In the name of Godisobc.com/files/2conf-isfahan.pdfHTTP://UI.CNF.IR/PPS 4 states that the global...

HTTP://UI.CNF.IR/PPS 1

In the name of God


Conference Topics:

-Active Peptides and their Industrial Applications

-Protein and Enzyme Engineering and their Applications

-Protein Diseases

-Folding, Structure and Stability of Proteins

-Biophysical Chemistry of Proteins and Peptides

-Application of Proteins and Enzymes in Environmental Issues

-Proteomics

-Protein Drugs and Biomarkers

-Protein Applications in Nanotechnology

-Protein Purification

-Protein- Protein Interactions

-Protein- Ligand Interaction

-Bioinformatics in Protein Researches

Scientific Chair: Prof. Abdol-Khalegh Bordbar

Executive Chair: Dr. Asghar Taheri-Kafrani


Protein and peptide Therapeutics – The future is here

In the two past decades protein and peptide therapeutics revolutionized the countenance of the

contemporary medicine and initiated effective therapies for numbers of refractory diseases. Since

1982, when the first therapeutic protein – recombinant human insulin – was introduced, the

global market of biotechnology drugs has been still growing. In 2008 more than 130 molecules

were approved for clinical use by FDA and at present there are almost 170 proteins and peptides

in use.

Today biopharmaceutics include: recombinant hormones, interferons, interleukins, hematopoietic

growth factors, tumor necrosis factors, blood-clotting factors, thrombolytic drugs, enzymes,

monoclonal antibodies (2nd generation) and vaccines. Today, protein and peptide drugs have

been successfully applied in treating various human illnesses including diabetes, dwarfism,

myocardial infarction, congestive heart failure, cerebral apoplexy, multiple sclerosis,

neutropenia, thrombocytopenia, anaemia, hepatitis, rheumatoid arthritis, asthma, Crohn’s disease

and cancers therapies.

The 1st generation of biopharmaceutics is dominated by structures based on the native

sequences, identical with the proteins/peptides naturally occurring in the body tissues, whereas in

the 2nd generation we find drugs with improved properties, especially PK, biodistribution,

higher specificity, efficacy and minimized side effects. To achieve these desired features, the

structures are deliberately modified by covalent attachment of the chemical compounds,

introduction of certain changes within the sequences of the protein, fusions of two or more

peptide chains or replacement of the sugar residues. The main challenge for the next, already 3rd

generation of recombinant drugs, seem to be the new route of administration, new formulations

and consequently even higher efficiency and safety.

In 2003, the global market for therapeutic proteins was worth $37 billion, more by almost 19%

than in the previous year, and achieved sales of over $90 billion in 2010. Much of this market is

dominated by erythropoietins and monoclonal antibodies, which treat common diseases such as

anaemia, arthritis and cancer. At the same time the global market for pharmaceuticals reached

approximately $650 billion in the same year. Therefore, therapeutic proteins covered

approximately 13.8% share of the global pharmaceutical market in 2010, a considerable

proportion of the total. According to the GBI research in the report “Therapeutic Proteins Market

to 2017 - High Demand for Monoclonal Antibodies will Drive the Market” the market is likely to

grow and to reach $141.5 billion in 2017. After Global Industry Analysts, Inc. in the “Protein

Drugs – Global Market Report”, nearly 400 types of protein drugs are in the process of

development and global market for protein drugs is estimated to reach $158.2 billion by 2015.

However the expiration of the patents of key protein therapeutics on the one hand and budget

limitations on the other will result in opening the market to biosimilar versions of first generation

drugs. Finally Research and Markets in “Global Protein Therapeutics Market Forecast to 2015”


states that the global market for biopharmaceutics is still growing and is likely to reach the level

of $143.4 by 2016.

Without any doubts there is still a lot to be done in the protein and peptide recombinant drugs.

Their development always means years of efforts and high risk. Though, even if only one is

successful, the success will be outstanding.

This conference includes both lecture and poster presentation sessions, covering the latest

findings across many topics in protein and peptide sciences including: Application of Enzymes

in Medicine and Industry - Quantitative and Analytical Proteomics -Enzyme Engineering -

Protein Chemistry - Protein Folding and Dynamics - Bioactive Peptides and Their Applications -

Proteins and Metabolic Diseases - Drug Proteins and Protein Biomarkers - Advanced

Technologies in the Field of Protein Research and Development - Application of Proteins in

Nanotechnology - Protein-Drug and Protein-Protein Interactions - Innovation in Protein

Purification and Quantification –Bioinformatics - Plant Proteins and Associated Diseases.

Also four scientific workshops in the related fields will go on in parallel to the main event. We

hope that this PPS conference can create a forum for useful dialogues between Iranian

researchers committed to protein and peptide sciences.

Scientific Chair: Prof. Abdol-Khalegh Bordbar

Executive Chair: Dr. Asghar Taheri-Kafrani


Scientific Committee of PPS Conference:

Dr. Abdolkhalegh Bordbar

Dr. Abdollah

Derakhshandeh

Dr. Abolfazl Barzegar

Dr. Abolghasem Abasi

Kajani

Dr. Abolghasem Esmaeili

Dr. Adeleh Divsalar

Dr. Ali Mohammad

Tamadon

Dr. Ali Zarrabi

Dr. Ali Akbar Moosavi-

Movahedi

Dr. Ali Akbar Saboury

Dr. Amir Razmjou

Dr. Asghar Taheri-Kafrani

Dr. Davoud Biria

Dr. Gholamhossein Riazi

Dr. Hamid Amiri

Dr. Hamidreza Karbalaei

Dr. Hasan Mohabatkar

Dr. Hedayatollah

Ghourchian

Dr. Karim Mahnam

Dr. Khosro Khaje

Dr. Mahmoud Amin lari

Dr. Mandana Behbahani

Dr. Maryam Nikkhah

Dr. Mehdi Sahihi

Dr. Mehran Habibi rezaei

Dr. Mehran Miroliaei

Dr. Mehrnaz Keyhanfar

Dr. Mohammad Rabani

Khorasgani

Dr. Mohammad Reza

Dayer

Dr. Mohammad Ali

Asadollahi

Dr. Mohammad Mahdi

Alavianmehr

Dr. Mohammad Reza

Mofid

Dr. Mojtaba Amani

Dr. Mostafa Rezaei

Tavirani

Dr. Nematollah Gheybi

Dr. Raheleh Masoudi

Dr. Rahman Emamzadeh

Dr. Reza Hasan sajedi

Dr. Reza Yousefi

Dr. Said Balalaei

Dr. Saman Hosseinkhani

Dr. Samaneh Zolghadr

Dr. Seyed Hamid Zarkesh

Esfahani

Dr. Seyed Jafar Mousavi

Dr. Seyed Mahmoud

Ghafari

Dr. Younes Ghasemi


Executive Committee:

Dr. Asghar Taheri-Kafrani

Afrouz Khalili

Elham Shirani

Fahimeh Andarzian

Fereshteh Enami

Fereshteh Mohagheghiyan

Ghazaleh Es-haghi

Javad Abbasabad Arabi

Mahkame Amirbandeh

Masumeh Alamdaran

Nesa Rafaati

Parisa Dehghani

Parisa Rabiei

Reyhaneh Kord Sedehi

Rezvan Kazemi

Sadegh Khorrami

Shohreh Esmaeli

Yasaman Boroumand

Zahra Abdollahi

Zahra Milanian


Table of Contents

Oral Presentation Abstracts: ................................................................................................................... 20

Modeling the DSC profile of irreversible thermal denaturation of proteins undergoing aggregation .. 20

Bioactive peptides from egg-whites of different avian species .............................................................. 21

Modified lysozymes as novel broad spectrum natural antimicrobial agents ......................................... 22

Molecular dynamics simulation for designing and predicting of bimolecular functions ....................... 23

Small substrate, big surprise. Structure and function of dihydroxyacetone kinases ............................. 24

Synthesis of therapeutic peptides and novel bioactive peptides ........................................................... 25

Cubic nanoparticles preparation to deliver protein drug (PAL36) to brain cells for possible treatment

of multiple sclerosis (MS) ........................................................................................................................ 26

The effect of the aptameric ligands’ length on the binding affinity to the analogous protein targets:

evaluation of aptamers specific to plasma coagulation factor VIIa against recombinant form of this

protein..................................................................................................................................................... 27

Antidiabetic effect of walnut peptides on blood glucose level concentration in alloxan-induced

diabetic rats ............................................................................................................................................ 28

Weak interaction at nanoparticles alter function and conformation of proteinase k ........................... 29

Evaluation of structure, stability and chaperoning function of R12C human αA-crystallin under

oxidative stress ....................................................................................................................................... 30

Application of β-casein nano-vehicles for oral drug delivery systems in cancer therapy ...................... 31

Homo-FRET in labeled proteins by steady-state fluorescence anisotropy, revising the theory,

rethinking the assumptions .................................................................................................................... 32

Effect of surface engineering at nano scale on the protein adsorption and bacterial adhesion of

polymeric and metallic substrates .......................................................................................................... 33

Spectroscopic and molecular docking studies on interaction of prodigiosin with β-Lactoglobulin ....... 34

Virtual screening of piperine analogs as survivin inhibitors and their molecular interaction analysis by

using consensus docking, MD simulation, MMPB/GBSA and alanine scanning techniques .................. 35

Heterologous expression and functional characterization of multiple isoforms of rice metallothionein

................................................................................................................................................................ 36

Assessment of antibacterial and antioxidant activity of silver nanoparticles produced by reduced

glycated casein adducts .......................................................................................................................... 37


QM/MM spectroscopic investigation of the structure of the light-driven enzyme protochlorophyllide

oxidoreductase (LPOR) ............................................................................................................................ 38

Computer-aided design of new Typrostatin-A derivatives as simultaneous effective inhibitors of αβ-

tubulin and breast cancer resistance protein ......................................................................................... 39

Evaluation of the kappa carrageenan-chitosan nano magnetics efficiency on purification of P. indica

pectinase ................................................................................................................................................. 40

Nerve growth factor precursor and its role in alzheimer’s disease ........................................................ 41

Conformational studies of Human hemoglobin and insulin upon interaction with MTBE ..................... 42

Molecular dynamics simulations of surfactant peptides wrapping single-walled carbon nanotubes ... 43

N-methyl phenylalanine-rich peptides as potential blood -brain barrier shuttles ................................. 44

Free radical scavenging and denaturation-inhibiting effects of peptides from fish skin in vitro and in

food model system ................................................................................................................................. 45

Antibacterial evaluation of Bis (2-methyl-1H-imidazole-κN3) silver (I) dichromate (VI) by autodock vina

function ................................................................................................................................................... 46

Looking for a generic inhibitor of amyloid-like fibril formation among tri hetero cyclicsmall molecules

................................................................................................................................................................ 47

The crucial role of a Ω–loop the stability and activity of the Exo–inulinase ........................................... 48

Different strategies for designing protein inhibitors, agonists and super-agonists ............................... 49

rh-IGF-1 (mecasermin): expression, purification and formulation ......................................................... 50

Functionalized superparamagnetic nanocarriers in enzyme engineering: Highly dispersive, stable and

robust biocatalysts .................................................................................................................................. 51

Lens antioxidant defense mechanism plays an essential role against oxidative stress induced structural

damages of crystallin proteins ................................................................................................................ 52

Memory prison of protein ...................................................................................................................... 53

Isolation of α glucosidase inhibitor producers, Bacillus sp. RP073 and virgibacillus sp. RP072 from

Persian Gulf. ............................................................................................................................................ 54

Potential application of β-lactoglobulin for presence in nano scale oral drug delivery systems ........... 55

Poster Presentation Abstracts: ............................................................................................................... 56

Optimal isolation and purification of lens α-Crystalline protein ............................................................ 56

Molecular dynamics simulation of new cyclotide from viola tricolor .................................................... 57


The impact of vitamin C on amyloid structure of treated bovine serum albumin with potassium

sorbate .................................................................................................................................................... 58

Structural intermediates of bovine serum albumin upon treatment with potassium sorbate .............. 59

Survivin gene cloning in bacterial host DH5α ......................................................................................... 60

Association of APOE and BDNF polymorphisms with alzheimer’s disease in south of Iran. .................. 61

A molecular dynamics simulation investigation into the dissociation constants (Kd) of Mn(II) binding on

the structure and stability of calprotectin using Molecular Dynamics Simulation ................................. 62

Preliminary antibacterial evaluation of the chemical compositions in mono and dinuclear cobalt(II)

complexes of 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl) propane ligand .............................................. 63

A Study on Zn(II) coordination in the present of Ca(II) in human calprotectin binding sites using

molecular dynamics simulations ............................................................................................................. 64

Chaperone-like activity of new deep eutectic solvents (DESs) ............................................................... 65

Creating hierarchical nanostructures with TiO2 nanoparticle and brush polymer, a promising approach

for protein repellence behavior of biomaterial ...................................................................................... 66

Protective effect of zinc ions against protein misfolding: a dose dependent phenomenon .................. 67

Computational study of interaction between prostate-specific membrane antigen and truncated

PSMA aptamer ........................................................................................................................................ 68

Stabilization of Ca2+ regulated photoprotein aequorin by deep eutectic solvents (DESs) ..................... 69

Effect of conventional and microwave heating on glycation of bovine serum albumin through maillard

reaction ................................................................................................................................................... 70

Study of the interaction of apigenin and epigallocatechingallatewith α-Lactalbumin and their

inhibitory effect on the formation of α-Lactalbuminamyloid fibrils ....................................................... 71

A spectroscopic study on the interaction of blood carrier protein of albumin with a new designed

Palladium complex .................................................................................................................................. 72

Min impact study on catalase of Helicobacter pylori through simulation docking ................................ 73

The survey of the effect of crocin and saffranal in terms of the inhibition of the formaion beta sheets

in neurodegenerative diseases in vitro and in silico ............................................................................... 74

Prediction of triple mutation roles on the sweetness and function of brazzein according to

bioinformatical studies ........................................................................................................................... 75

Mutation at calcium binding site in cyclomaltodextrinase improve enzyme thermostability: A

bioinformatic study ................................................................................................................................. 76

Rashid

Highlight


Application of albumin glycation products to increase the yield of phytase production in a

recombinant bacterial expression system .............................................................................................. 77

Analysis of the interactions between putrescine and bovine pancreatic trypsin by spectroscopic

techniques ............................................................................................................................................... 78

Fabrication and characterization of nano bio-composites scaffolds contains silk fibroin protein and

mcm-41 for tissue engineering applications ........................................................................................... 79

Theoretical study of effect of N232S, F251L and R242H mutations in myosin protein structure .......... 80

Theoretical study of the effect of mutation F117L osteoprotegerin protein on its binding to RANKL

protein by modeling methods ................................................................................................................ 81

Fabrication and charactenization of nano bio-composite scaffold for use in tissue engineering .......... 82

Investigation on the binding of metoprolol tartrate to β-lactoglobulin using spectroscopic techniques

................................................................................................................................................................ 83

Induction of point mutations in human growth hormone molecule using specific primers .................. 84

Co-immobilization of acetylcholine esterase and choline oxidase for determination of acetylcholine in

the brain of rat ........................................................................................................................................ 85

The role of glutamate oxidase in electrochemically measurement of glutamate neurotransmitter in rat

brain ........................................................................................................................................................ 86

Analysis the binding interactions of bisdemethoxycurcumin, diacetylcurcumin and

diacetylbisdemethoxycurcumin with bovine α-lactalbumin by experimental and theoretical analysis 87

An investigation into the molecular mechanisms of the bacterial for designinga competent genetic

construct for benzene biodegradation ................................................................................................... 88

The optimization of expression of recombinant denileukin diftitox in soluble form ............................. 89

Protective effect of polyphenols against mitochondrial membrane permeabilization induced by HEWL

aggregates ............................................................................................................................................... 90

Immobilization of Termomyces lanuginosus xylanase enzyme on functionalized graphen oxide and

determination of activity and thermal stability ..................................................................................... 91

Covalent binding of xylanase enzyme on functionalized superparamagnetic graphene oxide

nanoparticles and evaluation of activity and pH stability....................................................................... 92

Investigation the effects of different osmolytes on the structure of trypsin ......................................... 93

Bagging algorithm for protein thermostability prediction based on pseudo amino acid composition . 94

Efficient synthesis of novel eptifibatide analogous ................................................................................ 95

Bioactive peptides from egg-whites of different avian species .............................................................. 96


In silico study of molecular interaction between cel-D7 (a novel drivative of celastrol) and proteasome

using the autodock software .................................................................................................................. 97

Improvement of Bacillus subtilis ZH1 biosurfactant production ............................................................ 98

Probing the interaction of chemotherapeutic drug of 5-fluorouracil and milk carrier protein of -

lactoglobulin ........................................................................................................................................... 99

Identification of RCC in structure of large envelope protein S of HBV and molecular modeling ......... 100

Antimicrobial activity of heat stable peptides in Iranian native Bacillus strains with probiotic potential

.............................................................................................................................................................. 101

Preparation and characterization of monoclonal antibody against carcinoembryonic antigen and

immunohistchemistry evaluation ......................................................................................................... 102

Construction of BSA nanogels-loaded doxorubicin and its anti-carcinoma effect on MES-SA/DX5 .... 103

Medical applications of antimicrobial peptide ..................................................................................... 104

Study of the interaction change between the cytosolic components of the NADPH oxidase in cell free

system ................................................................................................................................................... 105

Exploring of the assembly process of the NADPH oxidase complex via the structural changes of p47phox

and p67phox subunits .............................................................................................................................. 106

Effects of fermentation by cocci lactic acid bacteria isolated from Iranian dairy products on the

immunoreactivity of Cow's milk caseinate ........................................................................................... 107

A thermodynamic study on the interaction of propolis and human hemoglobin ................................ 108

Studding the solubility of EGFP upon replacing valine 12 by lysine, using bioinformatics tools .......... 109

Enhanced green fluorescent protein instability upon replacing phenylalanine 226 by alanine .......... 110

Assesment of cow’s milk β-lactoglobulin allergenicity reduction using cocci lactic acid bacteria isolated

from Iranian dairy products .................................................................................................................. 111

Computer-aided evaluation of M4 protein (a truncated version of IL-24) with Bioinformatics tools . 112

Promotion of antioxidant peptides of tomato waste seed meals by bacillus subtilis submerged

fermentation ......................................................................................................................................... 113

Comparison of radical scavenging activity of tomato and grape meal peptides by bacillus subtilis

submerged fermentation ...................................................................................................................... 114

Glutathione S-transferase protein of some cultivated wheat in Iran ................................................... 115

Studying structures and processes involved in the transfer across nuclear pore complexes using

molecular dynamics simulation ............................................................................................................ 116


Investigating the interaction of antibacterial peptide “LLAA” with the bacterial membrane using

molecular dynamics simulation. ........................................................................................................... 117

The effects of a novel phenanthroline-imidazole derivative of platinum complex on the structure and

function of bovine liver catalase ........................................................................................................... 118

Stability of the recombinant enzyme in Lepidiumdrabaperoxidase (LDP) against heat and hydrogen

peroxide ................................................................................................................................................ 119

Effect of lysine residue acetylation on the structure of apomyoglobin ............................................... 120

Effect of spacer length of the synthetic cationic urethane gemini surfactants on the secondary

structure of insulin ................................................................................................................................ 121

Superior cytotoxicity of serum albumin on microglial cells upon hetero-seeding effect of amyloid

peptide .................................................................................................................................................. 122

Prediction and evaluation of myelin oligodendrocyte glycoprotein (MOG) antigenic epitopes .......... 123

Evaluation of MHC class I binding properties of designed peptides for DNA vaccine for induction of

multiple sclerosis tolerance in human .................................................................................................. 124

Cloning and expression of soluble extracellular domains 1-3 of human VEGF receptor-2 in Pichia

pastoris .................................................................................................................................................. 125

Study of the interaction of myricetin and Morin hydrate with bovineα-Lactalbumin ......................... 126

Protective effects of hydroalcohol extract of Zingiber Officinale on the functional disorders and

histological damages in Iron-induced renal toxicity in rats .................................................................. 127

Human asf1a c-terminal tail phosphorylation favours formation of stable secondary structures in this

intrinsically disordered peptide ............................................................................................................ 128

Bioinformatics analysis of Aspartyl/asparaginyl β-hydroxylase protein ............................................... 129

Cloning and heterologous expression of catalytic subunit of rice (Oryza Sativa) acetohydroxy acid

synthase in Escherichia coli ................................................................................................................... 130

Interaction of arachidonoyl serotonin with beta-casein nanoparticles: spectroscopy and molecular

modelin studies ..................................................................................................................................... 131

Interaction of serotonin with beta-casein nanoparticles: spectroscopy and molecular modelin studies

.............................................................................................................................................................. 132

An efficient synthesis of exenatide as an anti-diabetic drug ................................................................ 133

Preparation and biodistribution assessment of 68Ga-Bleomycin as a possible PET imaging ................ 134

The application of HER2 protein in cancer detection using graphene functionalized with specific DNA

sequences ............................................................................................................................................. 135


Construction of BMP-2 agonists based on nanobody (VHH) ................................................................ 136

Application of bovine serum albumin- carbon nanotubes conjugated system for fabrication of highly

sensitive arsenic aptasensor ................................................................................................................. 137

Structural and functional characterization of reduced glycated adduct of bovine β-casein................ 138

Construction, expression and purification of diabody against human vascular endothelial growth

factor in bacterial system...................................................................................................................... 139

Inhibition of kanamycin-resistant bacteria by designing 10–23 deoxyribozyme targeted to kanamycin

resistance mRNA ................................................................................................................................... 140

Investigating on the synergistic inhibitory effect of aspirin and propolis on the glycation of human

hemoglobin by fructose ........................................................................................................................ 141

Comparison on the inhibitory effects of propolis on the structural changes of glycated human

hemoglobin resulted glucose and fructose ......................................................................................... 142

Subcloning, Expression, and Activity Assay of Recombinant Luciferin Regenerating Enzyme from

Lampyris Turkestanicus (T-LRE) in Yeast ........................................................................................... 143

ASA rater: A web based software for classifying surface accessibility of protein residues from the

structure ................................................................................................................................................ 144

Studying the effect of changing the wettability of polypropylene films on the protein adsorption .... 145

Molecular modeling of Zika virus NS5 and evaluating its interaction with human targets using In-silico

approach ............................................................................................................................................... 146

Extraction optimization, purification and characterization of a protease enzyme from fruits of

Withania coagulans .............................................................................................................................. 147

Designing, development and assessment a series of novel genetic constructs for aromatic

hydrocarbons bioremediation based on investigation of bacterial dioxygenases ............................... 148

Enhancing extraction efficiency of heterologously expressed recombinant prostate stem cell antigen

in Ecoli ................................................................................................................................................... 149

The properties of biosurfactant produced by Lactobacillus rhamnosus ATCC 7469 ............................ 150

Investigate the mechanism of the BAX, a pro-apoptotic protein, activation through SMBA1, an anti-

cancer treatment: a molecular modeling and molecular dynamics study .......................................... 151

Effect of mare (Equus caballus) caseins and whey proteins on breast cancer cells ............................. 152

Endolysins as new class of antimicrobial agents against pathogenic bacteria ....................... 153

Study on the interaction of novel cationic platinum complexes with human serum albumin ............ 154

Rashid

Highlight


Spectroscopic and dynamic properties of arachidonoyl serotonin- β-Lactoglobulin complex: A

molecular modeling and chemometric study ....................................................................................... 155

Purified milk fractions and bioactive peptides, unknown source of health for Iranian people ........... 156

Design of ubiquitin conjugated peptide of toxoplasma gondii SAG1 antigen for presentation on MHC

class I ..................................................................................................................................................... 157

T-cell epitope prediction of different antigen for developing Toxoplasma gondii vaccines ................ 158

Kinetics of xantho-oligosaccharide production by xanthan degrading enzymes from Paenibacillus sp.

strain AS7 .............................................................................................................................................. 159

A thermodynamics study on the interaction of Allura Red AC with calf thymus DNA ......................... 160

Molecular cloning of a Bacillus licheniformis BR1390 α-amylase gene and biochemical characterization

of the recombinant enzyme .................................................................................................................. 161

Investigation on the effect of food colorant Allura Red AC on the bovine serum albumin by various

spectroscopic techniques...................................................................................................................... 162

Efficient synthesis of argirelin acetate as anti-wrinkle peptide ............................................................ 163

Thermostable alginate lyase from Pseudomonas aeruginosa strain 293 ............................................. 164

PH stability of alginate lyase from pseudomonas aeruginosa strain 293 ............................................. 165

Memory prison of protein .................................................................................................................... 166

Effects of Silver Nanoparticles on Protein Pattern and Antioxidant Enzymes Activities of Canola

(Brassica napus L.) Under In vitro Conditions ....................................................................................... 167

Spectroscopy study on interaction of amaranth with bovine serum albumin (BSA): a thermodynamic

approach ............................................................................................................................................... 168

Development a broad-spectrum immunotoxins based on in-silico ligands assay ................................ 169

Structural alterations in hemoglobin by glycation; prevention by ferulic acid and p-coumaric acid. .. 170

Protein glycation and anti-AGE agents; possible role in treatment of glycation-associated diseases. 171

A simple bioluminescence method for determination of benserazide by inhibitory effect on aequorin

in biological sample ............................................................................................................................... 172

Cognition enhancing and neuromodulatory propensity of satureiahortensis extract against lysozyme

induced cognitive impairments in rat hippocampus. ........................................................................... 173

Protective effect of 1, 3, 5 tri fluoro phenyl benzene against lysozyme oligomerization and amyloid-

mediated cell death in PC12 cells. ........................................................................................................ 174


Structural study of wnt-pathway inhibitors, Mesd and dkk1 on LRP6, potentials for anti-cancer peptide

design .................................................................................................................................................... 175

Lactopeptides are natural antibiotics can be replace with artificial antibiotics ................................... 176

Investigation of the antifouling and protein adsorption properties of polyethersulfonemembranes by

titaniadioxide nanoparticles coating .................................................................................................... 177

Interaction of human serum albumin with the resveratrol in the presence of nanoparticles and EMF

(up to 1 MHz) ......................................................................................................................................... 178

Interaction between silver nanoparticles and human serum albumin revealed by fluorescence

spectroscopy in the presence of resveratrol ........................................................................................ 179

Comparison of phytase production in submerged and solid state fermentation of a strain of

Aspergillus niger and investigation of 3 various solid media containing wheat bran as the basic

substrate ............................................................................................................................................... 180

Hydrolysis of collagen-containing wastes as a renewable nitrogen source ......................................... 181

In silico evaluation of binding affinity of zanamivir, peramivir, and laninamivir octanoate drugs

compared with oseltamivir to the neuraminidase in influenza A (H1N1) ............................................ 182

The simulation and evaluation of fever temperature effects on the active site of neuraminidase

protein receptor in influenza A (H1N1) virus in the in silico ................................................................. 183

Investigation of binding interactions of apigenin and morin hydrate with beta-lactoglobulin............ 184

Exploring the thermal stability and activity of proteinase K in the presence of spermidin by biophysical

techniques and molecular dynamic simulations .................................................................................. 185

Investigation of the effect of spermine on the interaction between ADA and its substrate using

computational methods........................................................................................................................ 186

Study of laccase activity of Bacillus spores by zymogeraphy ............................................................... 187

Study of expression and activation of engineered coagulation factor IX with propeptid of protrombin

.............................................................................................................................................................. 188

Identification of biologically active recombinant human erythropoietin (rHuEPO) glycoforms .......... 189

Thermodynamic stability of β-lactoglobulin in the presence of cetylpyridinumbromide: UV-Vis

spectroscopy andmdocking studies ...................................................................................................... 190

Investigating Interaction of DNA and protein immobilized gold nano particles with nitrocellulose

membranes ........................................................................................................................................... 191

Prediction 3D structure of IGFBP3 using homology modeling and molecular dynamic ....................... 192


An investigation on the interaction of antibacterial peptides "aurein 1.2" with the bacterial membrane

using molecular dynamics simulation ................................................................................................... 193

Luciferase mutation at K329 position by SDM for proteolytic stability ................................................ 194

Determination of 3-D structure of human HMGB4 protein using MODELLER software ...................... 195

Antiadhesive activity of a biosurfactant isolated by Lactobacillus acidophilus onSerratiamarcescens

strains .................................................................................................................................................... 196

Fermentative production of lysine by Corynebacterium glutamicum from different nitrogen sources

.............................................................................................................................................................. 197

Optimization of different carbon sources for production of L-lysine by Corynebacterium glutamicum

.............................................................................................................................................................. 198

In silico comparison of structural features of envelope protein of zika virus with the homologous

proteins of two close viruses ................................................................................................................ 199

Activation of EF-hand II of photoproteinaequorin by replacement of its calcium-binding loop .......... 200

Bioinformatics design of deoxyribozyme 10-23 targeted to beta-lactamase mRNA for inhibition of

ampicillin-resistant bacteria ................................................................................................................. 201

Prediction of the mode of interaction between monoterpenes and the nitroreductase from

Enterobacter cloacae by docking simulation ........................................................................................ 202

Molecular modeling, docking and molecular dynamics simulation approaches to assessment binding

of coumarin to β-casein ........................................................................................................................ 203

Exploring binding properties of coumarin with Bovine β-Casein: multispectroscopic and chemometrics

studies ................................................................................................................................................... 204

Measurement of dioxin contamination in water samples by a bioluminescence method .................. 205

Role of the pre- molten globule structure in amyloid fibril formation ................................................. 206

Nano-liposomal lipid peroxidation as a consequence of the diabetic albumin glycation .................... 207

Gold nanoparticles-capped mesoporous silica for enzyme responsive controlled release of doxorubicin

in cancer therapy .................................................................................................................................. 208

Isolation of ACE-inhibitory peptide produced by enzymatic activity of goat milk whey proteins ....... 209

The presence of JC virus VP1 capsid of genotype 2B in rheumatoid arthritis patients in Isfahan, Iran210

In Silico analysis of single nucleotide polymorphisms (SNPs) and screening of mutations affecting

protein stability and function of KRAS protein ..................................................................................... 211

Computational molecular docking studies of bioactive peptides from milk proteins as angiogenesis

converting enzyme inhibitors with antihypertensive effects ............................................................... 212

Rashid

Highlight

Rashid

Highlight


Molecular docking and quantitative structure--activity relationships(QSAR) studies of herbal

compounds in Iris pseudopumila (Iridaceae)asacetylcholinesterase inhibitorsin alzheimer's disease

treatment .............................................................................................................................................. 213

Study of the binding of warfarin drug to β- lactoglobulin by UV- visible and isothermal titration

calorimetry techniques ......................................................................................................................... 214

Fabrication of gold nanorod assemblies on BSA amyloid fibril scaffolds ............................................. 215

The effect of modified tryptophan residues on kinetic, thermodynamic and structure of

mashroomtyrosinase ............................................................................................................................ 216

Covalent immobilization of glucoamylase on superparamagnetic graphene oxide Fe3O4

nanocomposites .................................................................................................................................... 217

Functionalized superparamagnetic chitosan nanoparticles in enzyme engineering: A highly dispersive,

stable and robust biocatalyst ................................................................................................................ 218

Investigation on physicochemical properties of [Ni (FIP) 2] (OAC)2 complex and its interaction with ct-

DNA and Its effect on ct-DNA stability .................................................................................................. 219

An in-silico investigation on the structure and function of the Phenanthrene degradative bacteria

enzymes, an introduction to development of anti-cancer probiotics .................................................. 220

The effect of time and temperature incubation on bacterial phytase activity .................................... 221

Thermal stability of lactoperoxidase stabilized on modified magnetic nanoparticle ........................... 222

Effect of over-expressing Apaf-1 on apoptosis induction ..................................................................... 223

Studying the presence of hemolysin BL and NHE subunit genes in Iranian native Bacillus strains with

probiotic potential by PCR .................................................................................................................... 224

Inhibition of angiogenesis signaling pathways by synergic administration of VEGF antibody along with

endostatin derived peptide in the human umbilical vein endothelial cells.......................................... 225

Evaluation of antioxidant activity in peptides of fermented soybean meal by Lactobacillus rhamnosus

.............................................................................................................................................................. 226

Production of antioxidant peptides from soybean meal by Bacillus subtilis ........................................ 227

Theoretical design of a new vaccine for multiple sclerosis (MS) .......................................................... 228

The effect of temperature on the formation rate of liposome of DSPC and CHOL by coarse-grained

molecular dynamics simulations studies .............................................................................................. 229

Purification of sugar beet pulp induced pectinase from P. indica by chitosan-PVA magnetic beads

.............................................................................................................................................................. 230

Rashid

Highlight


Investigating the role of DADLE on 6-OHDA-induced cell toxicity in human neuroblastoma cells SH-

SY5Y as an in vitro model of Parkinson’s disease ................................................................................. 231

Interactions of β-lactoglobulin with Lovastatin .................................................................................... 232

Efficient synthesis and purification of buserelin acetate...................................................................... 233

A thermodynamic approach of the interaction between human serum albumin and a new synthesized

platinum complex ................................................................................................................................. 234

Computational analysis of miR-423 mediated drug response in breast cancer ................................... 235

Evaluation of dioxin contaminations in fish oil samples by bioluminescence method ........................ 236

Characterization of electrospun gelatin nanofibers crosslinked with tannic acid ................................ 237

Kinetics and spectrofluorimeteric the studies of catalase in presence of spermidine ......................... 238

Effect of TiO2 nanoparticle on structural stability and activity of catalase .......................................... 239

Separation and precipitation of β –lactoglobulin from commercial whey preparations by NaCl salting

out at low pH......................................................................................................................................... 240

Proteins and peptides in camel milk ..................................................................................................... 241

Efficient synthesis and purification of octreotide acetate as a somatostatin agonist analogue .......... 242

Optimization of carbon source for phytase production in submerged fermentation of a strain of

Aspergillus niger and comparison of enzyme activity between immobilized and free spores ............ 243

An investigation on the structure and function of the cell surface prostate-specific antigens for

development a new generation of immunotoxins ............................................................................... 244

A comparative study of effects of canola meal bioactive peptides, antibiotic, probiotic and prebiotic

on growth performance, some blood parameters, intestinal morphology and gut microflora in broiler

chicks ..................................................................................................................................................... 245

The investigation of stability of functionalized alkyl-peptide self-assembly innanofiber form by

molecular dynamics simulation ............................................................................................................ 246

Beta keratin solubilization: a new method for blocking sulfydryl groups ............................................ 247

Antioxidant and metal chelating ability of feather keratin................................................................... 248

Binding of carbon nanotube to carcinoembryonic antigen: A the oretical approach .......................... 249

Peroxynitrite-modified human α-Crystallin subunits indicate improved chaperone-like activity and

enhanced protection against copper-mediated ascorbic acid oxidation ............................................. 250

Investigation the use of plants as host for protein production ............................................................ 251

Immobilization of human serum albumin on modified graphene oxide nanosheets .......................... 252

Rashid

Highlight


A combined spectroscopic and molecular docking approaches to probing binding of daidzein to β-

lactoglobulin ......................................................................................................................................... 253

VEGF-A epitope prediction aim to exploiting in angiogenesis stimulation in order to tissue restoration

using magnetic nanoparticles ............................................................................................................... 254

Molecular docking study of HCV proteins with phytochemical compounds from Prangos uloptera DC

.............................................................................................................................................................. 255

Investigation the antibacterial effect of peptides derived from cow's milk protein (caseinate)

hydrolysis by lactic acid bacteria .......................................................................................................... 256

Immobilization of human serum albumin protein on metal-organic framework material .................. 257

Investigation the antibacterial effect of peptides derived from cow's milk protein (Betalactaglobulin)

hydrolysis by lactic acid bacteria .......................................................................................................... 258

Prediction of post-translational glycosylation of proteins .................................................................... 259

Effectiveness of a number of natural product in improving viability of probiotic bacteria in Iranian

diary product ......................................................................................................................................... 260

Effect of Polyoxometalates (POMs) on glioblastoma cancer cells ........................................................ 261

Prediction of phosphorylation sites of proteins from their amino acid sequence ............................... 262

Functionalized superparamagnetic graphene oxide nanoparticles as a matrix for glucose oxidase

immobilization ...................................................................................................................................... 263

Immobilization of glucose oxidase on superparamagnetic/chitosan nanoparticles ............................ 264

Comparing the physiochemical properties and alpha helix percentages of different organisms’ Lactate

dehydrogenases by bioinformatics tool ............................................................................................... 265

Studying the effect of changing the micro/nano roughness and wettability of polypropylene (PP) films

on the protein adsorption ..................................................................................................................... 266


Oral Presentation Abstracts:

Modeling the DSC profile of irreversible thermal denaturation of

proteins undergoing aggregation

Mojtaba Amani, Ali-Akbar Moosavi-Movahedi2

1Department of Biochemistry, Faculty of Medicine, Ardabil University of Medical Sciences (ArUMS), Ardabil,

Iran. 2Biophysical Chemistry lab, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran.

Abstract

Some proteins are the cause of fatal diseases in human being and animals. These diseases arise

when a misfolded form of a protein appears and forms aggregates. Aggregates of the misfolded

form may convert the normally folded protein to its misfolded state and hence promote the

aggregation. A model has been proposed in which a misfolded protein triggers misfolding of

other proteins and aggregation. The equation describing the heat capacity on temperature has

been formulated and the theoretical DSC profiles were plotted. The effects of different variables

on theoretical profile and cases in which aggregated protein profile resembles reversible

unfolding will be discussed.

Keywords: Thermal denaturation, Aggregate, Heat capacity.


Bioactive peptides from egg-whites of different avian species

Ladan Aminlari1, L. Hajipour2, M. Tavana3, M.M. Mohammadi3

1Department of Food Hygiene, School of Veterinary Medicine.

2 Department of Food Science and Technology School of Agriculture.

3Department of Biochemistry, Shiraz University, Shiraz, Iran.

Abstract

The aim of this study was to isolate and compare bioactive peptides from egg-white of quail,

duck and chicken and to determine their antimicrobial and antioxidant properties. The egg-white

proteins were diluted, the major proteins precipitated by trichloroacetic acid (TCA), centrifuged

to remove the precipitate and the supernatant were subjected to Sephadex G-25 gel-filtration

chromatography to isolate the peptides. The bioactive properties of the fractionated peptide were

determined. The elution pattern of peptides obtained by gel filtration chromatography of egg

white from different species of birds were different with different properties of the fractions. The

peptide fractions exhibited high antimicrobial and antioxidant properties. Most of the peptides

which were eluted at the final stage of gel-filtration chromatography showed the highest

antimicrobial properties against E. Coli and Bacillus Cereus. The results suggested that it is

possible to partially purify peptides from egg white of birds with potentially important functional

properties by a simple, one step chromatographic procedure. These peptides might substitute the

antioxidant and antimicrobial agents of chemical origin currently used in food and

pharmaceutical industries.

Keywords: Bioactive peptides, Egg whites, Quail, Duck, Chicken.


Modified lysozymes as novel broad spectrum natural antimicrobial

agents Mahmud Aminlari, M1, 2, Ladan Aminlari3, Mohammadi Hashemi2, Armin Mirzapour2

1Departement of Biochemistry, School of Veterinary, Medicine, Shiraz University, Shiraz,

Iran.

2Departement of Food Science and Technology, College of Agriculture, Shiraz Univ., Shiraz,

Iran.

3Departement of Food Hygiene, School of Veterinary Medicine, Shiraz Univ., Shiraz, Iran.

Abstract

In recent years much attention and interest have been directed toward application of

natural antimicrobial agents in foods the objective of this study was to identify and

assess antimicrobial systems in natural sources. Some naturally occurring proteins have

received considerable attention and are being considered as potential antimicrobial

agents natural antimicrobials can be found in milk (lactoferrin, lactoperoxidase,

globulins, fatty acids), eggs (lysozyme, transferrin, globulins, avidin,ovoinhibitors),

plants (phenolics : cloves, allspice, oregano, rosemary, sage, thyme,; flavanoids : fruits,

juices ; thiosulfinates (allicin in garlic), catechins (in green tea ), glucosinolates (in

horseradish, mustard). Our laboratory is currently involved in isolation, characterization

and modification of antimicrobial proteins from milk and egg white and in their

application in foods and pharmaceutical industries. Lysozyme kills bacteria by

hydrolyzing the peptidoglycan layer of the cell wall of certain bacterial species, hence

its application as a natural antimicrobial agent has been suggested. However,

limitations in the action of lysozyme against only gram-positive bacteria have prompted

scientists to extend the antimicrobial effects of lysozyme by several types of chemical

modifications. During the last 2 decades extensive research has been directed toward

modification of lysozyme in order to improve its antimicrobial properties. This seminar

will report on the latest information available on lysozyme modifications and examine

the applicability of the modified lysozymes in controlling growth of gram-positive and

gram-negative bacteria in vitro and in vivo. The results of modifications of lysozyme

using its conjugation with different small molecule, polysaccharides, as well as

modifications using proteolytic enzymes will be reviewed. These types of modifications

have not only increased the functional properties of lysozyme (such as solubility and

heat stability) but also extended its antimicrobial activity. In conclusion this review

demonstrates that modified lysozymes are excellent natural agents which can be used in

food and pharmaceutical industries.

Keywords: Chemical-enzymatic modifications, Conjugation, glycation, Lysozyme,

Maillard reaction, Natural antimicrobial.


Molecular dynamics simulation for designing and predicting of

bimolecular functions

Abolfazl Barzegar

Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.

Abstract Molecular dynamics simulation (MDS) is computer simulation with atoms and/or molecules

interacting using particular rules of physics. MDS can provide the critical detail regarding

specific particle motions as a function of time. It is important tool for understanding the physical

basis of the structure and function of biological macromolecules. Current MDS of biomolecules

typically allow using a very large number of atoms that are involved over timescales of many

nanoseconds. Herein, the MD simulation process was applied for the aim of designing peptides

to functionalize carbon nanotubes based on the aromatic residue numbers and also designing new

fullerene derivatives as anti-HIV drugs. Data indicated that stacking interaction between the

aromatic residue and π electrons of nanotube is important for dispersing carbon nanotubes. Also,

we found that the fulleropyrrolidine derivatives with one and two acetoxy-hydroxyl groups, as

new carbon naostructures of fullerene-based compounds which possibly have potential use as

effective HIV-1 protease inhibitors. The usage of MDS provides new insight into biomolecular

design strategies for future nano-biomedical applications.

Keywords: Molecular dynamic; AIDS, Fullerene, Carbon nanotube; Aromaticity.


Small substrate, big surprise. Structure and function of

dihydroxyacetone kinases

Bernhard Erni

Departement of Chemistry and Biochemistry, University of Bern, Switzerland.

Abstract

Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes which utilize

either ATP (in animals, plants, bacteria) or phosphoenolpyruvate (PEP, in bacteria) as source of

high-energy phosphate. The PEP-dependent kinase of E. coli consists of three subunits: DhaK is

a stable homodimer that binds Dha covalently by a hemiaminal linkage between an imidazole-

nitrogen of a histidine and the carbonyl carbon of Dha. DhaL contains a tightly bound ADP,

which - in contrast to the nucleotide of the ATP-dependent kinases - does not exchange but is

rephosphorylated in situ by DhaM. DhaM transfers phosphoryl groups from the general

phosphorylcarrier proteins HPr and enzyme I of the bacterial phosphotransferase system (PTS).

PEP→EI (His)→HPr(His)→DhaM(His)→DhaL(ADP)→DhaK(Dha) DhaR is the transcription

activator of the dhaKLM operon. It is a member of the AAA+ family of enhancer binding

proteins. The kinase subunits DhaL and DhaK act antagonistically as coactivator and corepressor

by mutually exclusive binding to the sensing domain of DhaR. In the presence of Dha, DhaL is

dephosphorylated, DhaL::ADP displaces DhaK and stimulates DhaR activity. In the absence of

Dha, DhaL::ATP accumulates. DhaL::ATP does not bind to DhaR. DhaR::DhaKinactive +

DhaL(ATP) + Dha → DhaR::DhaL(ADP)active + DhaK::DhaP

Keywords: Dihydroxyacetone, Substrate, Enzymes, Phosphoryl groups.


Synthesis of therapeutic peptides and novel bioactive peptides

Saeed Balalaie1, 2

1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416

Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Abstract

Peptides have a huge potential as drugs. They can be considered as “Natural Pharmaceuticals”.

The importance of peptides as pharmaceutical compounds has increased significantly and

peptide drugs have an essential role in pharmaceutical market. Meanwhile, today, following the

sequencing of the human genome, peptides have become a focus of biotechnological research.

Techniques have been developed for an easier, faster and cost effective synthesis of peptides.

Throughout the course of its story, the synthesis of pharmaceutical peptides and synthesis of

bioactive peptides has served as a principal driving force for discovering new chemical

reactivity, testing the power of existing synthetic methods, and enabling biology and medicine.

This talk will highlight elements of our efforts for: a) Synthesis of pharmaceutical peptides, Such

as GnRH analogues, Triptoreline, Leuprolide, Desloreline, Fertireline, Buserelin, Onclogy

peptides, Octrotide, Octrotate. b) Combining of solid and solution phase peptide synthesis with

new approaches such as multicomponent reactions for the synthesis of pseudo peptides and

investigation of their biological activities. c) Synthesis of novel cyclopeptides through Ugi

ligation/click reaction to construct the cyclopeptides which have a triazole moiety and also

lipophilic moieties. d) Combination of bioactive heterocyclic skeletons with active peptides.

Keywords: Therapeutic peptides, Bioactive peptides, Multicomponent reactions, Protected amino

acids, Cyclopeptides, Disulphide bridges.


Cubic nanoparticles preparation to deliver protein drug (PAL36) to

brain cells for possible treatment of multiple sclerosis (MS)

Behjat Nafari1 and Abbasali Palizban2

1Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.

2Department of Clinical Biochemistry, Isfahan University of Medical Sciences, Isfahan, Iran.

Abstract

Many peptides and proteins are being used because of potential therapeutics. Delivery of these

peptide/protein drugs is one of the biggest difficulties for clinical application. Taking advantage

of nanoparticles encapsulated protein to target specific cells and prevent degradation, we

investigated how to deliver nanoparticles containing protein drugs to brain cells by crossing

blood brain barrier. Poly (lactic acid-co-glycolic acid) (PLGA) and Poly (L-lactic acid) (PLA),

first used for structures. PLGA and PLA are degradable and then metabolized by the Krebs

cycle. Avidin were conjugated with fatty acids in sodium deoxycholate (2%). Avidin-

stearatolyated /palmitolyated -PLGA (50/50) nanoparticles were prepared with encapsulated

PAL36 protein (Trade Mark). The Nanoparticles were characterization using FT-IR for chemical

binding, SEM for morphology, zeta potential for nanoparticle size, UV-Vis spectrometer for

PAL36 protein drug release behavior and entrapment efficiency (% EE). The FT-IR results show

that NHS-fatty acids were properly conjugated to Avidin. The scanning electron microscopy

experiment revealed cubic morphology for nanoparticle with size of 100-400 nm. The % EE and

drug loading were calculated to be 59% and approximately 1, respectively. Avidin on the surface

of nanoparticles which encapsulated protein of PAL36 enables potentially add biotinylated

ligand to the formulation of nanoparticles to improve specific targeting brain cells. Currently we

are looking to establish a method to understand how to deliver these particles containing PAL36

to human brain cells for treatment of Multiple Sclerosis (MS) patients.

Keywords: PLGA, Cubic Nanoparticle, Avidin-fatty acid conjugated, Multiple Sclerosis (MS).


The effect of the aptameric ligands’ length on the binding affinity to

the analogous protein targets: evaluation of aptamers specific to

plasma coagulation factor VIIa against recombinant form of this

protein

Maryam Tabarzad1, Marzieh Jafari2, Nastaran Nafissi-varcheh3

1 Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

2 Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ahvaz Jundishpur University of Medical

Sciences, Ahvaz, Iran.

3 Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical

Sciences, Tehran, Iran.

Abstract

Aptamers are single stranded oligonucleotides comparable in selectivity and affinity to the

monoclonal antibodies, in addition to several strategic properties in design, development and

applications. Ease of design and development, simple chemical modification and the attachment

of functional groups, easily handling and more adaptability with analytical methods, small size

and adaptation with nanostructures are valuable characteristics of aptamers in comparison to

large protein based ligands. Among a broad range of aptamers’ targets, proteins and peptides

have significant position. Aptamers, especially DNA aptamers, as nucleic acid based affinity

ligands are more stable than monoclonal antibodies for protein purification or analysis.

Coagulation factor vii (FVII) is a plasma serine protease that has a significant role in coagulation

process and natural human hemostasis. Activated FVII (FVIIa) specific RNA aptamers were

developed previously with the aim of therapeutic applications. FVIIa specific DNA aptamers

were also presented in a patent considering plasma protein purification. In this study, two of the

aptameric DNA oligonucleotides that showed acceptable affinities for coagulation factor VIIa

purification from plasma, were selected to evaluate their affinity against a recombinant form of

FVIIa. Results showed the binding affinity of the 40 nucleotides aptamer was more than 81

nucleotides aptamer sequence. This might be the results of more probability of conformational

adaption in aptamer 3D structure when encounter minor differences in target molecule.

Therefore, this aptamer could be optimized in order to develop aptamer based affinity

chromatography process for this form of recombinant coagulation factor VIIa.

Keywords: Aptamer, Coagulation factor VIIa, Plasma, Recombinant, Conformational adaption.


Antidiabetic effect of walnut peptides on blood glucose level

concentration in alloxan-induced diabetic rats

Raheleh Jahanbani1, Mahmood Ghaffari1, Kourosh Vahdati2, Maryam Salami3, Ameneh

Rezayof 4, Zahra Ghasemzadeh4, Ali Akbar Moosavi-Movahedi1,5

1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

2 Department of Horticulture, University of Tehran, College of Aburaihan, Pakdasht, Tehran, Iran.

3Department of Food Science and Engineering, University College of Agriculture & Natural Resources, University

of Tehran, Karaj, Iran.

4Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.

5Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.

Abstract

In view of the fact that synthetic drugs for control of diabetes has some side effects and cannot

be use in the period of pregnancy, researchers have shown an increased interest in the use of

natural products to induced hypoglycemic effect. The present study was carried out to evaluate if

walnut peptides exert any effects on pancreatic ß cells in alloxan-induced diabetic rats and to

observe and determine the morphology of islets of animals from different treatment groups.

Twenty eight male Wistar rats (weighting 220-240 g at the start of experiments) were divided

into four groups. The first group was served as control and received no treatment. The second

group was served as diabetic control which they received 120 mg/kg of alloxan. The other two

groups were diabetic rats which were injected with 0.5 mg/kg of glibenclamide or 200 mg/kg of

walnut peptide for 21 days. Blood glucose readings and body weight were monitored during the

treatment period. Histological analysis was carried out on the pancreas and the kidneys of

animals in the treated and control groups. Our results showed that walnut peptides reduced

hyperglycemia in the diabetic animals. Histological analysis also indicated that walnut peptides

may be able to regenerate the damaged islets in the diabetic rats. Walnut peptides as a

nutraceutical agent may have potential regenerative effects towards the diabetic rats and can be

considered in different industries.

Keywords: Hyperglycemia, Alloxan, Walnut peptide, Rats.


Weak interaction at nanoparticles alter function and conformation

of proteinase k

Mansoore Hosseini Koupaei1, Behzad Shareghi1, Ali Akbar Saboury2, 3, Fateme Davar4, Aboulfazl

Semnani5

1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box.115, Iran.

2 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.


4 Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.

5Department of Chemistry, Faculty of Science, University of Shahrekord, Shahrekord, Iran.

Abstract

Weak protein- nanoparticle (Np) interactions are studied in a low binding regime as a model for the soft

protein corona around nanoparticles in complex biological fluids. No covalent interaction between

proteinase K (a serin protease) and zinc oxide nanoparticles (around 30nm) shows significant alteration in

conformation and enzymatic activity. Enzyme inhibition is accompanied by changes in the proteinase K

conformation. Changes in the stern- Volmer quenching constant and the fluorescence quenching of the

proteinase K suggesting a more polar location of Trp residues. Far-UV circular dichroism (CD) studies

showed that zinc oxide nanoparticles could change the secondary structure of proteinase K via increasing

in the content of α-helix structure. The thermodynamic parameters also indicated that the binding of

proteinase K on nanoparticles was spontaneous and the hydrogen bonds played a major role in interaction

of enzyme (proteinase K) with nanoparticles (zinc oxide).

Keywords: Proteinase K- nanoparticle, Weak interaction, CD- enzyme inhibition.


Evaluation of structure, stability and chaperoning function of R12C

human αA-crystallin under oxidative stress

Kazem Khoshaman and Reza Yousefi

Protein Chemistry Laboratory (PCL), Department of Biology, Shiraz University, Shiraz, Iran.

Abstract

The oxidative stress in eyeball which occurs under chronic hyperglycemia and during

inflammation has been already indicated in the pathogenesis of cataract disorders. As the main

fraction of soluble lens proteins, α-crystallin has been indicated to play a vital role in the

maintenance of eye lens transparency. In the current study, the cataractogenic R12C mutant αA-

crystallin and its wild-type protein counterpart were incubated under oxidative stress for various

times. Then, several spectroscopic techniques and gel mobility shift analyses were applied to

investigate stability and structural/functional properties of these recombinant proteins. Upon

incubation with hydrogen peroxide, extensive disulfide covalent cross-linking was induced in

R12C mutant protein. Also, hydrogen peroxide-induced cross-linking was accompanied with an

important reduction in stability and significant loss of chaperone activity of this mutant protein.

The obtained results suggest that individuals carrying the R12C mutation are at an increased risk

to develop early-onset cataract under medical conditions such as diabetes mellitus and

inflammation which are associated with oxidative stress.

Keywords: αA-crystallin, Hydrogen peroxide, Disulfide cross-linking, Chaperone, Cataract.


Application of β-casein nano-vehicles for oral drug delivery systems

in cancer therapy

Adeleh Divsalar1 and Ali Akbar Saboury2

1Department of Biological Sciences, Kharazmi University, Tehran, Iran.


Abstract

The clinical applications of platinum drugs are limited due to poor water solubility, low

stability, interactions with healthy tissues, and severe side effects. Then, in the present study, we

have explored a novel protective nano-platform based on the self-assembly of β-Casein (β-CN)

copolymers for the oral delivery of a platinum drug. Initially, affinity and stoichiometry of

association of Pt (II) complex to β-CN was characterized by fluorescence spectroscopy. Then,

the influences of pH and protein concentration on the formation of a colloidally-stable

nanocarrier system composed of drug-loaded β-CN in the absence and presence of chitosan

were investigated using dynamic light scattering (DLS)/zeta potential analysis and scanning

electron microscopy (SEM). Finally, the bioefficacy and cytotoxicity of Platinum drug loaded

in β-CN nanoparticles were evaluated on colorectal carcinoma HCT116 cells and compared with

the free drug. The results obtained from the DLS and SEM analyses are proof for the formation

of the β-CN -Platinum drug nanoparticles with very good colloidal stability and average particle

sizes of 200-250 nm. Treatment of colorectal carcinoma HCT116 cells with free and

encapsulated platinum drug indicated that the cytotoxicity and cellular uptake of the drug

was enhanced when entrapped in β-CN nanoparticles. Finally, it can be concluded that the β-

CN nanoparticles containing platinum drug can be a very promising candidate for the use in oral

drug delivery for cancer treatment.

Keyword: β-CN, Pt (II) complex, Bioavalibility, Nanocarrier, Oral drug delivery.

http://www.wikigenes.org/e/mesh/e/3796.html

http://www.wikigenes.org/e/mesh/e/3796.html


Homo-FRET in labeled proteins by steady-state fluorescence

anisotropy, revising the theory, rethinking the assumptions

Zahra Zolmajd-Haghighi1, Quentin Hanley2, Aliakbar Saboury1

1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2School of Science and Technology, Nottingham Trent University, Nottingham, UK.

Abstract

Oligomerization of proteins are involved in many biological functions and mal-functions. Model

systems that simulate such phenomena can be used to monitor oligomerization of proteins. Techniques based on Resonance Energy Transfer between identical fluorophores (homo-FRET)

can uncover the oligomerization state of proteins. Homo-FRET causes the fluorescence

anisotropy of the system to decrease when the number of identical fluorophores within energy

transfer distance increases. Theories that describe these systems applied an assumption of equal

fluorescence efficiency for all sites that means emission intensity of fluorophores do not change

when in close proximity with each other in a cluster. However, most fluorophores in close

proximity show either self-quenching or emission enhancement. Bovine serum albumin (BSA)

solutions that were fractionally labelled with FITC was chosen to mimic aggregation of

fluorescently labeled proteins. Previous theories were then applied to analyze the data and to fit

the results. The analysis showed that the model system did not follow the assumption of equal

fluorescence efficiency and by applying the assumption the cluster sizes were under-estimated. It

was also shown that applying the assumption of equal fluorescence efficiency would over-

estimate the cluster size in systems that show enhancement of emission upon proximity of

fluorophores. Modified analytical expressions were then presented for fully labeled and

fractionally labeled systems that show a range of quenching or enhancement behavior and the

experimental results of BSA were analyzed.

Keywords: Oligomerization, Bovine serum albumin (BSA).


Effect of surface engineering at nano scale on the protein adsorption

and bacterial adhesion of polymeric and metallic substrates

Amir Razmjou, Parisa Moazzam, Fatemeh Noorisafa

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box

73441-81746, Isfahan, Iran.

Abstract

Protein adsorption is the first of a complex series of events that regulates many phenomena at the

nano-bio interface, e.g. cell adhesion, biofilm formation, in vivo inflammatory responses and

protein crystallization. Understanding of how nanoscale morphology and hierarchical structure

influences protein adsorption and cell adhesion is strategic for providing insight into all of these

processes. The tendency of proteins attachment to the surface depends on the material properties

such as surface energy, structure, texture, and relative charge distribution. Here a systematic

superhydrophobic and superhydrophilic surface modification were done to find out the rule of

surface morphology and chemistry on the biomaterial- cells interactions. In this study surface

modification via grafting technique in the surface of polymer and metal alloys were done to

investigate the effect of modification on the biomaterials biocompatibility. A systematic

characterization was conducted to elucidate the role of each parameters on the protein adsorption

and bacterial adhesion. The aluminum surfaces were characterized by SEM, EDAX, XPS, AFM,

FTIR, contact angel (CA) goniometry, surface free energy (SFE) measurement, MTT, Bradford,

Lowry and microtiter plate assays and also flow cytometry and potentiostat analyses.

Engineering the surface wettability towards superhydrophilicity/superhydrophobicity has been

found an impressive technique to enhance biocompatibility and reduction in protein-material

interactions.

Keywords: Protein adsorption, Super hydrophobicity, Super hydrophilicity, Hierarchical

nanostructured surfaces.


Spectroscopic and molecular docking studies on interaction of

prodigiosin with β-Lactoglobulin

Banafsheh Rastegari and Hamid Reza Karbalaei-Heidari

Molecular Biotechnology Laboratory, Department of Biology, Faculty of Science, Shiraz University, Shiraz 71454,

Iran.

Abstract

β-Lactoglobulin (β-Lg), the major whey protein in bovine milk, has a high affinity for

encapsulating poor souble drugs in oral drug delivery. Prodigiosin is a family member of

tripyrrole red pigments called prodiginines which shows attracting increasing interest because of

their antimicrobial, antimalarial, immunosuppressive and remarkable selective anticancer

activities. In this study, the interaction of prodigiosin with β-Lg was investigated through far-UV

circular dichroism (CD) spectroscopy, fluorescence spectroscopy and molecular docking studies.

Prodigiosin interacts with the central calyx of β-Lg with association constant of 1.99 × 104 M-1

to form 3:2 complexes at 300 K. The results indicated that binding of prodigiosin to β-Lg caused

strong fluorescence quenching of protein through static quenching mechanism. Hydrophobic

interactions are the major forces in the stability of Prodigiosin–β-Lg complex with entropy-

driving mode. CD spectra showed slight conformational changes in β-Lg due to the binding of

prodigiosin. Moreover, pH-dependent interaction survey confirmed that the prodigiosin binds to

residues located in the central calyx of β-Lg with association constant of 1.99 × 104 , 1548 and

184 M-1 in pH 7.4, 5.5 and 3.0, respectively.

Keywords: Prodigiosin, β-Lactoglobulin, Fluorescence, CD, Molecular docking.


Virtual screening of piperine analogs as survivin inhibitors and

their molecular interaction analysis by using consensus docking,

MD simulation, MMPB/GBSA and alanine scanning techniques

Elham Sattarinezhad, Abdol-Khalegh Bordbar, Najmeh Fani

Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran.

Abstract

Survivin, as a potential target for cancer therapeutics, is essential for tumor cell proliferation and

viability. In this study, consensus docking of AutoDock and AutoDock Vina was carried out in

order to improve the reliability of docking in a virtual screening of a library of 2497 Piperine

derivatives as a novel group of survivin inhibitors. The initial docking of these compounds into

the binding site of survivin, using AutoDock Vina program, resulted in the selection of the

top100 derivatives with the highest binding affinities. A subsequent screening was done on these

100 compounds by recalculation of the binding energies using the Auto Dock program.

Considering the obtained binding energies, the top two highest ranked compounds, as well as

piperine, were selected and subjected to three independent10 ns molecular dynamics (MD)

simulations in order to further validate the proposed binding modes and interactions.

Subsequently, the contributions of van der waals interactions, electrostatic forces, and the polar

and non-polar solvation in the total binding free energies were calculated using the

MMPB/GBSA methods and the entropy component as a further refinement of the total free

energy was calculated by the nabnmode module of AMBER. In addition to MMBP/GBSA

methods, the contribution of each active site residue to the total binding free energy was assessed

using alanine scanning. The results represent a key role by the hydrophobic forces in the

molecular interactions and elucidate the binding modes of Piperine analogs for further

experimental studies.

Keywords: Survivin, piperine, Consensus docking, MD simulation; MMPB/GBSA; Alanine

scanning.


Heterologous expression and functional characterization of multiple

isoforms of rice metallothionein

Azar Shahpiri, Mohsen Zarei, Rezvan Mohammadi Nezhad, Iman Soleimanifard, Soheil Piezadeh

Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111,

Iran.

Abstract

Metallothioneins (MTs) are a superfamily of low-molecular-weight, cysteine (Cys)-rich proteins

that are believed to play important roles in protection against metal toxicity and oxidative stress.

Plants have several MT isoforms, which are classified into four types based on the arrangement

of Cys residues. In this study, four rice (Oryza sativa) MT isoforms OsMTI-1b, OsMTI-2a,

OsMTI-3a and OsMTII-1a that belong to type 1, type 2, type 3 and type 4, respectively, were

heterologously expressed in Escherichia coli as carboxy-terminal extensions of glutathione-S-

transferase (GST). The tolerance of E. coli cells expressing GST–OsMTI-1b, GST-OsMTI-2b

and GST-OsMTI-3a considerably increased to Ni2+, Cd2+ and Zn2+ through the accumulation of

more metal ions compared with cells expressing GST alone. However, the tolerance of cells

expressing GST-OsMTII-1a protein increased slightly only to Ni2+. The recombinant MTs were

extracted from E. coli cells and purified using affinity chromatography. The apo forms of these

MTs were provided by acidification and then were exposed to Cd2+ , Ni2+ and Zn2+. The UV

absorption spectra and competitive reactions of in vitro Cd2+/Ni2+-incubated proteins with 5-5_-

dithiobis(2-nitrobenzoic) acid revealed that GST–OsMTI-1b, GST-OsMTI-2b and GST-OsMTI-

3a are able to form Cd/Ni/Zn-thiolate clusters. However these different rice MT isoforms has

different ability in binding to different metals. The recombinant form of GST-OsMTII-1a was

not able to bind metals. In addition none of new strains were not able to bind Cu2+.

Keywords: Metallothionein, Rice, Metal-binding characterization.


Assessment of antibacterial and antioxidant activity of silver

nanoparticles produced by reduced glycated casein adducts

Zohreh Tavaf1,3, Mohammad Tabatabaei1, Farhad Panahi2, Tanaz Sadeghian3, Ali Khalafi-Nezhad2

1Department of Pathobiology, Schools of Veterinary Medicine, Shiraz University, Shiraz, Iran.

2Department of Chemistry, Shiraz University, Shiraz, Iran.

3Protein Chemistry Laboratory (PCL), Department of Biology, Shiraz University, Shiraz, Iran.

Abstract

The inappropriate antibiotic prescribing and use have been identified as major factors in the

emergence of antibiotic resistance. The cariogenic bacterium Streptococcus mutans (S.mutans) is

the major cause of dental caries worldwide. Due to their effective antibacterial and antiviral

properties and lower propensity to develop resistance, silver nanoparticles (AgNPs) have

recently gained much attention. In the current study, we report an economically green route for

the synthesis of biocompatible AgNPs, employing reduced glycated adducts of whole casein

fraction (gWCF) from bovine milk as the reducing/capping agents. We applied different

spectroscopic techniques and microscopic assessment for characterization of AgNPs. moreover,

the antimicrobial properties of AgNPs against S. mutans were evaluated, using zone of inhibition

method. According to the results of our study, gWCF demonstrates significant ability for the

efficient synthesis of stable AgNPs which indicated reasonable size ranges. Additionally, the

AgNPs produced in the presence of gWCF exhibited promising antibacterial properties against

cariogenic bacterium S.mutans. Overall, this study recommends the application of reduced

glycated casein adducts (gWCF) as a novel and important source of biomaterials for the

economic and efficient production of relatively stable AgNPs with reasonable antibacterial

properties against cariogenic bacteria S. mutans.

Keywords: Silver nanoparticles (AgNPs), Antimicrobial properties, Streptococcus mutans,

Whole casein fraction (WCF), Glycation.


QM/MM spectroscopic investigation of the structure of the light-

driven enzyme protochlorophyllide oxidoreductase (LPOR)

Samira Gholami1, AbdolKhalegh Bordbar1 , Marco Garavelli2, Ivan Ravilta2, Artur Nenove3, Mehdi

Davari4, Marco Bocola4, Ulrich Schwaneberg5

1 Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.

2 Laboratoire de Chimie, Ens de Lyon, Site Jacques Monod - 46 allée d'Italie, 69364 Lyon cedex 07, France.

3 Dipartimento di chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy. 4 Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany.

5 DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany.

Abstract

POR, catalyzes one of the latter steps in the chlorophyll biosynthesis pathway, the trans addition

of hydrogen from NADPH (as cofactor) across the C17–C18 double bond of the D-ring of

Pchlide (protochlorophyllide) to produce Chlide (chlorophyllide). Regarding to the lack of the

crystal structure of LPOR a full identification of the reaction pathway at room temperature, the

identification of the initial intermediate state(s) involved, and the nature of structural changes

that lie at the origin of the activation process, still is unclear in this enzyme. In this paper, we

first present a refined homology model of the ternary POR enzyme of T.elongatus based on the

previous ssPOR model. In this model, missing parts and the orientation of the active site residues

was refined and the binding mode of the substrate and cofactor was corrected. Molecular

dynamics simulations suggested that coordination number of central magnesium is 6 in both free

and bound Pchlide, as previously also proposed in FLN spectra. QM/MM spectroscopic

investigations revealed that there is no any characteristics shift in the first band of the absorption

spectra (Qy) from solvent to protein, and the Qy is not influenced by the environment and the

magnesium coordination number, therefore linear absorption cannot undoubtedly be used to

justify the reported experimental shift in Qy solvent to protein. However, computational transient

IR spectra of the enzyme-substrate complex was in agreement with the experimental one which

led to re-assigning of the important peaks involved in the catalytic reaction and validating the

accuracy of our model.

Keywords: Light-driven protochlorophyllide oxidoreductase (LPOR), Protochlorophyllide,

homology modeling, QM/MM calculations, Computational spectroscopy.


Computer-aided design of new Typrostatin-A derivatives as

simultaneous effective inhibitors of αβ-tubulin and breast cancer

resistance protein

Najmeh Fani, Abdol- Khalegh Bordbar, Elham Sattarinezhad

Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.

Abstract1

In the first part of this paper, docking method was employed in order to study the

structure−activity relationships (SAR) for a group of previously synthesized and designed

Tryprostatin-A (TPS-A) derivatives (which considered in our previous study as potent inhibitors

of αβ-tubulin) in the binding site of breast cancer resistance proteins (BCRP). The results

represent that these compounds bind to the binding site of BCRP with relatively suitable binding

energies and therefore could be potential inhibitors of both αβ-tubulin and BCRP proteins. In the

second part, virtual molecular docking method was utilized with the aim of design novel

analogues of TPS-A with significant inhibitory effect on both αβ-tubulin and BCRP proteins. For

this purpose binding energies and binding poses of a library of TPS-A derivatives in the binding

sites of αβ- tubulin and BCRP have been investigated using molecular docking calculations.

Molecular docking results revealed that a group of 37 compounds among them exhibit strong

anti-tubulin and anti-BCRP activity.

Keywords: Tryprostatin-A, Breast cancer resistance Protein, αβ-tubulin, Molecular docking,

Structure−activity relationships.


Evaluation of the kappa carrageenan-chitosan nano magnetics

efficiency on purification of P. indica pectinase

Parisa Fathi Rezaei1, Shahab Ghanbari1, Saleh Shahaabivand1, Gholamreza Mahdavinia2

1Department of Biology, Faculty of Science, University of Maragheh, Maragheh, Iran.

2Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.

Abstract

Pectinases are one of the most important industrial enzymes and hydrolyze pectin to galacturonic

acid. Pectin is one of the main polysaccharides in plant cell wall. Pectinases have a large number

of applications in food industries and biomass conversion. Various methods are used for

pectinase purification from microbial sources including precipitation and chromatography.

Nowadays many studies focused on purification and immobilization of enzymes on magnetic

beads. In this investigation purification of Piriformospora indica pectinase on kappa

carrageenan-chitosan nano magnetics was investigated. P. indica was cultured on YPG medium

supplemented with pectin. The slurry was filtered by centrifugation at 10,000 rpm at 4 ºC for 15

min. Later the supernatant was incubated with kappa carrageenan-chitosan nano magnetics at 4

ºC overnight with continues shaking. The enzyme was desorbed from nano magnetics by

phosphate buffer. The protein content of samples was determined by Bradford assay. Based on

the results, the protein content of the solutions treated with kappa carrageenan-chitosan nano

magnetics was elevated significantly in comparison to untreated solutions. In conclusion, kappa

carrageenan-chitosan nano magnetics could open new insights for purification of pectinase and

the optimization of its immobilization on magnetic beads is running in our group.

Keywords: P. indica, Pectinase, Pectin, Carrageenan-chitosan, Nano magnetics.


Nerve growth factor precursor and its role in alzheimer’s disease

Raheleh Masoudi

Shiraz University, Biology Department, Shiraz, Iran.

Abstract

Nerve growth factor (NGF) is one of the key factors in neuronal survival and function. In

Alzheimer’s disease (AD), there is increase in the level of NGF precursor, proNGF.

Interestingly, no change in the level of NGF mRNA has been detected. There is controversy

regarding the biological activity of proNGF. While some researches show the neurotrophic

activity of this protein, others believe that this protein is apoptotic. NGF binds to TrkA receptor

with high affinity while proNGF has more affinity for p75NTR receptor which could lead to

neuronal death. We have already shown that the ratio of TrkA to p75NTR may determine the

apoptotic or neurotrophic activity of proNGF. In this review, we focus on the role of this

precursor in Alzheimer disease considering that the level of its receptors alter in AD. Moreover,

its relation with amyloid beta and tau will be discussed.

Keywords: Alzheimer’s disease, Pro nerve growth factor, Apoptotic, Neurotrophic.


Conformational studies of Human hemoglobin and insulin upon

interaction with MTBE

Parvaneh Maghami1, 3 , Masoumeh Valipour1,4, Mostafa Sadeghpour5, Mohamad Ali Khademian6,

Khadijeh Mosavi6 , Ali Akbar Moosavi-Movahedi1,2



3Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.

4Department of Cellular and Molecular biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz,

Iran.

5Office of Health, Safety and Environment (HSE) Oil Ministry, Tehran, Iran.

6Office of Health, Safety and Environment (HSE) Oil Ministry, Bandar Mahshahr, Iran.

Abstract

Methyl tertiary butyl ether (MTBE) is the most widely used motor vehicle fuel oxygenate since it

reduces harmful emissions due to gasoline combustion. The emission of MTBE into the

environment occurs mainly during the production, distribution, storage, and use of gasoline.

There is evidence that MTBE is a toxic substance in higher dose that may have adverse effects

on both animals and humans. Due to MTBE is well absorbed after inhalation, oral, or dermal

exposure it is necessary to clear the molecular mechanism of it. Hemoglobin (Hb) and insulin are

most functional proteins in blood and play critical role in oxygen transport and regulation of

glucose in body respectively. The aim of this study was to analyze and compare structural

changes of Hb and insulin in the presence of different concentrations of MTBE. Our result shows

that different structural changes in hemoglobin and insulin in the presence of MTBE by

spectroscopic methods. According to fluorescence and circular dichroism spectroscopy, insulin

formed a molten globule (MG)-like structure in the presence of MTBE under physiological pH

while heme degradation was observed in hemoglobin structure. To delineate the mechanisms

involved in MTBE-protein interactions, the formation of reactive oxygen specious (ROS) was

measured by chemiluminesence technique. As a result, the interaction of MTBE with cited

proteins which possess different conformational states in order to carry their biological functions

would be different.

Keywords: Methyl tertiary butyl ether, Molten-globule, ROS, Insulin, Heamoglubin.

https://www.google.com/search?biw=1280&bih=699&q=Hemoglobin+and+insulin+are+most+functional+protein+in+blood+and+play+critical+role+in+oxygen+transport+and+regulation+of+glucose+in+our+body+respectively&spell=1&sa=X&ved=0ahUKEwjEwfWk8LzLAhVDD5oKHfhLDboQvwUIGSgA




Molecular dynamics simulations of surfactant peptides wrapping

single-walled carbon nanotubes

Karim Mahnam2 , Alireza Mansouri2,3 , Abolfazl Barzegar2

1 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.

2Department of Biophysics, Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.

3Department of Young Elites scientific Site, Iran.

Abstract

The non-covalent interaction of single-walled carbon nanotube (SWCNT) with surfactant

peptides makes them soluble in biological media for application in nanomedicine, drug delivery

and gene therapy. In this study, ten surfactant peptides with the length of 8 residues were

designed using Lys, Trp, Tyr, Phe and Val amino acid residues. 300 ns MD simulation was

performed for free surfactant peptides in water and surfactant peptides near to a (6 6) carbon

nanotube. Our results indicate that the binding affinity of peptides to SWCNT increase with the

increase aromatic residue content. Among of aromatic residues, the peptides containing Trp

residues have higher binding affinity to SWCNT than the peptides with Phe or Tyr residue. The

results of binding affinity showed aromaticity parameter is more important than the

hydrophobicity in binding peptides to SWCNT. In addition, steric hindrance between aromatic

residues and the distance between them is important for binding free energy of peptides to

SWCNT.

Keywords: Single-walled carbon nanotubes, Surfactant Peptide, Molecular dynamics simulation,

Binding free energy.


N-methyl phenylalanine-rich peptides as potential blood -brain

barrier shuttles

Morteza Malakoutikhah1, † Meritxell Teixidó, Ernest Giralt2


Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10, E-08028

Barcelona, Spain.

Abstract

The blood-brain barrier (BBB) protects the brain from harmful substances in circulating blood

and regulates the entry of particular molecules from blood into the central nervous system

(CNS). This physical and enzymatic barrier is the major bottleneck for the delivery of

therapeutic agents to the brain. The BBB is formed by endothelial cells that are sealed through

tight junctions, which significantly block paracellular transport. To bypass the BBB and deliver

drugs to the brain, several strategies have been used: temporarily opening the BBB,

administration of very high doses of a drug, and direct injection of a drug into the spinal cord.

However, these approaches imply risks of infection and toxicity and, in addition, require

qualified personnel.1, 2 here several peptide families containing N-methylated amino acids were

designed and synthesized using solid phase peptide synthesis (SPPS). The permeability and

lipophilicity of these compounds were studied by parallel artificial membrane permeability assay

(PAMPA) and immobilized artificial membrane chromatography (IAMC) to select the best

peptides in terms of length, terminal groups, and amino acid replacement to be used as carriers

that pass through a model of the blood-brain barrier (BBB) by passive diffusion. Furthermore,

the enzymatic stability of these peptides in human serum and their cell viability by MTT assay

were tested. These peptide families showed great stability and nontoxicity. The three peptides

that showed the greatest permeability were coupled to levodopa, GABA, Nip, and ALA to

examine their passive BBB permeation by means of PAMPA and their lipophilicity by IAMC.

Unaided, these nonpermeating drugs alone did not cross the PAMPA barrier and the BBB

passively; however, the peptides tested as potential BBB shuttles transferred them by passive

transfer through the PAMPA phospholipid. The permeability of peptides that showed the highest

permeability in PAMPA was also examined in bovine brain microvessel endothelial cells

(BBMECs).3,4 These peptide-based BBB shuttles can open up the possibility to overcome the

formidable obstacle of the BBB, thereby achieving drug delivery to the brain.

Keywords: Blood-brain barrier, N-methyl phenylalanine, Parallel artificial membrane

permeability assay (PAMPA), Immobilized artificial membrane chromatography (IAMC).


Free radical scavenging and denaturation-inhibiting effects of

peptides from fish skin in vitro and in food model system

Mehdi Nikoo1

1Department of Fisheries, Faculty of Natural Resources, Urmia University, Urmia, West Azerbaijan 5756151818,

Iran.

Abstract

From the skin of fish the peptide with amino acid sequence of proline-alanine-glycine-tyrosine

and molecular weight of ~406 Da was isolated from using RP-HPLC and antioxidant activity and

cryoprotective effect of the peptide and skin gelatin hydrolysates in vitro and in fish mince

model system was investigated. Peptide showed scavenging activity against free radicals (DPPH,

ABTS and hydroxyl). Addition of peptide into model system lowered the peroxide and

thiobarbituric acid-reactive substances when compared to the control, most probably due to their

free radical scavenging potency. Based on low-field proton nuclear magnetic resonance analysis,

peptides in hydrolysates prevented the displacement of water molecules between the different

muscles compartments, thus stabilizing the water associated with myofibrils (as reflected by T21)

induced by freeze–thawing. Peptides were able to retard protein oxidation as indicated by the

retarded protein carbonyl formation and lower loss in sulfhydryl content. As determined by

differential scanning calorimetry, at freeze-thaw cycle 0, enthalpy (ΔH) of myosin ranged from

1.49 to 1.84 mJ mg-1 and control mince had significantly lower ΔH than those with added 25 and

50 ppm of peptide. After 6 freeze-thaw cycles, ΔH of myosin in minces with added peptide was

higher than that of the control. Enthalpy of the second peak (actin) at freeze-thaw cycle 0 ranged

from 0.29 to 0.46 mJ mg-1 and higher ΔH was found for minces with added 25 ppm peptide.

Furthermore, when gelatin hydrolysates were added, higher transition temperature (Tmax) of

myosin and higher enthalpy of myosin and actin was observed.

Keywords: Free radicals, Peptides, Fish skin protein, Denaturation-inhibiting effect, Food model

system.


Antibacterial evaluation of Bis (2-methyl-1H-imidazole-κN3) silver

(I) dichromate (VI) by autodock vina function

Faeze Hashemi*1, Azizolla Beheshti1, Hossein Motamedi2

1Department of Chemistry, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran. 2Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.

Abstract

A novel silver complex [Ag(C4H6N2)2]2Cr2O7(1) has been synthesized and fully characterized by

single crystal X-ray diffraction ,UV–Vis, elemental analysis and FT-IR techniques. The

antibacterial tests of free 2-methylimidazole ligand, Ag2[CrO4] and its complex 1 were studied

by using molecular docking technology and antibacterial test in vitro. The 3 three-dimensional

(3D) structures of the 5 compared compositions an 2-methylimidazole ligand and

[Ag(C4H6N2)2]2Cr2O7 were established by Autodock vina function The antibacterial activity

studies of the free 2-methylimidazole ligand, Ag2[CrO4] and its complex 1 show that, the ability

of these compounds to inhibit growth of the tested bacteria. Molecular-docking investigations

between the five standard antibiotic, free 2-methylimidazole ligand, complex 1 and fragment of

bacterial DNA and five biological macromolecule enzymes (receptors) were carried out. The

results of docking studies confirm that the antibacterial activities of these compounds.

Keywords: Molecular-docking, scoring function, Antibiotic experiment in vitro, Bacterial DNA.


Looking for a generic inhibitor of amyloid-like fibril formation

among tri hetero cyclicsmall molecules

Hassan Ramshini and Najmeh Annabestani

Biology Department, Payam Noor University, 19395-4697 Tehran, I.R. of Iran.

Abstract

A range of diseases is associated with amyloid fibril formation. Despite different proteins being

responsible for each disease, all of them share similar features including beta-sheet-rich

secondary structure and fibril-like protein aggregates. A number of proteins can form amyloid-

like fibrils in vitro, resembling structural features of disease-related amyloids. Given these

generic structural properties of amyloid and amyloid-like fibrils, generic inhibitors of fibril

formation would be of interest for treatment of amyloid diseases. Several natural and synthetic

flavone derivatives have been reported to inhibit formation of amyloid fibrils or to remodel

existing fibrils. These studies suggest that heterocyclic aromatic small molecules are effective as

amyloid inhibitors. At the present study, we have evaluated 7Tri Aryl Benzene derivatives to

reduce amyloid fibril formation by hen egg white lysozyme (HEWL) and its associated

cytotoxicity. The inhibitory effect of the compounds was investigated against hen egg white

lysozyme (HEWL) fibrillation. The molecules were tested using ThT, AFM and MTT assay. We

found all 7 compounds able to inhibit HEWL aggregation in a dose-dependent manner. Our

study showed that these compounds also inhibit the cytotoxic activity of aggregated HEWL

toward cell culture. In conclusion, we found the core structure of the compounds plays the

primary inhibitory role and the side chain groups of the compounds modulate their effects.

Keywords: Lysozyme, Amyloid aggregation, Tri ArylBenzene, Cytotoxicity.


The crucial role of a Ω–loop the stability and activity of the Exo–

inulinase

Maryam Rezaei Arjomand1, Mehran Habibi–Rezaei1, 2, Gholamreza Ahmadian3

1School of Biology, College of Science, University of Tehran, Tehran, Iran. 2Nano–Biomedicine Center of Excellence, Nanoscience and Nanotechnology Research Center, University of

Tehran, Tehran, Iran. 3Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and

Biotechnology, Tehran, Iran.

Abstract

Inulinases are considered in the food and medical industries. They especially have industrial

potential for production of high–fructose syrup (HFS), inulooligosaccharides, and bioethanol.

Inulinases are members of family 32 (GH32), (CAZy) (http://www.cazy.org/) and are divided

into endo– and exo–inulinases. Endo–inulinases (EC 3.2.1.7) hydrolyse internal (2→1) β–D–

fructosidic linkages in inulin and produce inulooligosaccharides while exo–inulinases (EC

3.2.1.80) hydrolyse (2→1) β–D–fructofuranose linkages from the non–reducing end of the inulin

to release D–fructose and a D–glucose. Here, we report the deletion of a juxta active site loop

fragment (74YGSDVT79 sequence) from third Ω–loop of the exo–inulinase (PDB ID: 1Y4W) from

Aspergillus niger to study its structural and functional importance. To investigate the flexibility

of this region, molecular dynamics simulations for 80 ns were performed in two parts of the

native and mutant (Δ6SL) enzymes. MD simulation data were shown that deleted region has a

role in increasing the rigidity of the enzyme. Moreover, molecular docking was performed to

compare the interactions in the active sites of native and Δ6SL enzymes with fructose. The

functional thermostability, kinetic parameters and activation energy (Ea) of the catalysis of both

enzymes indicate on the importance of the deleted sequence on the catalytic performance of the

enzyme. In conclusion, juxta active site loop fragment not only plays an important role in the

stability of the enzyme, it involves in the enzyme catalysis through lowering the activation

energy of the catalysis and effective improving the catalytic performance.

Kewword: inulinase, molecular dynamic, enzyme catalysis.


Different strategies for designing protein inhibitors, agonists and

super-agonists

Sayyed Hamid Zarkesh Esfahani1, Zeinab Monajjemi Rarani2

1Sayyed Hamid Zarkesh Esfahani, PhD, Immunology, Department of Biology, Faculty of Sciences, University of

Isfahan, Isfahan, Iran.

1Zeinab Monajjemi Rarani, MSc student, Microbiology, Department of Biology, Faculty of Sciences, University of

Isfahan, Isfahan, Iran.

Abstract

Proteins do not function in isolation; it is their interactions with one another and also with other

molecules (e.g. DNA, RNA) that mediate metabolic and signaling pathways, cellular processes,

and organismal systems. Protein–protein interactions are central to most biological processes.

Many human diseases can be traced to aberrant protein–protein interactions, either through the loss

of an essential interaction or through the formation of a protein complex at an inappropriate time

or location. The inhibition of these aberrant associations is of obvious clinical significance. In

some cases, the nonfunctional proteins due to mutations may cause diseases in human. Growth

hormone deficiency in children that leads to dwarfism is an example of such diseases that can be

successfully cured using recombinant human growth hormone.

A range of approaches are being developed to generate inhibitors, agonists and super-agonists of

protein–protein interactions that may form useful therapeutics for human disease. These

therapeutic proteins proved to be very efficient and have improved the management of many

diseases that were incurable for centuries. Protein agonists and antagonists have raised the hope for

treatment of many other diseases and are one of the biggest market in pharmaceutical industries.

Multiple approaches have been developed to prevent or mimic the effects of proteins including:

recombinant protein production, anti-receptor antibodies, soluble receptors, mutant proteins,

siRNAs, small molecule inhibitors, etc.

Keywords: protein, agonist, antagonist, super-agonist


rh-IGF-1 (mecasermin): expression, purification and formulation

Mohammad Reza Mofid

Department of Biochemistry, School of Pharmacy and Bioinformatics Research Center, Isfahan University of

medical sciences, Isfahan, Iran.

Abstract

Insulin-like growth factor-1 (IGF-1) is a single chain polypeptide made up of 70 amino acids

with three helix and three disulfide bonds. IGF-1 is mainly secreted by the liver as a result of

stimulation by growth hormone (GH). More than 99% of IGF-1 in blood is in complex with IGF

binding proteins (IGFBPs). IGFBP-3 is the major IGF binding moiety in plasma. Mecasermin

(rh-IGF-1 with point mutation T4I) is a pharmaceutically noticed recombinant protein.

Mecasermin has a 20 times longer half-life than IGF-1 in plasma. The object of present research

is over- production of Mecasermin by employing effective factors in order to achieve more

native protein and reduce extensive losses of product during purification.

After production of Mecasermin in E. coli, purification of the protein was performed by

extraction of Inclusion body, solubilization in 6M Gdn-HCl, refolding, purification by gel

filtration column and further formulation of them. The analyses of mecasermin were

accomplished by SDS-PAGE, Western-blot, ESI-MS, ELISA of IGF-1, Endotoxin assay, SEC

chromatography and biological assay.

Here we set up an over- production method with novel and efficient downstream purification to

achieve both high quantity and quality of mecasermin.

Keyword: Mecasermin, Purification, SEC chromatography, Recombinant protein.


Functionalized superparamagnetic nanocarriers in enzyme

engineering: Highly dispersive, stable and robust biocatalysts

Asghar Taheri-Kafrani, Asieh Soozanipour and Maryam Royvaran

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan,

Isfahan, 81746-73441, Iran.

Abstract

Immobilized enzymes are used as biocatalysts for analytical purposes in diagnostics and for

preparative purposes in large scale industrial processes. Immobilization can increase the half-life,

improve the stability, and increase the catalytic activity of an enzyme. It facilitates the separation

and recovery of the catalyst from the reaction products, and allows for multiple use of the

biocatalysts. Herein, we demonstrated synthesis of silica-coated modified magnetite

nanoparticles via cyanuric chloride activation, magnetic nanoparticles supported hyperbranched

polyglycerol (MNP/HPG) and graphene oxide nanosheets decorated with superparamagnetic iron

oxid nanoparticles (SPGO) as convenient nano platforms for immobilization of enzymes. Then,

an important industrial enzyme, xylanase, was immobilized on the nanocarriers to produce robust

biocatalysts. A variety of analytical tools was used to study the morphological, structural and

chemical properties of the biocatalysts. Additionally, the results of biocatalyst systems exhibited

the substantial improvement of reactivity, reusability and stability of xylanase due to this

strategy, which might confer them a wider range of applications.

Keywords: Functionalized magnetite nanoparticles, Immobilization, Xylanase, Enzyme activity.


Lens antioxidant defense mechanism plays an essential role against

oxidative stress induced structural damages of crystallin proteins

Reza Yousefi

Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.

Abstract

α, β, and γ-crystallins are present at extremely high concentration (>300 mg/ml), accounting for

more than 90% of the total soluble proteins in the lenticular tissues. Due to their remarkable

longevity, lens crystallins accumulate a substantial amount of post-synthetic modifications on their

structures which ultimately culminate in development of cataract disorders. The generation of

reactive oxygen species in the lenticular tissues occurs from a variety of sources which may

subsequently induce protein structural damages, accelerates the rate of ascorbic acid oxidation and

catalyzes non-enzymatic glycation of lens crystallins. Using different spectroscopic methods, gel

mobility shift assay, and lens culture assessment, we indicated important capacity of antioxidant

defense mechanism of eye lens against various structural and functional damages of lens

crystallins which induced under oxidative sates. We believe that under normal conditions lens

antioxidant defense mechanism effectively prevent these structural and functional insults. However

mass production of oxidative agents in the lenticular tissues, under a variety of conditions such as

diabetes, aging, senile cataract, infection and exposure to sunlight may overcome the capacity of

the antioxidant defense mechanism leading to lens opacification.

Keywords: Lens crystallins, Oxidative stress, Antioxidant, Structural damages, Dehydroascorbate.


Memory prison of protein

Gholamhossein Riazi1, Shahryar Pooyan, Nima Allahyari

Neuroorganic Lab, Department of Biochemistry, Institute of Biochemistry and Biophysics (I.B.B),

University of Tehran, Tehran, Iran.

Abstract

The mechanism of information custody in biological specious in perhaps the most

complex subject among life’s processes to study such mechanism has been tested since

several centuries ago. Based on fractal theory, the human memory of mimics small

molecules such of proteins, complex globular structure of proteins in protect candidate for

keeping information so called memory. Primary sequence and geometry of third and

fourth structure would be involved in memory of biological organisms. Naturally more

complexity drives the protein to more ability for prisoning information inside.

Microtubules proteins which in a polymer of thousands of tubulin monomer, with

hydrophobic pocket changing hydrophobic pocket structure has been shown to the very

stable while microtubule protein, as to as vesicle transporter at the time.

Keywords: Memory, Microtubules, Complexity, Fractal theory.


Isolation of α glucosidase inhibitor producers, Bacillus sp. RP073

and virgibacillus sp. RP072 from Persian Gulf.

Roya pournejati, Samira Rezaei, Hamid Reza Karbalaei-Heidari

Molecular Biotechnology Laboratory, Department of Biology, Faculty of Science, Shiraz University, Shiraz 71454,

Iran.

Abstract

Diabetes mellitus is an advanced metabolic disorder which shows increase of blood glucose level

followed by serious damages in several organs such as kidney, nerves and retina. Alpha-

glucosidase is a key enzyme which produces by epithelial cells of duodenum and helps to digest

of foods by hydrolyzes of starch and disaccharides. Inhibitors of this enzyme have suitable

potential for using indiabetes mellitus type 2 treatment as a drug. These compounds can delay the

absorption of carbohydrates through the intestine and consequently reduces the blood sugar and

insulin level immediately after feeding. Secondary metabolites are organic molecules that are not

involved in the normal growth and development of an organism, but have great importance for

human health due to their bioactive properties such as antibacterial, antitumor, anti-

inflammatory, immunosuppressant, and etc. In the present investigation, 39 bacterial marine

isolates from coastal area of Persian Gulf were selected and screened for production of secondary

metabolites with the ability to inhibit rat α-glucosidase. The results showed that the two isolates

which were characterized by 16S rDNA sequencing as Bacillus sp. strain RP073 and

Virgibacillussp. strain RP072 capable of producing secondary metabolites in TSB medium

during incubation at 30 oC after 5 days which have inhibitory effects on rat alpha-glucosidase.

Methanolic extract of the isolates biomass show 88% and 66% inhibition on the enzyme activity,

respectively.

Keywords: Alpha glucosidase inhibitors, Secondary metabolite, Bacillus, Persian gulf.


Potential application of β-lactoglobulin for presence in nano scale

oral drug delivery systems

Behafarid Ghalandari1, 2, Adeleh Divsalar3, Ali Akbar Saboury4, 5

1Department of Medical Nanotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran.

2Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran.

3Department of Cell & Molecular Biology‚ Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.

4Institute of Biochemistry and Biophysics‚ University of Tehran, Tehran, Iran.


Abstract

The possibility of biopolymers presence in nano scale oral drug delivery system is one of the

most interest topics in nanobiotechnology. β-lactoglobulin (β-LG) as a globular milk whey

carrier protein can be candidate for this aim due to its unique structure and physicochemical

properties. In this study, we investigated the design and production of β-LG nanoparticles as

nanocarrier for anticancer metal based drugs. First, β-LG interaction with oxalipalladium was

examined using fluorescence spectroscopy. Results showed that drug was bind to β-LG with

molar ratio of 1:1 by driving force of hydrophobic and predominant contribution of static

quenching mechanism. Then, β-LG nanoparticles were prepared and characterized using

dynamic light scattering (DLS) and scanning electron microscopy (SEM) and equilibrium

dialysis methods. The results show that the lowest size of nanoparticles were formed close to

isoelectric point of β-LG in the presence of low methoxyl pectin (LMP) with colloidal stability

and spherical shape. On the other hand, the equilibrium dialysis results show that the rate of drug

release in the simulated gastrointestinal tract from β-LG nanoparticles in the presence of LMP is

very low so that it can be concluded β-LG nanoparticles are resistant to acidic medium. In

addition, the highest rate of in vitro drug release is occur in the simulated terminal ileum fluid

and simulated colon fluid during simulated release time. Consequently, based on our findings β-

LG is potential biopolymer and promising candidate for presence in nano scale oral drug delivery

system.

Keywords: β -LG, Oral drug delivery, Nanoparticle, Fluorescence spectroscopy, Release.


Poster Presentation Abstracts:

Optimal isolation and purification of lens α-Crystalline protein

Shohreh Yazdani1,2, Reza Khodarahmi1, Khosrow Khajeh2

1Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

2Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

Alpha Crystalline as measure of structural protein of eye lens contains two subunits αA and αB

Crystalline. Due to its chaperon-like activity, this protein plays a preventive role in a number of

disorders such as neurodegenerative disease and cataract. For research studies, it is necessary to

develop simple and efficient strategy for isolation of the target protein of interest. Here we

designed an appropriate procedure that yields a proportion of purified α-Crystalline through a

combination of extraction of crude protein from bovine eye lenses followed by several steps of

centrifugation and sequential dialysis by the same buffer at different molarities. The efficacy of

the purification step was evaluated using electrophoretic resolution at each stage and non-

specific peroxidase activity.

Keywords: α-Crystalline, Isolation, Purification.


Molecular dynamics simulation of new cyclotide from viola tricolor

Rayeheh Vafaee and Mahboobeh Zarrabi

Biotechnology Department, Biological Sciences Faculty, Alzahra University, Tehran, Iran.

Abstract A current trend in pharmaceutical industry is to produce medications by using peptide. They tend

to develop stable drugs with new functionality as an oral administration. Accordingly, with

respect to their properties, cyclotides are the best choice. The cyclotides are antimicrobial

circular peptides that have a variety of biological activities such as anti-HIV, anti-tumor,

cytotoxic, hemolytic activity and etc. They keep their functionality in the presence of

denaturation circumstances as proteolysis, GndHC16M and such like. On the other hand, a new

cyclotide is obtained from a local species of Viola Tricolor in the north part of Iran. They

motivate us to study the stability of this kind of cyclotide in the water solvent via considering

different parameters including potential energy, RMSD, Gyradius and solvent accessible surface.

In the beginning, the cyclotide tertiary structure model has been built by Modeller software.

Hence, we run several simulations based on Molecular Dynamics by means of GROMACS

software. Corresponding results are presented and discussed in detail in this paper.

Keywords: Cyclotide, Molecular dynamics, Antimicrobial, Gromacs, Modeller.


The impact of vitamin C on amyloid structure of treated bovine

serum albumin with potassium sorbate

Elham Vahdatahar, Fereshteh Taghavi, Ali Akbar Moosavi-Movahedi

Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.

Abstract

Vitamin C (ascorbate) is a powerful antioxidant that through scavengering reactive oxygen and

nitrogen species performs its antioxidant activities. Evidence is suggested that vitamin C can

interact with radicals and oxidant substances and by this way the reaction of these substances

with protein and other soluble components is prevented strongly. The potassium sorbate is a food

preservative and previous researches refer to its role in protein structural changes through

creation of glycotoxins(Maillard products and reactive radicals).The formation of amyloid

structures is initial result of these structural changes which lead to amyloid aggregate and

amyloid -like fibril. In order to investigate the effect of vitamin C on amyloid structural changes

in treated bovine serum albumin with potassium sorbate, ThT and circular dichroism techniques

were used. Incubation of protein with potassium sorbate at 55 ° C caused distinc changes in the

secondary structure of protein and creation of amyloid structure which were in associasion with

ThT intensity increament. But the presence of vitamin C in the studied time interval (24,72,120

hours) considerably reduced the intensity of ThT. This result can be considered as the deterrent

effect of vitamin C on formation of amyloid structure of bovine serum albumin and importance

of this vitamin for designing of anti-amyloid drugs.

Keywords: Bovine serum albumin, Potassium sorbate, Vitamin C, Amyloid aggregates, Amyloid

-like fibril.


Structural intermediates of bovine serum albumin upon treatment

with potassium sorbate

Elham Vahdatahar, Fereshteh Taghavi, Ali Akbar Moosavi-Movahedi

Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.

Abstract: Today with the growing population, the need for food preservative is highly felt. Potassium

sorbate is a food preservative which is vastly used in the production of Dairy products, baked

foods, juices, frozen fruit, bread, cakes, food products, including fish, processed vegetables,

spices, jams, vegetables and gelatin products, fast food, and drinks. The toxicity of this substance

on the cells was confirmed by previous experiments. The aim of present study is to investigate

structural changes of bovine serum albumin (BSA) due to use of potassium sorbate. To evaluate

structural changes of BSA, intrinsic fluorescence and to investigate the changes in

hydrophobicity, ANS assay have been used. The results of intrinsic fluorescent study showed

reduction in intensity according to treatment of BSA with Potassium sorbate. It is worth

mentioning that the results of ANS study represents increase of intensity according to increase in

hydrophobic patches in protein surface, partially unfolding and creation of intermediate structure

of protein. Then in the next step decrease of intensity at wavelength 390nm, represents reduction

of available hydrophobic patches as a result of creation of intermediates and after that protein

aggregation to achieve greater stability. It is obvious that, understanding of protein intermediate

formation and restructure process can play a crucial role in designing of inhibitory mechanisms

for these structures.

Keywords: Bovine serum albumin, Potassium sorbate, Intermediate structure, Hydrophobic

patches.


Survivin gene cloning in bacterial host DH5α

Rashid Hooshdarpoor1, Maryam Moradi1, Mohsen Alipoor2, Farangis Ataei 1*, Saman Hosseinkhani1

1 Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.

2 Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.

Abstract

Survivin (BIRC5), is the smallest family member of the family of inhibitors of apoptosis proteins

(IAPs). Survivin is a 142-amino acid, 16.5 kDa protein encoded by a single gene located on the

human 17q25 chromosome. Survivin is a multifunctional protein that inhibits apoptosis,

regulates cell division and enhances angiogenesis. Survivin is preferentially and highly expressed

in cancer cells, with low expression in the most normal non-dividing adult tissues. The integral

role of survivin in cancer cell, division and survival makes it an attractive therapeutic target to

inhibit cancer cell growth and drug screening. In this study, wild type of survivin gene was

cloned in pDB2 eukaryotic vector for future investigation. In order to molecular cloning of

survivin gene, total RNA was extracted from breast cancer cells, MCF-7, and then survivin

cDNA was synthesized by reverse transcriptional (RT)-PCR. Thereafter, survivin gene was

amplified by PCR with PrimeSTAR®HS Taq DNA Polymerase (Takara). Then PCR product

and pDB2 vector were restricted by Hind III and Nhe I at 37 °C for 8 h and ligated at 22 °C for 4

h and then 4 °C overnight. The ligation mixture was transformed into E.coli DH5α and screened

by antibiotic (50 μg/ml ampicillin) selection. Plasmid DNA was isolated from positive colonies

(selected by colony PCR) and sequenced (Macrogen, Korea) to check inserted DNA for future

cell survival investigation.

Keywords: Survivin, MCF-7, PDB2, Cloning, Cancer.

Rashid

Highlight


Association of APOE and BDNF polymorphisms with alzheimer’s

disease in south of Iran.

2, Ali Javadpour1, Raheleh Masoudi1Zohreh Harati

1 Department of Biology, College of Science, Shiraz University, Shiraz, Iran.

2 Research Center for Psychiatry and Behavior Sciences, Shiraz university of Medical Science, Shiraz, Iran.

Abstract

Alzheimer’s disease (AD) is a neurodegenerative disorder and, in elderly people, is the most

common cause of dementia. Accumulation of beta-amyloid plaques and neurofibrillary tangles in

brain are two major pathological hallmarks of AD. Apolipoprotein E, the most important

cholesterol carrier in the brain, plays a role in clearance of amyloid plaques. APOE has three

major alleles E2, E3 and E4. E4 allele is an important risk factor for AD. Brain-derived

neurotrophic factor (BDNF) promotes neuronal survival and synaptic plasticity and is

downregulated in AD. BDNF Val66Met polymorphism (rs6265) decrease secretion of BDNF and

subsequently memory impairments and loss of hippocampal volume. The aim of this study was

to investigate the association of these three polymorphisms with risk of AD in a population of

South of Iran. 67 patients and 62 healthy controls were included in this case-control study. Two

groups were genotyped for this polymorphisms using Allele specific PCR or amplification-

refractory mutation system (ARMS). The difference in allelic and genotype frequency between

case and control groups was assessed using chi-square and regression logistic statistical analysis.

There was a significant association between E4 allele of APOE gene and risk of AD (OR= 2/9,

95% CI= 1/18- 7/16, P= 0/02). However, no association was found between BDNF

polymorphism and risk of AD in this population. This study was the first in Iran which

investigate the association between rs6265 BDNF polymorphism and risk of AD. Combination

of this polymorphisms and their association with AD was also investigated.

Keywords: Alzheimer’s disease (AD), APOE, BDNF, Allele specific PCR, South of Iran.


A molecular dynamics simulation investigation into the dissociation

constants (Kd) of Mn(II) binding on the structure and stability of

calprotectin using Molecular Dynamics Simulation

Faezeh Hashemi*, Mohammad Reza Dayer, Azizolla Beheshti

Department of Chemistry, Faculty of Science, Shahid Chamran University, Ahvaz, Iran.

Abstract

Human Calprotectin (CP) is an antimicrobial protein that competes with pathogens for transition-

metal binding belongs to Ca(II)-binding proteins of the S100 family. Crystallographic

characterization of CP heterotetramer () indicate the presence of two His4 and two His3Asp

binding sites at subunits interface. The dissociation constants for calcium-insensitive binding

Mn(II) for His4 and His3Asp binding sites were reported as 194 ± 203 nM (for Kd1) and 21 ± 5

μM (Kd2) respectively. In order to understand the role of Ca(II) in dynamic properties of protein

and its effect on dissociation constants (Kd) of metal ions, we decided to simulate calcium and

manganese bound and free structures of CP's structures in native like conditions of 310K

temperature, 1 atm of pressure and in a rectangular box of water with 6.163x6.721x6.268 nm of

dimensions for up to 10ns period. Our results indicate that the presence of Ca(II) stabilize CP-

Mn(II) complex via conferring more negative potential energy probably through their

interactions as electrolyte with negatively charged groups when contrasted to free CP. Our

findings also analysis indicate that in calcium-bound form of CP His4 binding site exhibits

higher affinity for Mn(II) in contrast to at His3Asp binding site. Based on Irving williams and

hofmeister series for calcium and manganese are expected to be of destabilizing nature for

proteins but our data show that in case of CP these two elements provide essential flexibility and

stability CP those are absolutely necessary for native function of the protein.

Keywords: Molecular dynamics simulation, Calprotectin, Dissociation constants.


Preliminary antibacterial evaluation of the chemical compositions in

mono and dinuclear cobalt(II) complexes of 1,1,3,3-tetrakis(3,5-

dimethyl-1-pyrazolyl) propane ligand

Faeze Hashemi1 , Azizolla Beheshti*2, Mohammad Reza Daye 2, Hossein Motamedi2

1Department of Chemistry, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran. 2Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.

Abstract

Two new mono- and dinuclear Co(II) complexes namely [Co(tdmpp)Cl2]2.H2O (1) and

[Co2(tdmpp)Cl4] (2) were prepared by one- pot reaction in methanol as a solvent. These

compounds have been characterized by single crystal X-ray diffraction, elemental analysis,

infrared spectroscopy, antibacterial activity and computational studies. The in vitro antibacterial

activity studies of the free tdmpp ligand, compounds 1 and 2 show that, the ability of these

compounds to inhibit growth of the tested bacteria increase progressively from tdmpp to the

dinuclear complex 2. Molecular-docking investigations between the five standard antibiotic, free

tdmpp ligand, complexes 1, 2 and five biological macromolecule enzymes (receptors) were

carried out by using Autodock vina function. The results of docking studies confirm that the

metal complexes are more active than the free ligand. This is consistent with the results obtained

by the antibacterial activities of these compounds.

Keywords: Mono and dinuclear Co (II) complexes, Gromacs, Molecular-docking investigation,

In vitro antibacterial activity.


A Study on Zn(II) coordination in the present of Ca(II) in human

calprotectin binding sites using molecular dynamics simulations

Faezeh Hashemi*, Mohammad Reza Dayer, Azizolla Beheshti

Department of Chemistry, Faculty of Science, Shahid Chamran University, Ahvaz, Iran.

Abstract

Calprotectin (CP) is an antimicrobial protein produced and released by neutrophils that inhibits

the growth of pathogenic microorganisms by sequestering essential metal nutrients in the

extracellular space. CP is a tetramer made up of two heterodimer of S100A8 and S100A9. The

two proteins belong to Ca(II)-binding proteins of the S100 family. In this work, for a better

understanding of the role of Ca(II) and Zn(II) on the dynamics of CP, were studied using

Molecular dynamics simulations. The simulations were carried out on Ca(II)-free and Ca(II)-

bound, Zn(II)-free, Zn(II)-bound, Ca(II)- CP-Zn(II) models, using crystal structures obtained

from the Protein Data Bank, and trajectories at 37 ºC and 1 atmosphere pressure for 10ns period.

Our molecular dynamic analysis confirmed that Ca(II) binds to both seven-coordinate,

“canonical” sites and five-coordinate, “non-canonical” sites. Also, the simulations demonstrated

that Ca(II) and Zn(II) ions can stabilize the conformation of their binding site. During simulation,

due to CP structure alteration, the RMSD of Ca(II)-CP-Zn(II) is slightly lower than its free state.

Although the Zn(II) and Ca(II)-binding to CP leads to decreased activity of the protein, the

RMSF curve illustrated that Ca(II)-CP-Zn(II) complex has lower flexibility and mobility than

CP-Zn(II). Taken together, these data provide a working model whereby CP responds to

physiological Ca(II) gradients to become a potent Zn(II) chelator in the extracellular space. The

results of this study indicated that although Zn (II) in Irving-Williams series of proteins known to

be stable, its natural presence to create flexibility in the protein structure CP is absolutely

necessary.

Keywords: Molecular dynamics simulation, Calprotectin, Zn (II), Ca (II).


Chaperone-like activity of new deep eutectic solvents (DESs)

Foruzan Niknaddaf1, Reza Hasan. Sajedi1, Akbar Heydari2


2Department of organic Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

Green solvents such as natural deep eutectic solvents (DESs) have recently been shown to

prepare liquid media like intracellular water space of the cells. For this reason, and because of

the solvents are biodegradable, inexpensive andnon-toxic, DESs have gained much attention in

many fields. DESs are mixtures of a salt and a hydrogen bond donor which have lower melting

point in comparison with the individual components. In this study, some artificial chaperones

have been utilized as one of the components of the solvents. Artificial chaperones are small

molecules with chaperone-like activity against forms of protein aggregation. In the present work,

the synthesis of three kinds of DES is reported, including choline chloride (ChCl): lacticacid,

lactic acid: L-glutamine andlactic acid: L-arginine. Chaperone-like activity of these solvents has

been studied by DTT-induced and dilution-induced aggregation of hen’s egg white lysozyme in

400 nm. Single factor experiments have been done to investigate the effects of chaperone-like

activity, including the amount of DES, the concentration of protein and the incubation time.

DTT-induced aggregation carried out indifferent concentrations of DESs (1, 2.5, 5 and 10

%(v/v)). All concentrations showed full inhibition of protein aggregation and enhancement in the

yield of refolding. Our findings suggested that the use of molecular chaperones increases the

efficiency of chaperone-like activity deep eutectic solvents.

Keywords: Deep eutectic solvents, Artificial chaperone, Protein aggregation, DTT-induced

aggregation, Refolding.


Creating hierarchical nanostructures with TiO2 nanoparticle and

brush polymer, a promising approach for protein repellence

behavior of biomaterial

Fatemeh Noorisafa and Amir Razmjou

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box

73441-81746, Isfahan Iran.

Abstract

Advanced surface modification approaches of biomaterials alongside the advent of sophisticated

analytical techniques have provided a great opportunity to understand how the physicochemical

characteristics of materials determine cell–surface dynamics at molecular and atomic scale.

Appropriate molecular and cellular response to biomaterial surfaces is essential for implants and

biomedical devices. The tendency of proteins attachment to the surface depends on the material

properties such as surface energy, structure, texture, and relative charge distribution. Engineering

the surface wettability towards superhydrophilicity has been found an impressive technique to

enhance biocompatibility and reduction in protein-material interactions. In this study surface

modification of polyurethane plates by poly ethylene glycol thin layer via grafting technique and

TiO2 nanoparticle entrapment in the brush polymer was investigated with respect to the surface

chemistry and surface structure to increase the biocompatibility. A systematic characterization

was conducted to elucidate the role of each parameter on the biocompatibility and biofilm

formation. The surface protein absorption capacity reduced by 8.7 times and based on MTT

assay the modification has no toxic effect on HeLa cells. The modified samples have also the

ability to reduce the biofilm formation by 71%. In general, when a micron-nano scale roughness

appeared on PU surface, the impact of morphological changes on the biocompatibility, protein

adsorption and biofilm formation becomes significantly higher than that of the surface chemistry

alteration.

Keywords: Protein adsorption, Biocompatibility, Superhydrophilicity, Hierarchical surfaces.


Protective effect of zinc ions against protein misfolding: a dose

dependent phenomenon

Sepideh Noorzadeh1 and Mohammad Reza Dayer2

1Nourdanesh institute of higher education of Meymeh, Esfahan, Iran.

2Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Abstract

Protein misfolding is an inherited character of certain small proteins that expressed in life

threatening diseases such as Alzheimer’s disease, cystic fibrosis and prion-associated spongiform

encephalopathies (bovine spongiform encephalopathy and Creutzfeldt-Jacob’s disease). The

precise mechanism and factors facilitate amyloidogenic process are not well understood. Here an

aliphatic alcohol of ethanol was used to induce amyloid fibrils and to simulate misfolding

process in human insulin as a model protein. Using different techniques of UV-Vis, fluorescence,

CD, FTIR spectroscopy we measured protein turbidity at 398nm, melting temperature at 280nm,

Thioflavin T (ThT) fluorescence quenching, protein secondary structure determination at Far-UV

CD and FTIR to study insulin misfolding at different concentrations of ethanol at the presence

and absence of Zinc ions concentrations. Our findings indicate that I-ethanol at optimum

concentration of 20%(v/v) accelerates insulin misfolding and reduces ThT fluorescence by 38%.

II-Zinc ions at high concentrations of ≥25mM prevent insulin misfolding induced by ethanol

while lower concentrations of Zinc ions accelerates insulin misfolding even at the absence of

ethanol. III-Our data also show that 25mM concentration of Zinc ions increase insulin melting

temperature by 5 degree centigrade. IV-Far-UV CD and FTIR experiments reveal that 20%

ethanol increases beta structure content of insulin by 10% while it is abolished at the presence of

25mM concentration of Zinc ions. Based on our findings and previous reports we can conclude

and hypothesize that zinc ions at high enough concentrations by stabilizing hexamer associations

with native conformation, prevent their dissociation to monomer forms and subsequently to

protofibriles, the structures that facilitate protein misfolding.

Keywords: Misfolding, Zinc ions, Amyloidogenic disease, Ethanol.


Computational study of interaction between prostate-specific

membrane antigen and truncated PSMA aptamer

Farzaneh Namazifar1, Masoud Ayatollahi-Mehrgardi1, Mehdi Sahihi2

1Analytical Chemistry Group, Department of Chemistry, Isfahan University, Isfahan, Iran.

2 Physical Chemistry Group, Department of Chemistry, Isfahan University, Isfahan, Iran.

Abstract

Cancer is a class of diseases characterized by out-of-control cell growth. There are over 100

different types of cancer, and each is classified by the type of cell that is initially affected.

Prostate cancer is the most common cancer types with increasing PSMA protein on the surface

of prostate cancer cells as a biomarker for detect of this cancer. Aptamers are

oligonucleotide or peptide molecules that bind to a specific target molecule. Here, we used RNA

structural prediction and protein/RNA docking algorithms that enabled us to predict the

interaction between A9g, a truncated RNA aptamer to prostate-specific membrane antigen

(PSMA), with great potential for targeted therapeutics. In addition, the modeled RNA tertiary

structure and protein/RNA docking predictions revealed key nucleotides within the aptamer

critical for binding to PSMA and inhibiting its enzymatic activity. Finally, this work highlights

the utility of existing RNA structural prediction and protein docking techniques that may be

generally applicable to developing RNA aptamers for therapeutic use.

Keywords: Cancer, Truncated aptamer, Prostate specific membrane antigen (PSMA), Molecular

docking.

https://en.wikipedia.org/wiki/Oligonucleotide

https://en.wikipedia.org/wiki/Peptide


Stabilization of Ca2+ regulated photoprotein aequorin by deep

eutectic solvents (DESs)

Negin Nazari Moghadam1, Reza Hasan Sajedi1, Akbar Heydari2, Bijan Ranjbar3


2Department of organic Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran.

3Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract Deep eutectic solvent (DES) is a fluid generally composed of two or three cheap and safe

components that are capable of self-association, often through hydrogen bond interactions, to

form a eutectic mixture with a melting point lower than that of each individual component. DESs

exhibit similar physico-chemical properties to the traditionally used ionic liquids, while being

much cheaper, non-toxicity and environmentally friendlier. Generally, proteins are best stored at

about 4°C in clean, autoclaved glassware or polypropylene tubes. Storage at room temperature

often leads to protein degradation and/or inactivity, commonly as a result of microbial growth.

Several kinds of photoproteins, including aequorin, isolated from hydrozoan jellyfishes and

hydroids. Aequorin is a photoprotein that emits light upon binding calcium. When Ca2+ binds to

the photoprotein, the 2-hydroperoxycoelenterazine decomposes into coelenteramide and CO2,

accompanied by the emission of light.The purpose of this study is to investigate the protein

stability in the presence of some DESs at room temperature and increase its thermostability. In

this work, the stability of aequorin has been studied in choline chloride: urea and choline

chloride: glycerol (choline chloride (ChCl) as the salt and urea (U) and glycerol (G) as the

hydrogen bond donor). The results showed that after incubation of apoaequorin by 20% ChG and

2.5% ChU at room temperature, aequorin activity was increased to 1.5 and 3 times, respectively.

Also, interestingly aequorin thermostability was increased at 70 ºC and 80 ºC in the presence of

10% ChG, wherease ChU had no effect on the protein thermostability.

Keywords: Deep eutectic solvents, Aequorin, Protein stability.


Effect of conventional and microwave heating on glycation of bovine

serum albumin through maillard reaction

Farzaneh Nasrollahzadeh1, Mehdi Varidi2, Arash Koocheki3, Farzin Hadizadeh4

1, 2, 3 Department of Food Science and Technology, Ferdowsi University of Mashhad, Mashhad, Iran.

4 Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.

Abstract The aim of present study was to evaluate the effect of Microwave (MH) and conventional

heating on the glycation progress of a model protein, bovine serum albumin (BSA) via Maillard

reaction. For this purpose, three different weight ratios (1:1, 1:3 and 1:5) of BSA and

maltodexrin (MD) were chosen and thermal treatments were done at 90 ºC. Conjugation was

confirmed by o-phthaldialdehyde (OPA), absorbance at 420, UV absorbance and CIE lab

parameters. Statistical analysis showed significant differences between MH and water bath

heating (WH) in reduction of free amino groups and increase in Abs 420 and UV absorbance.

The value of L*and a* were increased in the time of heating. However, dramatic difference

between MH and WH was not seen (p>0.05). The least and the greatest glycation percent were

observed about 9% in both WH and MH during 15 min, and 66.65% by MH in 120 min,

respectively. It showed that graft reactions under MH were much faster than those by WH and

microwave can accelerate the rate of Maillard reaction.

Keywords: Bovine serum albumin, Maillard reaction, Microwave heating, Conventional heating.


Study of the interaction of apigenin and epigallocatechingallatewith

α-Lactalbumin and their inhibitory effect on the formation of α-

Lactalbuminamyloid fibrils

Zahra Nadermohammadi and Fakhrosadat Mohammadi

Department of Chemistry, Institute for Advanced Studies in Basic Science, Gavazang, Zanjan, Iran.

Abstract:

Amyloid fibrillogenesis of almost twenty different proteins followed by deposition of amyloid

fibrils in organs results in several neurodegenerative disorders such as Alzheimer's, Parkinson's,

Huntington's diseases and type II diabetes. Bovine α-Lactalbumin (BLA) is an acidic Ca2+-

binding protein that forms amyloid fibrils at low pH. At present there is no effective treatment

for these diseases and all drugs have failed in different stages of clinical trials. However

identification and development of small molecules that can inhibit fibrillation is an interesting

subject of research. Flavonoids are small natural polyphenols found in many grapes, fruits,

berries, vegetables and herbs as well as other plants. These small polyphenols act as fibrillation

inhibitors. Natural polyphenolic compounds are introduced as appropriate candidates for

inhibition of amyloid formation. In the present study, the inhibitory activities of apigenin and

epigallocatechingallate as two bioactive flavonoids on the amyloid fibrillation of bovine alpha-

lactalbumin as an appropriate model protein for in vitro fibrillation were investigated using

thioflavin T (ThT) fluorescence and atomic force microscopy (AFM). Also, the binding

interaction evaluations were carried out using fluorescence quenching, fluorescence resonance

energy transfer (FRET), synchronous fluorescence and molecular docking approaches.The

binding parameters including binding constant and number of binding sites, thermodynamic

parameters, and distance between the bound ligands and tryptophan residues of alpha-

lactalbumin were determined from the fluorescence experiments. The amyloid fibrillation assays

showed that both apigenin and epigallocatechingallate have considerable capability to inhibit

amyloid fibrillation of alpha-lactalbumin.

Keywords: Amyloid fibrils, Flavonoids, α-Lactalbumin.


A spectroscopic study on the interaction of blood carrier protein of

albumin with a new designed Palladium complex

Akram Najaran1, Adeleh divsalar2, Ali Akbar Saboury3, Nasim Hayati Rudbari1

1Department of Science and Research Branch, Islamic Azad University, Tehran, Iran.

2 Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.


Abstract

Human serum albumin (HAS) is the major protein component of human plasma and has very

important roles in transporting of various drugs, smaller organic compounds and inorganic ions.

In the present study, the interaction of human serum albumin (HSA) and a new designed

Plladium complex was studied by using different spectroscopic techniques of fluorescence and

circular dichroism (CD) at two temperatures of 25 and 37 C. By the analysis of fluorescence

spectra, it was observed that the palladium complex has an ability to quench the intrinsic

fluorescence of protein through a static quenching procedure. The number of binding sites and

the association binding constant as well as thermodynamic parameters of palladium complex

were calculated at both temperatures according the quenching methods. Also, far-UV-CD spectra

of the protein in the absence and presence of various concentrations of complex represented that

the regular secondary structure of protein did not show any significant alterations. From above

results, it can be concluded that the new design palladium complex can bind to blood carrier of

HSA without any alteration in secondary structure of protein which can be considered in

designing of new anticancer drugs with low cytotoxicity in future.

Keywords: Palladium complex, HSA, Fluorescence, Quenching.


Min impact study on catalase of Helicobacter pylori through

simulation docking

Pardis Naderi -Dehkordi and Fatemeh Raiesi

Islamic Azad University, Shahrekord Branch, Shahrekord Iran.

Abstract

The purpose of this article is to study the effect of mint on catalase of Helicobacter pylori using

simulation docking. The effect of mint on Helicobacter pylori catalase docking procedure was

carried out in this way on catalase compounds were mint. Docking with the software Autodock 4

were done. Mint extract contains: (Chrysophanol, Mentol, Terpinolene) results showed

chrysophanol that the binding energy (-6/33 kj/mol) are the best and can be used as medicine.

Helicobacter pylori is a gram-negative, curved s-shaped bacterium, which also has a non-cultural

cocoid form with rounded ends The species name stems from: helico, meaning helical or spiral

shape, bacter, meaning bacteria, and pylori, refering to pylorus region of the stomach. This

pathogen possesses five to seven distinct flagella and grows best when cultured at 37°C.

Interestingly, in resting individuals, 37°C is the stomach's temperature - the targeted organ;

however, the bacteria is able to withstand temperatures as low as 25°C. The purpose of this

article is to study the effect of mint on catalase of helicobacter pylori using simulation docking.

The effect of mint on helicobacter pylori catalase docking procedure was carried out in this way

on catalase compounds were mint. Docking with the software Autodock 4 were done. Mint

extract contains: (Chrysophanol, Mentol, Terpinolene) results showed chrysophanol that the

binding energy (-6/33 kj/mol) are the best and can be used as medicine.

Keywords: Helicobacter pylori, Mentha longifolia, Docking, Catalase.


The survey of the effect of crocin and saffranal in terms of the

inhibition of the formaion beta sheets in neurodegenerative diseases

in vitro and in silico

Tahereh Naderi Jelodar1, Marzihe Dehghan1 , Ali Akbar Saboury1, Mohamad Ali Ebrahimi2

, Atiyeh

Ghasemi1

1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 2Department of Agriculture Biotechnology, Payame Noor University, Tehran, Iran.

Abstract

Aggregation of proteins is a major feature of the pathogenesis of many neurodegenerative

diseases such as Alzheimer's, Parkinson and Prion. Lysosyme plays an important role in creation

systemic amyloid diseases. Lysosyme aggregation was observed under laboratory conditions,

high temperature and highly acidic pH. In this study, structural properties and kinetics of protein

in the presence of effective material of Saffron namely safranal and crocin were investigated

individually using fluorescence method, circular dichroism, SEM and docking. In the

fluorescence of ThT, the emission intensity decreased after adding the protein that had been

incubated with safranal and crocin separately with increasing concentration of treatments and

increasing incubation time. The results showed beta-amyloid sheets were separated from each

other and they lead to inhibit protein aggregation. The binding of ANS marker to hydrophobic

surface protein caused to increase emission intensity and subsequently to decrease the surface

hydrophobicity. To determine the probable impact of safranal and crocin on the secondary

structure of lysozyme, CD spectrophotometer was used in the long-wavelength ultraviolet. The

study showed that the formation of amyloid fibrils decreased in the various concentrations of

crocin and safranal. To prove the exact mechanism of the mentioned effect, the incubated

samples were surveyed by SEM. Docking method were performed to demonstrate the results of

inhibitory activity of compounds on the process of protein aggregation and to determine the

interaction region of compounds with crocin and safranal. Docking analysis revealed crocin and

safranal interact to the central hydrophobic region of lysozyme through Van der Waals

interaction. Hydroxyl group in crocin through hydrogen bonds connected to the hydrophilic

amino acids of lysosyme such as aspartic acid, lysine, serine and threonine while there is just one

hydroxyl group in safranal that through hydrogen bonds connected to aspartic acid in lysozyme.

As a consequence, crocin and safranal prevent the formation of aggregation in the beta sheets

which induce neurodegenerative diseases. Crocin have more potent than safranal .

Keywords: Safranal, Crocin, Fluorescence, Circular dichroism, Docking.


Prediction of triple mutation roles on the sweetness and function of

brazzein according to bioinformatical studies

Ziba Mirzaei, Soraya Pirmohammadi, Vahab Jafarian

Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.

Abstract

Recently, Brazzein due to of convenient features such as sweetness potential, high solubility,

tolerate a wide temperature range and pH to reduce the risk of diseases such as diabetes and

obesity sugar consumption is taken into consideration. Our and another previous theoretical and

experimental studies had shown that replacing the glutamic acid9, alanine19 and glutamic acid41

residue with lysine, a single mutation, increased power sweets Brazzein. Therefore, in this study

to examined the role of triplemutation in structure and function of possible designed protein.

Following theoretical and bioinformatics studies with using the Moderller9v7 software, single

(E9K, A19K, E41K) and triplemutation (E9K/A19K/E41K) done and three-dimensional

structure of the mutants were modeled using chimera software. The best model according to the

ModEval program, Spdbviewer Software and SAVES server selected on the basis of structural

parameters, biochemical and physical properties of wild protein and mutated were examined

findings. Experimental results from single mutations showed that the brazzein double mutant has

been stable and is expected to have more power sweets than single mutation. Check results and

match it with single mutations experimental results indicate that the triplemutant Brazzein has

been stable and is expected to power more sweets than to have a single mutation.

Keywords: Brazzein, Triplemutation, Sweetness, Bioinformatic studies.

.


Mutation at calcium binding site in cyclomaltodextrinase improve

enzyme thermostability: A bioinformatic study

Ziba Mirzaee and Vahab Jafarian

Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.

Abstract

Cyclomaltodextrinases are multidomain and often dimeric proteins from glycoside hydrolase

family 13 (GH13), and catalyzes the degradation of cyclomaltodextrins or cyclodextrins to

maltose and glucose, Analysis of the native cyclomaltodextrinase sequence with GenBank code

KT633577, has predicted the presence of two Ca2+ binding sites. The aim of this study was to

evaluate and select appropriate mutation in first Ca2+ binding sites to improve thermostability of

the enzyme. For this purpose, the mutations were designed using structural and sequence

analysis tools such as ProtParam, ProtScale. Then, Rosetta Bachrub server and MODELLER

program were used for construction of the three-dimensional structure of WT and mutant and the

best model were selected for further studies with programs under the SAVES server as well as

ModEval program. Upon selection of the best model based on the structural features, the status

of interactions and physico-chemical properties of wild-type and mutant were evaluated. Based

on our study, it was revealed that replacement of Asparagine149 by Aspartic acid, the possibility

of binding to Ca2+ increased through the aspartate carbonyl oxygen and enzyme's thermostability

was significantly improved by increasing in ionic interactions and salt bridges.

Keywords: Cyclomaltodextrinase, Modeling, Mutation, Thermostability, Calcium binding site.


Application of albumin glycation products to increase the yield of

phytase production in a recombinant bacterial expression system

2, Bijan Bambaei1Rezaei-Mehran Habibi ,1Naeini-Sadat Mirtavousi-Fateme

1School of Biology, College of Science, University of Tehran, Tehran, Iran.

2National Institute for Genetic Engineering and Biotechnology, Tehran, Iran.

Abstract

Phytases (EC 3.1.3.8, EC 3.1.3.26, EC 3.1.3.72) are enzymes that hydrolyze stepwise release of

phosphate from phytate (myo-inositol (1, 2, 3, 4, 5, 6) hexakisphosphate) therefore are proposed

as an animal feed additive to enhance the value of plant material in animal feed by liberating

phosphate. Phytate has a negative impact on the availability of the phosphate and valuable trace

elements; about 80 percent of the phosphorous exist in the bound form as phytate in plant-based

feed and due to its high negative charge under physiological condition, renders the absorption of

minerals and trace elements. In this study, the detergency effect of morph aggregated form of the

serum albumin prepared upon a time dependent protein glycation, then fibrillation are explored

to increase the periplasm to medium secretion of the phytase in an engineered phytase

heterologous expression system. Experiments were designed using response surface

methodology (RSM) approach in which various parameters were optimized including aggregate

concentration and state of fibrillation. The products of albumin fibrillation were added to the

recombinant bacterial culture before and after growth of bacteria that are assigned as pre-

treatment or post-treatment modes, respectively. As a result, the product of albumin glaycation

represented the highest efficiency at 20 days of albumin fructation products, determined through

phytase activity assay in the supernatant of culture centrifugation product in pre- treatment mode.

In conclusion, the serum albumin glycation products are effectively used to enhance the yield of

phytase production most probably upon detergency effect on the bacterial outer membrane.

Keywords: Glycation, Phytase, Detergency effect, Response surface methodology, Serum

albumin.


Analysis of the interactions between putrescine and bovine

pancreatic trypsin by spectroscopic techniques

Lida Momeni1, Behzad Shareghi 2, Ali Akbar Saboury 3

1 Department of Biology, Faculty of Science, University of Payam Noor, Tehran, Iran. 2 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O.

Box.115, Iran. 3 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

Abstract

Information on protein stability is essential to study protein structure, activity, and interactions

with ligands. The interaction of putrescine with trypsin was investigated by using different types

of spectroscopic techniques in an aqueous medium at two temperatures of 25 and 35°C. The

enzyme activity of Trypsin showed that putrescine increased the activity of the enzyme and its

thermal stability was increased by enhancing the concentration of putrescine. Far- UV circular

dichroism (CD) studies showed that putrescine could change the secondary structure of trypsin

via increasing the content of the α- helix structure and decreasing the β-sheet. The fluorescence

spectroscopic experiments revealed that putrescine had the ability to quench the intrinsic

fluorescence of trypsin through a static quenching procedure. The intrinsic fluorescence of

trypsin was decreased in the presence of putrescine due to the excited-state proton transfer. The

binding constant was determined using the Stern-Volmer equation. The thermodynamic

parameters also indicated that the binding process was spontaneous and that hydrogen bonds and

van der Waals forces played a major role in the interaction of putrescine with trypsin. Moreover,

the increased thermal stability of trypsin might be due to the lower surface hydrophobicity and

the higher hydrogen bond formation after putrescine enhancing, which was reflected in the

increase of UV absorbance, the quenching, as well as the increase of α-Helix content.

Keywords: Trypsin, Putrescine, Thermal stability, Fluorescence, Circular dichroism.


Fabrication and characterization of nano bio-composites scaffolds

contains silk fibroin protein and mcm-41 for tissue engineering

applications

and Abbas Teimouri Nafiseh mobadi

3697, Tehran, I. R. of Iran.-Department, Payame Noor University, 19395Chemistry

Abstract

A scaffold possessing certain desired features such as biodegradation, biocompatibility, and

porous structure could serve as a template for tissue engineering. In this regard, exploration of

new and suitable biomaterials is needed. Silk is a strong and lustrous natural fiber which mainly

contains protein polymer. Silk protein obtained from different silkworm species consists of two

totally different families of proteins, namely fibroin and sericin. Silk fibroin (SF) is used as one

of the most preferable biomaterials for fabrication of scaffolds and several new techniques are

being adopted to fabricate silk scaffolds with greater ease, efficiency and perfection. Mesoporous

MCM-41 is a bioactive material which is comprised of siloxane and silanol groups and offers

opportunities for modification of its surface via bonding organosilanes of desirable structure and

functionalities. In continuation of our recent study on the construction of composite scaffolds, in

this study nano bio-composite sponges were successfully prepared with an interconnected

porous structure and proper mechanical properties.The composite scaffold was characterized by

SEM, XRD, BET and FT-IR studies. In addition, the water uptake capacity, degradability and

biomineralization capability of the composite scaffolds were assessed.Cytocompatibility of the

scaffolds was also assessed by an MTT assay and cell attachment studies using Human Gingival

Fibroblast cells.The results showed the cells were found to attach to the pore walls within the

scaffolds and no signs of toxicity. Thus, we suggest that this nano bio-composite scaffold is a

potential candidate to be used for tissue engineering.

Keywords: Silk fibroin protein, Biomaterials, Tissue engineering, Scaffolds.


Theoretical study of effect of N232S, F251L and R242H mutations in

myosin protein structure

Karim Mahnam1 and Tayebeh Rabani2

1. Biology Department, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.

2. Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran.

Abstract

Mutations in muscle proteins are directly responsible for a class of human disease, such as

familial hypertrophic cardiomyopathy (HCM). Over than 75% of mutations accrue within the

myosin motor domain in four distinct functional regions: the ATP binding site, the actin binding

interface, the reactive sulfhydryl or converter region and the light chain binding domain. In this

study we decide to investigate the affect of there important mutation, i.e. N232S, F251L and

R242H mutations on structure of myosin. These mutations accrue in exon 8 and 9 MYH7 gene

and are near to region of binding myosin to actin and related to HCM disease. At fist 3D

structure of myosin was made by multiple template modeling (PDB codes : 4DB1 and 4P7H )

via modeler 10 and the best model was selected based on DOPE energy. Then this model was

used as starting structure for 10 ns MD simulation via Gromacs 5 package and final structure

(wild type structure) was obtained. Then N232S, F251L and R242H mutations created in wild

type and the mutated structures were used for MD simulation with the same condition of wild

type. Three loop of myosin are important for function and binding myosin to actin that contain

loop 1: Pro401-Lys412, loop2: Lys564-His575 and loop3: Ala621-Val646. Then the accessible

surface area of these loops in wild type and mutated structures were calculated. Our results

indicated that accessible surface area of loop 2 and 3 increase after mutation N232S and F251L.

Also the surface of all loops increase after mutation R242H. Then we can concluded that these

mutation lead to more tight binding of myosin to actin and cause to functional impairment of the

cardiac muscle.

Keywords: Myosin, Molecular dynamics simulation, N232S, F251L and R242H mutation,

Hypertrophic cardiomyopathy.


Theoretical study of the effect of mutation F117L osteoprotegerin

protein on its binding to RANKL protein by modeling methods

Karim Mahnam 1, Zahra Mousavi2, Razye Pourahmad2

1 Biology Department, Faculty of Sciences, Shehrekord University, Shahrekord, Iran.

2 Faculty of Science, Department of Genetics, Shahrekord University, Shahrekord, Iran.

Abstract

Osteoporosis is a multifactorial skeletal disease that characterized by low bone mineral density,

which leads to increase of bone fragility and fracture risk. Osteoprotegerin protein (OPG)

secreted by osteoblasts cells is a negative regulator of osteoclastogenesis that prevent activation

of osteoclast precursors. Polymorphism of the phenylalanine 117 to Leucine was seen in some

patient with osteoporosis in china people. Then it suggested that this mutation probably alters the

structure of OPG and leads to osteoporosis. The model of native and mutated OPG dimer protein

were built by modeler 10 and used for molecular dynamic simulation by Gromacs 4 for 10

nanoseconds in NPT ensemble in presence of water molecules and ions. Then the obtained

structure was docked to RANKL protein by HADDOCK web server. According to docking

results, both native and mutated OPG protein can bind to RANKL protein and have negative

binding energy. Then this mutation or polymorphism probably has no effect on osteoporosis

diseases.

Keywords: Osteoprotegrin (OPG), Docking, Mutations, Molecular dynamics simulations,

Modeling.


Fabrication and charactenization of nano bio-composite scaffold for

use in tissue engineering

Ghasem Mehranzadeh1, Abbas Teimouri1, Hossein Salehi2

1 Department of Chemistry, Payame Noor University, P. O. Box 19395-3697, Tehran, Iran.

2Department of Anatomical Sciences, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran.

Abstract

The urge to repair and regenerate natural tissues can now be satisfactorily fulfilled by various

tissue engineering approaches. Tissue engineering through the integrated use of cells, scaffolds

and regulatory molecules represents a promising approach towards functional tissue

replacements in regenerative medicine. Silk protein fibroin can be effectively used as a

scaffolding material in these treatments. Silk fibers are obtained from diverse sources, among

them, silk of silkworms is a good source for the development of biomedical device. Nano

diopside powders have been shown to be bioactive biomaterial for bone repair. Diopside was

synthesized through a novel sol-gel synthesis. In continuation of our recent study on the

construction of composite scaffolds, in this work, a bio-composite scaffold containing organic

materials and nano materials was prepared by freeze drying method. The silk fibroin (SF)/nano

diopside composite scaffold was characterized by SEM, XRD and FT-IR studies.The biological

response of MG-63 cells on nanocomposite scaffolds was very good in terms of cell attachment

and cell proliferation was analysed by MTT assay.This nano composite has suitable properties

for bio-applications such as bone tissue engineering application in the future.

Keywords: Tissue engineering, Silk fibroin, Nano diopside, Bone tissue.


Investigation on the binding of metoprolol tartrate to β-

lactoglobulin using spectroscopic techniques

Nayereh Mahdieh-Najafabadi, Asghar Zeini-Esfahani, Ali Asghar Rastegari

Department of Molecular and Cell Biochemistry, Islamic Azad University, Falavarjan, Esfahan, Iran.

Abstract

β-Lactoglobulin (β-Lg) is the major whey protein of bovine milk present at a concentration of 2–

3 g L–1. Its biological role is still not well-known. However, many studies have suggested that β-

Lg may play either nutritional or specific transporter role. Metoprolol tartrate (MPT), 1-[4-(2

methoxyethyl)phenoxy]-3-[(1-methylethyl)amino]-2-propanol tartrate, is a selective β-blocker

drug. In the present work, binding of MPT drug to β-Lg at pH 6.7, has been studied by UV-

Visible and circular dichroism (CD) spectroscopy methods. The binding constant for MPT/β-Lg

interaction has been found to be 103 M. The binding processes between protein and drug

molecules were endothermic and spontaneous owing to positive ∆H and negative ∆G values,

respectively. According to far- and near-UV CD results, these ligands have no apparent influence

on β-Lg secondary structure, however they partially destabilize its tertiary structure.

Keywords: β-Lactoglobulin, Metoprolol tartrate, UV-Visible spectroscopy, Circular dichroism

spectroscopy.


Induction of point mutations in human growth hormone molecule

using specific primers

Zeinab Monajjemi Rarani, Seyed Hamid Zarkesh Esfahani, Rahman Emamzadeh, Mohammad Rabbani

Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.

Abstract

Human growth hormone (hGH) or somatotropin is a protein consists of 191 amino acid and

22kDa molecular mass which is synthesized by the somatotropic cells of the pituitary gland and

is secreted into the blood. GH synthesis and secretion are controlled by at least two hypothalamic

hormones; growth hormone releasing hormone (GHRH) and somatostatin (SMS). Some

biological activities of GH include its ability to regulate protein synthesis, cell proliferation,

differentiation of pre adipocytes to adipocytes and development of the immune system. The most

significant bioactivities of GH are protein anabolism, nitrogen and phosphate retention. GH plays

these roles by binding to specific cell surface receptors that belong to the class I cytokine

receptor superfamily. GH deficiency results in dwarfism in children and metabolic changes in

adults (e.g. acromegaly and gigantism). GH antagonist is needed in conditions such as

acromegaly and pituitary tumors. There are different approaches for making antagonists for GH.

One method is introduction of different mutations in the molecule to inhibit its biological

activity. To this aim, it's necessary to determine important parts of hGH which have main role in

interaction with receptors. These parts then could be replaced by primer design and PCR. So, the

resulted molecule may have antagonist properties and could be used in clinical trials for

therapeutic aims. In this study, we designed primers by using Oligo7 and Gene runner softwares

to replace important residues in GH molecule.

Keywords: Human growth hormone, Somatotropin, Point mutation, Oligo7, Gene runner.


Co-immobilization of acetylcholine esterase and choline oxidase for

determination of acetylcholine in the brain of rat

Alireza Montazeri1, Hosna Tavakoli2, Gholamreza Herfehdost2, Hassan Tavakoli2

1Department of Biophysics, Islamic Azad University Science and Research Branch of Tehran, Iran.

2Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.

Abstract

Because of the essential role of acetylcholine (Ach) in several neurodegenerative diseases such

as Alzheimer and dementia, precise determination of ACh is very important for clinical

diagnosis. In this investigation an electrochemical biosensor is developed for measuring ACh in

the brain of rat. For construction of biosensor, acetylcholinesterase (AChE; E.C 3.1.1.7) and

choline oxidase (ChOx; 1.1.3.17) co-immobilized by nafion on the surface of glassy carbon

electrode. The nafion increased the stability and improves the constructed biosensor responses.

For brain sample preparation, five rats were sacrificed, their brains was extracted, homogenized

in buffer phosphate solution and centrifuged. The supernatant was utilized for ACh

measurement. The biosensor was located into the samples, the cathodic and anodic peak currents

as the responses of the biosensor were obtained through cyclic voltammetry. The known

concentration of the pure solution of ACh was used for drawing the calibration curve. The

biosensor responses were linear up to 1mM. The cathodic and anodic peak currents obtained

8.626µA, -1.523µA respectively and the concentration of ACh was estimated 51.84 µM. AChE

hydrolyzed acetylcholine to choline and acetate and in turn, ChOx, catalyzed the oxidation of

choline to betaine and H2O2. The H2O2 which formed in this reaction iselectrochemically

detectable by the biosensor. It is important to note that the amount of produced H2O2 during

enzymatic reactions was indirectly proportional to the concentration of ACh. Consequently, the

biosensor could measure the ACh concentration in the biological samples such as the brain of rat.

Keywords: Acetylcholine Neurotransmitter, Electrochemical biosensor, Choline oxidase,

Acetylcholine esterase, Co-immobilization.


The role of glutamate oxidase in electrochemically measurement of

glutamate neurotransmitter in rat brain

Alireza Montazeri1, Hosna Tavakoli2, Asgar Imamgholi2, Hassan Tavakoli2

1Department of Biophysics, Islamic Azad University Science and Research Branch of Tehran.

2Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.

Abstract Glutamate oxidase (GOx; EC 1.4.3.11) belongs to the oxidoreductases family that catalyzes the

oxidative deamination of L-glutamate (Glu) to ketoglutarate, ammonia and hydrogen peroxide,

H2O2. During this enzymatic reaction, the amount of H2O2, in which detectable by

electrochemical biosensor is proportional to Glu concentration. In this research, electrochemical

method was utilized for measuring Glu neurotransmitter in rat’s brain. In order to prepare the

brain sample, five adult rats were deeply anaesthetized by ether and their brain was dissected by

a transcardially perfusion. The brain was homogenized in phosphate buffer solution and

centrifuged. After that, the clear supernatant was picked up for measurement of Glu level. For

electrochemically determinationof Glu, GOx–based biosensor was fabricated by immobilization

of GOx at the surface of platinum electrode. To assess the biosensor performance, the cyclic

voltammetry experiment was performed and cyclic voltammograms was considered as biosensor

response. The calibration curve was sketched using different concentrations of pure Glu solution.

For Glu measurement, the biosensor was dipped in the brain sample. The concentration of H2O2

in which produced in presence of Glu and GOx, was electrochemically measured by GOx –

based biosensor. The peak currents of brain samples obtained 0.812 µA by cyclic voltammetry

experiments and considered as the responses of GOx – based biosensor. the calibration curve

was linear up to 1mM and the concentration of Glu in rat’s brain obtained 36.5 µM. The results

showed that the GOx had a crucial role in electrochemical measurement of Glu and GOx

biosensor can be applicable for analytical and clinical determination of Glutamate.

Keywords: L-Glutamate oxidase, Enzymatic biosensors, Electrochemical biosensor,

Neurotransmitter.


Analysis the binding interactions of bisdemethoxycurcumin,

diacetylcurcumin and diacetylbisdemethoxycurcumin with bovine

α-lactalbumin by experimental and theoretical analysis

and Fakhrossadat Mohammadi Marzieh Moeeni

Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-

66731, Iran.

Abstract

Milk proteins are one of the natural delivery systems for transporting drugs and bioactive

compounds. Biodistribution of drugs and minerals are affected by the extent and molecular

details of the binding of these proteins to the bioactive compounds. Bovine α-lactalbumin (BLA)

is an important whey protein which can be utilized as valuable vehicle for essential minerals. In

the present study the interaction of BLA with bisdemethoxycurcumin (BDMC),

diacetylcurcumin (DAC) and diacetylbisdemethoxycurcumin (DABC) as three bioactive

compounds was investigated by fluorescence quenching measurements and docking studies. The

stern-volmer equation was utilized to obtain the binding constants and the binding stoichiometry.

The extent of resonance energy transfer (FRET) and Forster’s distance between donor and

acceptor was estimated. Thermodynamic parameters confirmed that the final BDMC-BLA

complex was stabilized by hydrogen bonds, whereas the final DABC-BLA and DAC-BLA

complexes were stabilized by hydrophobic bonds which are in accordance with their chemical

structures. Theoretical and experimental studies verified that theTrp-26 has the most contribution

in the binding process. This considerable binding interaction between these curcuminoids and

BLA may be useful in enriching milk products by binding these anti-oxidant and anti-cancer

compounds to the proteins of the milk such as BLA. The considerable enhancement in the

nutritional value of milk can be obtained by these types of bindings.

Keywords: Alpha-lactalbumin, Disdemethoxycurcumin, Diacetylcurcumin,

Diacetylbisdemethoxycurcumin, Fluorescence quenching


An investigation into the molecular mechanisms of the bacterial for

designinga competent genetic construct for benzene biodegradation

Marzie Mozafari1 and Aliakbar Haddad-Mashadrizeh2, 3

1Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran. 2Cell and Molecular Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad,

Iran. 3Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

Benzene is one of the aromatic hydrocarbons and the most stable one that can enter to the human

body through various ways such as smoking, processed food products and contaminated drinks.

This compound could be accumulate into the various organs such as gastrointestinal and/or

metabolize at corresponding organs. This element and its derivatives recognized as carcinogenic

in the body and reported as carcinogenesis risks factor at higher concentration. In this regard,

destructive effects of this compound on stem cells, pronormoblasts, normoblasts and stomas have

been demonstrated. On the other hand, this element has key role in leukemia induction so that

called as leukemiagene. Considering, provide the solutions for decrease the resource of this type

of components, and or strategies for metabolisms without creation carcinogenic intermediates in

the body, could be provided promising vision for reducing negative effects of compulsory

attendance of it in communities, which are considered in this study via application of the

bioremediation potency of the bacteria and non-bacteria microorganisms for probiotic

development. Bearing in mind, investigations into the molecular mechanisms of the bacterial

were performance for designing a competent genetic construct for benzene degradation. In this

regard, a comprehensive profile of the bacterial microorganisms with the ability of metabolizing

aromatic hydrocarbons especially benzene were gathered and then molecular mechanisms and

key and effective enzymes in the process were determined. Sequences of the selected enzymes

were retrieved from data banks such as NCBI and UniProt. Molecular survey of them have been

taken via CD search, Motif Scan, InterProScan, Blast, MEGA6, Hex and ClusPro2.0programs.

Subsequently, new genetic constructs with capacity to benzene degradation have been designed

based on detection of the functional domains of selected enzymes, and the structural modelling

of them was done with Modeller program. Assessments the qualities of the minimized structures

were done via MOE and RAMPAGE programs. Moreover, binding affinity of designed enzymes

to benzene was performance by using of the PatchDock web server. The results of this study

while introducing some strains of Pseudomonas and Mycobacterium with the ability to digest

aromatic hydrocarbons, especially benzene, led to presented the structural and functional

domains of corresponding enzymes such as deoxygenates and monooxygenates. Moreover,

provide a series of optimized genetic construct with capacity to transforming probiotic strains

that ought to be examined in experimental condition.

Keywords: Benzene, Carcinogen, Cancer, Bioremediation, Probiotic.


The optimization of expression of recombinant denileukin diftitox in

soluble form

Bahareh Mortezagholi1, Reza Hasan Sajedi1*, Mehdi Zeinoddini2 , Khosro Khajeh3

1*Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

2Department of Bioscience and Biotechnology, Mallek Ashtar University of Technology, Tehran, Iran.


Abstract

Denileukin diftitox (trade name Ontak®) was constructed using recombinant DNA technology

(1999) to target malignant cells expressing the IL-2 receptor, after confirmation America Food

and Drug Administration (FDA) by Eisai Company became available. Recombinant Denileukin

diftitox is made by combining a part of the amino acid sequences for IL-2 followed by the

sequences for diphtheria toxin. In order to produce the recombinant protein, design of an

expression system is essential that E. coli is the most famous and widely used expression system

that has fast-growing production in mass volumes however high level expression of recombinant

Denileukin diftitox in E. coli leads to the formation of insoluble aggregation as inclusion body.

In this project, to provide optimal condition for expression of the Soluble form of the protein in

E. coli strain BL21 (DE3). For this purpose, with different temperatures, various concentrations

of IPTG and different times, expression performed and finally, protein in soluble form was

obtained. The protein solution was passed from the Ni-NTA affinity chromatography and soluble

proteins were isolated from the sedimentat. The SDS-PAGE was indicated the maximum

expression and high purity of the soluble protein.

Keywords: Denileukin diftitox, Aggregation, Soluble protein, High purity.


Protective effect of polyphenols against mitochondrial membrane

permeabilization induced by HEWL aggregates

Bijan Akbari1, Ali Akbar Meratan2, Mahshid Shafizadeh1, Shahin Ahmadian1

1 Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, 1417614411 Tehran, Iran.

2 Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.

Abstract

A growing body of evidence demonstrates that mitochondrial dysfunction is the earlier and the

most common character of a wide range of protein-deposition disorders, including

neurodegenerative diseases and peripheral disorders such as systemic amyloidosis and type II

diabetes. In regard to the mechanism of mitochondrial dysfunction, it has been proposed that

interaction of prefibrillar intermediates with mitochondrial membrane is a major determinant of

cytotoxicity. In line with this concept, compounds that interfere with the aggregate species to

bind lipid membranes may serve as therapeutic agents for the treatment of amyloid-associated

disorders. In the present study, the ability of two naturally occurring polyphenols including

resveratrol and curcumin in preventing the HEWL oligomer-induced membrane permeabilization

of mitochondria isolated from brain, liver and heart was investigated. Mitochondrial membrane

permeabilization was investigated following an approach involving the release of malate

dehydrogenase located in the mitochondrial matrix. Our results demonstrated that both

polyphenols effectively inhibit HEWL oligomer-induced membrane permeabilization in a

concentration-dependent manner. Polyphenol-induced protection was found to be more effective

in liver and heart compared to brain mitochondria. In conclusion, we suggest that resveratrol and

curcumin can effectively hinder mitochondrial membrane damage by HEWL oligomers and may

serve as important drug leads to alleviate mitochondrial dysfunction in neurodegenerative

diseases.

Keywords: Hen egg white lysozyme, Mitochondria, Membrane permeabilization, Oligomer,

Polyphenol.


Immobilization of Termomyces lanuginosus xylanase enzyme on

functionalized graphen oxide and determination of activity and

thermal stability

Vajihe Mehnati-Najafabadi1, Abdol-khalegh Bordbar2, Asghar Taheri- Kafrani3

1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.

2Department of Chemistry, University of Isfahan, Isfahan, Iran.

3Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University

of Isfahan, Isfahan, Iran.

Abstract

The covalent binding of xylanase enzyme on functionalized Graphen Oxide

was investigated. The structure, size, and magnetic properties of the

support and immobilized xylanase were characterized by transmission

electron microscopy (TEM), Fourier-transform infrared spectra (FTIR) and

thermo-gravimetric analysis (TGA). The TEM images showed that the

Enzyme was immobilized on support succesful. The FTIR results

demonstrated the successfully immobilization of xylanase on functionalized

magnetic nano particles Graphen Oxide (MNPsGO). Results from Bradford protein

assay and TGA indicated that xylanase was covalently attached to the

surface of magnetic support. Enzymatic activity, reusability, thermo-

stability, and storage stability of the immobilized xylanase were found

significantly superior to those of the free one. The Immobilized enzyme

exhibited maximal catalytic activity at 60 0 C and were found to keep high

more than 80% of the activity of free ones. Notably, xylanase-MNPsGO

showed quite impressive stability, even after 10 reaction cycles, it could

still retain more than 65% of the initial activity. Results indicated that the

MNPsGO could be a suitable support for Xylanase in food, chemical and

biofuel product industries.

Keywords: Xylanase, Immobilization, Graphen oxide, Enzyme stability, Enzymatic Activity.


Covalent binding of xylanase enzyme on functionalized

superparamagnetic graphene oxide nanoparticles and evaluation of

activity and pH stability

Vajihe Mehnati-Najafabadi1, Abdol-khalegh Bordbar2, Asghar Taheri- Kafrani3

1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran. 2Department of Chemistry, University of Isfahan, Isfahan, Iran. 3Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University

of Isfahan, Isfahan, Iran.

Abstract

The covalent immobilizayion of xylanase enzyme on functionalized

Graphen Oxide was investigated. The structure, size, and magnetic

properties of the support and immobilized xylanase were characterized by

transmission electron microscopy (TEM), Fourier-transform infrared spectra

(FTIR). The results from TEM and FTIR demonstrated that xylanase was

covalently attached to the surface of magnetic support. Enzymatic activity,

reusability, pH-stability, and storage stability of the immobilized xylanase

were found significantly superior to those of the free xylanase. The

Immobilized enzyme exhibited maximal catalytic activity at pH 6.5 and

were found to keep high more than 80% of the activity of free xylanase.

Notably, immobilized enzyme showed quite high stability, even after 10

reaction cycles, it could still retain more than 50% of its initial activity.

Results reflected that the immobilized xylanase could be an appropriate

matrix for xylanase in food, chemical and bevarage industries.

Keywords: Xylanase, Immobilization, Graphen oxide, Enzyme stability, Enzymatic Activity.


Investigation the effects of different osmolytes on the structure of

trypsin

Sheyda Mahmoodian, Behzad Shareghi, Elham Dadaie

Department of Biochemistry, College of Sciences, Shahrekord University, Iran.

Abstract

Trypsin EC (3.4, 21, 4) is a serine proteases that contains a water-soluble globular protein,

hydrolizing peptide binding.In this study the effects of different Osmolytes (i.e., sucrose,

erythrose, and tyrosine) on Trypsin enzyme structure was investigated .For all fluorimetry

experiments Spectrofluorophotometer device Shimadzu model RF-5103PC was used at 2

different temperatures (25 and 35 °C), pH 8, using an excitation wavelength of 280 nm and

emission wavelength of 340-290 nm. The Flourescence Spectrometry indicated that all

Osmolytes could quench the intrinsic Flourescence of Trypsin throuh static quenchin.

Furthermore, thermodynamic analysis indicated that the hydrogen bonds and Van der Waals

force are the dominant forces in interaction trypsin with the osmolytes.

Keywords: Trypsin, Osmolytes, The structure of the enzyme, Fluorescence.


Bagging algorithm for protein thermostability prediction based on

pseudo amino acid composition

Maryam Mahmoudi, Seyed Shahriar Arab, Javad Zahiri, Mozhgan Mozaffari Legha

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IRAN.

Abstract

Proteins in terms of thermal stability are divided into several categories at different temperatures.

Thermophile and hyperthermophile proteins have high thermal stability and are able to maintain

the structure and function at higher temperatures near or above the boiling point of water. The

mesophilic proteins are stable at lower temperatures. The role of thermal stable protein in design

of enzymes, protein engineering, drug design, medical and industrial processes cause them one

of interesting research fields in the recent years. Stability in the different temperature is

associated with the structural and sequence features of proteins. Identifying these features to

build an efficient computational model for termal stability prediction is of critical importance

due to the costs of in vitro studies. In this study, we exploited bagging algorithm using pseudo

amino acid composition feature to predict the protein thermostability. The results show that

pseudo amino acid composition is one of the most important feature in discrimination of

thermophilic and mesophilic proteins. Proposed model achieved accuracy of 96.9%.

Keywords: Protein thermostability, Thermophilic proteins, Mesophilic proteins, Structure and

sequence features, Machine learning methods, Bagging.


Efficient synthesis of novel eptifibatide analogous

Kazem Mahmoudzadeh1, Azam Monfared1, Saeed Balalaie2, 3

1University of Payame Nour, Tehran Branch

2Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416.

3Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Abstract

Eptifibatide is an antiplatelet drug of the glycoprotein IIb/IIIa inhibitor class. It is

a cyclic heptapeptide. It belongs to the class of the arginin-glycin-aspartat-mimetics and

reversibly binds to platelets. Eptifibatide has a short half-life. In continuation of our program for

the synthesis of some pharmaceutical active ingredients peptides which have disulfide bridge,

herein we report the synthesis of eptifibatide and their novel analogues using a combination of

solid phase peptide synthesis and solution phase. The novel analogues contain the ethylamide,

semicarbizide, and thiosemicarbazide which has been added at the C-terminal. The structure of

the synthesized compounds was confirmed based on HR-MS(ESI). The antiplatelet investigation

of the synthesized compounds compared to eptifibatide is in progress.

Keywords: Analogous, Eptifibatide, Antiplatelet.

https://en.wikipedia.org/wiki/Antiplatelet_drug

https://en.wikipedia.org/wiki/Glycoprotein_IIb/IIIa_inhibitor

https://en.wikipedia.org/wiki/Cyclic_compound

https://en.wikipedia.org/wiki/Heptapeptide

https://en.wikipedia.org/wiki/Half-life


Bioactive peptides from egg-whites of different avian species

Ladan Aminlari1, Leila Hajipour2, Maryam Tavana3, Mohamad Mohsen Mohammadi3

1Department of Food Hygiene, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.

2Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran.

3Department of Biochemistry, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.

Abstract

The aim of this study was to isolate and compare bioactive peptides from egg-white of quail,

duck and chicken and to determine their antimicrobial and antioxidant properties. The egg-white

proteins were diluted, the major proteins precipitated by trichloroacetic acid, centrifuged to

remove the precipitate and the supernatant subjected to G-25 Sephadex gel-filtration

chromatography to isolate the peptides. The bioactive properties of the fractionated peptide were

determined. The elution pattern of peptides obtained by gel filtration chromatography of egg

white from different species of birds were different with different properties of the fractions,

indicating that endogenous proteases had significantly different effects on the proteins of egg

whites of different species. The peptide fractions exhibited high antimicrobial and antioxidant

properties. Most of the peptides which were eluted at the final stage of gel-filtration

chromatography showed the highest antimicrobial properties against E. Coli and Bacillus Cerus.

The results suggested that it is possible substitute the antioxidant and antimicrobial agents of

chemical origin with peptides naturally present in egg-whites of duck, chicken and quail.

Keywords: Bioactive peptides, Egg white, Gel filtration chromatography, Antioxidant,

Antimicrobial properties.


In silico study of molecular interaction between cel-D7 (a novel

drivative of celastrol) and proteasome using the autodock software

Elmira Mohammadi1, Mohammadreza Mofid2 , Neda Fayyazi3, Sana Pirmardvand Chegini4, Ali Jahanian

Najafabadi1

1 Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of

Medical Sciences. Isfahan, Iran.

2 Department of Biochemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of Medical Sciences.

Isfahan, Iran.

3 Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of

Medical Sciences. Isfahan, Iran.

4 Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Univercity of Medical Sciences.

Isfahan, Iran.

Abstract

The proteasome is a multicatalytic enzyme complex with a molecular weight of 2.5 MDa.

Usually, the cellular proteasome is referred to as the 26S proteasome in accordance with its

sedimentation coefficient. The 20S proteasome is the catalytic core of the 26S proteasome

complex, which contains of four stacked rings that form a barrel with a central cavity. These

stacked rings include two non-catalytic α rings (each with seven nonidentical subunits) outside of

two catalytic β. The catalytic activity of the β rings are found within the β1(caspase or

peptidylglutamyl peptide-hydrolyzing-like (PGPH) activity), β2(trypsin-like activity), and

β5(chmotrypsin-like proteolytic activity) subunits. In all the three β-subunits, a threonine residue

at the amino terminal (Thr1) is considered to be the catalytically active amino acid. Inhibition of

proteasome have some biological effects especially in cancer inhibition; consist of: cell cycle

arrest and apoptosis. In various studies several natural compounds with proteasome inhibitory

activity were assessed such as celastrol. Cel-D7 is a novel derivative of celastrol with low cell

toxicity. In this study in silico intraction of cel-D7 with subunit β5, S1 pocket, of proteasom was

assessed with auotodock soft ware. Result from docking study revealed that this compound

intracted with minimum H bonding energy with Thr1 and also has intraction with Met45.

Keywords: Cel-D7, Celastrol derivative, Proteasome, Molecular docking.


Improvement of Bacillus subtilis ZH1 biosurfactant production

Atieh Motaghi Golshan, Jamshid Fooladi, Parichehr Hanach

Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.

Abstract

Biosurfactants are surface active agents produced by microorganisms. They have many

applications in food, pharmaceutical industries as natural emulsans and some of them have

biocidal, insecticidal activities. Bacillus subtilis biosurfactants are among the most powerful ones

as they reduce the surface tension of distilled water from 72 to 28 mN m-1 and are suitable for

bioremedation of oil-contaminated lands. We try to improve the biosurfactant production of

Bacillus subtilis ZH1 by adding both organic nitrogen source and inorganic nitrogen source in

the growth medium. Different concentration of ammonium dihyrogen phosphate, 1%, 1.5% and

2%, was added to the medium as the inorganic nitrogen source. Oil spreading test, using ODA

(Oil Displacement Area) as an index, is an indirect method for measuring the amount of

produced biosurfactant. These tests showed that 2% ammonium dihyrogen phosphate has larger

ODA and thus, improves the biosurfactant production.

Keywords: Biosurfactant, Bacillus subtilis, Improvement, Oil spreading test, Ammonium

dihydrogen phosphate.


Probing the interaction of chemotherapeutic drug of 5-fluorouracil

and milk carrier protein of -lactoglobulin

Amineh Leilabadi-Asl1, Adeleh Divsalar2, Ali Akbar Saboury3, Kazem Parivar1

1Department of Science and Research Branch, Islamic Azad University, Tehran, Iran.



Abstract

In the present study, the interaction and side effects of a chemotherapeutic anti-cancer drug of5-

Fluorouracil with milk carrier protein of β-lactoglobulin (BLG) was investigated using various

spectroscopic methods of fluorescence and circular dichroism at two temperatures of 25 and 37

°C. The analysis of fluorescence spectra showed that the addition of the 5-Fluorouracil to BLG

solution led to a significant reduction in the intrinsic fluorescence spectra of protein and then

quenched it. Values of the number of binding sites and the binding constants of 5-Fluorouracil on

protein were calculated at different temperatures according quenching method. Analysis of

Stern-Volmer curve of protein showed that the dynamic mechanism has a major role in

fluorescence quenching of BLG. Also, binding results have represented that there is 2 binding

sites on BLG for binding of 5-Fluorouracil at two temperatures of 25 and 37 °C, respectively.

Finally, according above results, it can be concluded that the anticancer drug of 5-Fluorouracil

can bind to carrier protein of BLG and changed the tertiary structure of it.

Keywords: β-Lactoglobulin, 5-Fluorouracil, Fluorescence, Binding site.


Identification of RCC in structure of large envelope protein S of

HBV and molecular modeling

Mojtaba mortazavi1, Safa Lotfi1, Masoud Torkzadeh1, Mehdi Rahimi1, Abdorrasoul Malekpou2, Mohsen

ModaresKia1

1Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate

University of Advanced Technology, Kerman, Iran. 2Gastroenterohepathology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.

Abstract HBV causes the death of over one million persons per year by liver failure or hepatocellular

carcinoma. The virus particle (virion) consists of an outer lipid envelope and an icosahedral

nucleocapsid core composed of protein. Recent studies suggest that rare codon clusters are

functionally important for protein activity. Here, for the first time we analyzed and reported rare

codon clusters in HBV genome and their protein structure. This analysis was performed using

the Sherlocc program that detects statistically relevant conserved rare codon clusters. By this

program, the rare codon cluster was identified in large envelope protein S (PF00695). For further

understanding of the role of these rare codon clusters, we studied location of these rare codon

cluster in structure of large envelope protein S. We identified some of critical residues near or

within rare codon cluster. It should be mentioned that characteristics of these critical residues

such as location and situation of side chains are important in assurance of the HBV life cycle.

The results of this study provide new and deep perspectives about structure of HBV proteins for

further researches and designing new drugs for treatment of HBV.

Keywords: HBV genome and proteins, Rare codon cluster, Sherlocc program, Ribosomal pauses.


Antimicrobial activity of heat stable peptides in Iranian native

Bacillus strains with probiotic potential

Mohsen Golnari Maranni1, Nastaran Bahrami2, Mohammad Rabbani3, Mohammad Ali Asadollahi1

1Biotechnology Department, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.

2Microbiology group, Nour Danesh non-profit higher education institute of Meymeh, Isfahan, Iran.

3Biology Department, Faculty of Science, University of Isfahan, Isfahan, Iran.

Abstract

Probiotics are beneficial microbes with healthy effects on their hosts and consumers. Recently

the use of Bacillus strains as probiotics has received a great deal of attention because of their

sporulation and resistance to stress conditions like low pH of the gastric fluid. Bacillus bacteria

could play a significant role in the gastrointestinal tract because of the high resistance of their

spores, immune-stimulatory and antimicrobial activities. Most of the antimicrobial substances

produced by Bacilli have peptide structures but some strains produce antibiotics belonging to

other chemical classes. In this study, the antimicrobial activity of heat stable peptides of Bacillus

isolates was investigated. Thirty-nine Bacillus strains were isolated from a variety of dairy

products, soil samples, vinegar, livestock excreta and poultry excreta samples. Isolates were

identified by biochemical and molecular methods. These Bacillus strains were screened for

probiotic characteristics and 14 strains were selected and investigated for antimicrobial activities

against potential bacterial pathogens such as S. aureus, S. enterica, Shigellea sonei, Listerai

monocytogenes, E. coli and S. pyogenes. These strains were identified as B. subtilis, B.

licheniformis, B. toyonensis, B. pumilus, B. coagulans, B. amiloliquifaciens, B. endophitycus and

B. siamensis. Three different experimental approaches (Spotting, Well Diffusion and Mixed

Culture) were used to detect antibacterial activities and results revealed that these activities could

be because of the presence of heat stable peptides.

Keywords: Bacillus, Probiotics, Antimicrobial activity, Heat-stable peptides.


Preparation and characterization of monoclonal antibody against

carcinoembryonic antigen and immunohistchemistry evaluation Mohammad Keyvanloo Shahrestanaki 1, Bratali Mashkani 1, Mahboobeh Alamdari 2, Mohammad Nadri 1,

Mohsen Sisakhti 3, Taiebe Kianosh 1, Seyed Isaac Hashemy1,5, Amir Hossein Jafarian Mohammad

Soukhtanloo 1,4,

1Department of Clinical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad,

Iran.

2Department of Biochemistry, School of Science, Payame Noor University, Mashhad, Iran.

3Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.

4Cancer Molecular Pathology Research Center, Ghaem Hospital, School of Medicine, Mashhad University of

Medical Sciences, Mashhad, Iran.

5Surgical Oncology Research Center, Imam Reza hospital, Faculty of Medicine, Mashhad University of Medical

Sciences, Mashhad, Iran.

Abstract

Carcinoembryonic antigen (CEA) considered as a tumor- associated antigen. It is a highly

glycosylated protein, which overexpressed in many different cancers, mainly in colorectal

cancer. Specific monoclonal antibodies (mAb) against this antigen provide helpful strategies for

detection of this antigen in serum and tissue, which in turn can be used for diagnostic and

therapeutic purposes. our goal was production of anti- CEA mAb. This mAb can detect CEA in

sera of patient with colon carcinoma and also can be used for immunohistochemical assays.

Briefly two male mice 6-old-week immunized with CEA. Anti-CEA levels of mAbs in sera

evaluated with designing indirect ELISA. Hybridoma cells produced by fusion of SP2/0

myeloma cells and spleen cells of immunized animals. After screening of fused cells in RPMI-

HAT, HT media, mAb secretion of each colon evaluated by indirect ELISA. Best clone (RM1)

selected and used for isotyping and immunohistochemistry analysis. Efficiency of fusion was

65%, which implicated fairly good immunization of animals. Isotype of RM1 determined IgG2b,

and kappa light chain. The affinity of this antibody estimated 5×10-6 M. According to

immunohistochemical analysis, predominant staining of gland lumina performs very well with

RM1. RM1 can be considered as a valuable tool for detecting CEA in the sera of patient with

colon carcinoma. RM1 shows very good immunohistochemical results in comparison to Dako

antibody and can be used for determining of this antigen in tissue and other related fluids.

Keywords: Carcinoembryonic antigen, Monoclonal antibody, Hybridoma.


Construction of BSA nanogels-loaded doxorubicin and its anti-

carcinoma effect on MES-SA/DX5

Zahra Kayani1, Abdol-khalegh Bordba1, 2, Omidreza Firuzi1, 3

1Biotechnology Department, University of Isfahan, Isfahan, Iran.

2Chemistry Department, University of Isfahan, Isfahan, Iran.

3Medicinal and natural products chemistry research center, Shiraz University of Medical Sciences, Shiraz, Iran.

Abstract

BSA nanogels (BSA ng) for the treatment of cancers were prepared successfully. These nanogels

were synthesized and used for loading doxorubicin as a nano-system for enhancing intracellular

uptake via endocytosis by cancer cells. The results indicated that BSA nanogels loaded with

doxorubicin (DBSA ng) can effect on drug-resistant MES-SA/DX5 cells compared with

doxorubicin. Increased therapeutic efficiency of doxorubicin loaded BSA nanogels were also

tested in MES-SA/DX5 cells and compared with doxorubicin. In addition, the cell accumulation

levels of DBSA ng in MES-SA/DX5 was time dependent for these nanoparticles. DBSA ng

(effective diameter: 109 ± 1.1 nm; polydispersity index: 0.193) could significantly boost cellular

accumulation of doxorubicin and overcome the drug efflux mechanism of MDR in resistant cell

lines. In conclusion, DBSA ng can be used as a potentially effective drug delivery system.

Keywords: BSA nanogel, Doxorubicin, MDR mechanism, drug delivery.

Keywords: BSA nanogels, doxorubicin, drug delivery, anti-carcinoma effect.


Medical applications of antimicrobial peptide

Sahar Kashkouli 1, Nasrin Molavi 1, Hossein Mazarei 1, Hadi Zare-Zardini 2, Azam Hashemi 2

1 Student of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran.

2 Hematology and Onccology Research Center, Shahid Sadoughi University of Medical Sciences and Health

Services, Yazd, Iran.

Abstract

Increasing use of antibiotics for treating infectious diseases has provided fields for creating

resistant strains, so that nowadays some bacterial strains are not under the influence of any of

today's common antibiotics. So today we should be looking for a suitable alternative to these

compounds so that we can be able to deal with this problem. Through this it has been determined

that antimicrobial peptides (AMPs) that produced by all organisms and play important role in

innate immunity, have significant effects against various microbes. These peptides are suitable

candidates for treatment and prevention of microbial infections. In this review, the properties,

mechanism and application of AMPs as potent antimicrobial drugs was discussed. Methods that

used in this study is a literature review of important research on AMPs. According to this review,

natural and modified AMPs have potent properties for application as antimicrobial drugs. These

peptides can be modified for reduction of side effects and then, obtained Food & Drug

Administration approval for any topical or systemic medical indications. AMPs are useful for

treatment of infectious diseases. However, their usefulness as a new class of antimicrobial drugs

still remains to be proven.

Keywords: Antibiotics, Antimicrobial peptides, Antimicrobial drugs, Infectious diseases.


Study of the interaction change between the cytosolic components of

the NADPH oxidase in cell free system

Gilda Karimi1 and Tania Bizouarn2

1 Department of Biological Sciences, Kharazmi University, Tehran, Iran.

2Laboratoire de Chimie physique, UMR8000, CNRS-Université Paris Sud-Orsay, Franc.

Abstract

The NADPH oxidase (NOX) is the major source of superoxide radicals in phagocyte cells. The

system is made of several cytosolic (p47phox, p67phox, rac) and membrane (gp91phox, p22phox)

proteins. We have constructed a cell-free Nox system in order to explore some aspects of the

functioning of this enzyme. Using various methods such as surface plasmon resonance (Biacore),

fluorescence measurements and kinetics measurements in cell free system, we are studying the

assembly process of NADPH oxydase of phagocyte. Our results confirm that p47phox subunit

helps the binding of p67phox on the complex but with less extend than found in the literature

secondly it increases the rate of superoxide production suggesting a true adaptor role of p47phox.

In addition, our experiments show that in our system, p47phox is not a competitor for the dimer

p67phox-p47phox which means that p47phox alone would not tightly bind to the flavocytochrome.

Finally we will present a comparison of EC50 obtained with various mutants of p47phox that

gives information on the domains that are involved in this assembly process.

Keywords: NADPH oxidase, Cell free system, Assembly process.


Exploring of the assembly process of the NADPH oxidase complex

via the structural changes of p47phox and p67phox subunits

Gilda Karimi

Department of Biological Sciences, Kharazmi University, Tehran, Iran.

Abstract

The NADPH oxidase (NOX) is the major source of superoxide radicals in phagocyte cells. The

system is made of several cytosolic (p47phox, p67phox, rac) and membrane (gp91phox, p22phox)

proteins. We have constructed a cell-free Nox system in order to explore some aspects of the

functioning of this enzyme. Our aim is to get new insights into the assembly process of the

NADPH oxidase complex and to investigate the structural modifications induced by the

assembly of its different partners. Using SRCD spectroscopy, we investigated the conformational

changes associated with the assembly process, the role of arachidonic acid in the process and the

conformation changes induced by post-translational modifications.

Keywords: NADPH oxidase, Assembly process, Structural changes.

.


Effects of fermentation by cocci lactic acid bacteria isolated from

Iranian dairy products on the immunoreactivity of Cow's milk

caseinate

Reihane Kordesedehi1, Mohammad Rabbani-khurasgani2, Asghar Taheri-Kafrani1, Rezvan Kazemi1

1Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.

2Departement of biology, Faculty of sciences, University of Isfahan, Isfahan, Iran.

Abstract

Bovine milk is the best substitution for infant's diet when breast feeding is not possible. Cow’s

milk contains 30–35 g of different proteins per litre. The coagulum of milk can be obtained

through the acidification of raw skim milk or action of renin which consists of four proteins

(αS1-, αS2-, β and к-casein). Caseins form ordered aggregates that termed micelles. Cow's milk

caseins play a basic role in persistent of cow’s milk allergy (CMA), so the feeding of an infant

allergic to cow’s milk casein may create serious allergenic reactions. Probiotic Lactic acid

bacteria (LAB) have long been used by consumers in fermented dairy products. It should be

highlighted that the proteolytic enzymes of LAB can reduce the allergenicity of hydrolyzed

proteins such as caseins. The aim of this study was to screen out cocci LAB from cow and camel

milk samples and evaluate their proteolytic activity on caseinate digestion and their ability to

degrade the main allergenic sequences. The ability of LAB supernatant to hydrolyze caseinate

was tested after growing the bacterial cells in milk citrate agar media (MCA) for 48 h at 37°C.

The effects of proteolytic activity of these bacteria on milk proteins were investigated using

SDS-PAGE and RP-HPLC techniques. The most effective bacteria for the hydrolysis of

caseinate were isolated. Residual antigenicity of these proteins was determined by competitive

ELISA test, using a pool of sera from cow’s milk allergy patients. The study findings show that

caseinate hydrolysates are less able to bind to IgE from serum of patients with allergy to cow's

milk. The results indicated that lactic acid fermentation can attenuate caseinate antigenity in

cow's milk. These bacteria can be used to reduce allergy in Iranian dairy products.

Keywords: Caseinate, Lactic acid bacteria, Cow’s milk allergy, Competitive ELISA.


A thermodynamic study on the interaction of propolis and human

hemoglobin

Fatemeh Kazemi1, Adeleh Divsalar2, Ali Akbar Saboury1


2Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.

Abstract

Propolis or bee glue is a resinous hive product collected by honey bees from buds and leaves

secretions of trees and has several biological properties such as antimicrobial, antifungal, anti-

aging, anticancer, anti-inflammatory, and antioxidant properties. In the present study, we have

investigated the structural changes in purified human hemoglobin (Hb) upon interaction with

propolis using various spectroscopic techniques at two temperatures of 25 and 37 C.

Fluorescence results have shown that adding of propolis extract to Hb solution lead to significant

reduction in intrinsic fluorescence of protein and can quench it. Also, the number of binding sites

and binding constants of this interaction calculated according quenching method at two

temperatures of 25 and 37 C. Binding analysis represented that there is one binding site for

propolis on the human at both of the temperatures of 25 and 37 C. Since during heme

degradation in Hb, two fluorescent compounds produces. Then, the induction of heme

degradation in Hb in the presence of various concentrations of Propolis was checked and results

showed that low concentrations of propolis did not induce any significant heme degradation in

Hb.From above results, it can be concluded that propolis can bind and interact with human Hb

without any significant structural changes which might be considered as an herbal drug with low

side effect.

Keywords: Hemoglobin, Propolis, Quenching, Hem degradation, Fluorescence.


Studding the solubility of EGFP upon replacing valine 12 by lysine,

using bioinformatics tools

Sheida Kazemi 1, Rahman Emamzadeh 2, Behnaz Safar 3

1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran 2Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran. 3Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.

Abstract

Enhanced green fluorescent protein (EGFP) has a β-barrel structure and a low molecular weight

of about 27 kDa. This fluorescent protein after excitation in 395 nm, emits a green beam of light

in 508 nm with no extra chemical ingredient or substrate. These features make it an appropriate

tag for detection of proteins expression, protein-protein expression and transformation or

transfection analysis. In spite of these application, its approximately low stability faced its usage

with difficulty. Thus altering EGFP to more soluble mutants is an attractive field of protein

engineering. In this study the protein 3D structure was built using SWISS-MODEL server and

based on homology modeling. Then the structure analyzed with SPDBV software and accessible

residues determined. Valine 12 as a non-polar and exposed residue was chosen. Finally valine 12

replaced with lysine and its solubility was studied using ESPRSSO (mbs.cbrc.jp/ ESPRSSO).

The result expressed that upon this mutagenesis, replacing valine 12 by lysine, protein solubility

might increase slightly. Regarding to the lysine feature as a polar and ionic residue this result has

been expected.

Keywords: EGFP, Mutagenesis, Solubility, Valine 12.


Enhanced green fluorescent protein instability upon replacing

phenylalanine 226 by alanine

Sheida Kazemi 1, Rahman Emamzadeh 2, Behnaz Safar 1

1 Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran.

2 Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran.

Abstract

Enhanced green fluorescent protein (EGFP) is a fluorescent protein that is widely used as a

protein reporter in conjugation with other proteins. This protein tag used for monitoring in time

of several biological phenomena in living cells. Although protein instability is a general

limitation in protein utilization assays. Thus protein engineering to achieve more stable protein is

an active field of search. In this study protein stability upon mutagenesis was predicted. PDB

file of EGFP was made using SWISS-MODEL server based on homology modeling. Then PDB

file was uploaded in HotSpot Wizard 1.7 server, and high mutability residues were evaluated.

Finally phenylalanine 226 was chosen and its stability was predicted upon replacing by alanine

using DUET server (http://bleoberis.bioc.cam.ac.uk/duet/stability). The mutation caused a

negative value of DDG (-2.265 Kcal/mol) which means manipulation of F226 has an unstable

effect on EGFP structure. This result represents that phenylalanine 226 may participate in

hydrophobic interaction with other residues in the β-barrel structure of EGFP, and thus replacing

of that by alanine caused a destabilizing effects.

Keywords: EGFP, Protein stability, DUET server, Hydrophobic interaction.

http://bleoberis.bioc.cam.ac.uk/duet/stability


Assesment of cow’s milk β-lactoglobulin allergenicity reduction

using cocci lactic acid bacteria isolated from Iranian dairy products

Rezvan Kazemi, Asghar Taheri-Kafrani, Reihane Kordesedehi

Department of Biotechnology, Faculty of Advanced Science and Technologies, University of Isfahan, Iran.

Abstract

The prevalence of food allergies has increased around the world, so the World Health

Organization (WHO) has declared it as a sixth human health problem. Nearly few foods are

responsible for the majority of considerable food-induced allergic reactions. Cow's milk proteins

(CMA) are the most important food allergens have been reported. Today, 4-8 % of children

under 3 years old suffer from allergy to cow's milk (CMA). The milk protein β-lactoglobulin (β-

lg) caused about 80% of all main cases of milk allergies for children and infants. Some studies

showed that the enzymatic activity of probiotic bacteria can reduce the potential allergenicity of

milk proteins. Therefore, in the present work, 20 kinds of traditional milk have been collected

from different regions of Iran, and 13 types of Lactic acid cocci bacteria have been isolated in

M17 broth and agar medium. The effects of proteolytic activity of these bacteria on milk proteins

were investigated using SDS-PAGE and RP-HPLC techniques. The most effective bacteria for

the hydrolysis of β-lg were isolated. Residual antigenicity of these proteins was determined by

competitive ELISA test, using a pool of sera from cow’s milk allergy patients. The study

findings show that β-lg hydrolysates are less able to bind to IgE from serum of patients with

allergy to cow's milk. The results indicated that lactic acid fermentation can attenuate β-lg

antigenity in cow's milk. These bacteria can be used to reduce allergy in Iranian dairy products.

Keywords: β-Lactoglobulin, Lactic acid bacteria, Cow’s milk allergy, Competitive ELISA.


Computer-aided evaluation of M4 protein (a truncated version of

IL-24) with Bioinformatics tools

Reza Ghavimi1, Mohammadreza Mofid2, Ali Jahanian Najafabadi1, Mohammad Keyvanloo2, Neda

Fayyazi3

1 Department of Pharmaceutical Biotechnology, Faculty ofPharmacy and Pharmaceutical Sciences, University of

Medical Sciences.Isfahan, Iran.

2 Department of Biochemistry, Faculty ofPharmacy and Pharmaceutical Sciences, University of Medical Sciences.

Isfahan, Iran.

3Department of PharmaceuticalChemistry, Faculty ofPharmacy and Pharmaceutical Sciences, University of Medical

Sciences. Isfahan, Iran.

Abstract

Fusion proteins (FPs) are chimeric proteins constructed by genetically fusing two or more

protein domains together by a linker molecule. In most cases a cell penetrating or apoptosis

inducing peptide along with another protein domain as a targeting moiety are participated in

structure of FPs. FPs have wide applications in biological and pharmaceutical research such as

protein purification, drug delivery, tumor targeting and designing of anticancer drugs. IL-24 is a

cytokine with 206 aa that could selectively induce apoptosis in cancer cells without harming

normal cells. An N-terminal truncated molecule, M4 having amino acid residues 104–206 of IL-

24, contains essential domains required for cancer-specific apoptotic activity of this molecule, so

by connecting of M4and targeting moiety with a suitable linker, itcan be applied in the structure

of FPs.According to growing importance of FPs, bioinformatics evaluation of M4 can reveal

some new avenues for structure manipulating to increase itsapplication value. Thus, the aim of

this study was evaluation of M4 using bioinformatics tools. In this study, virtual cloning of M4

in pET32a+ vector performed step by step by Vector NTI® Software (Thermo Fisher Scientific)

and some of M4 features evaluated by bioinformatics tools. Finally, interaction of M4 evaluated

by docking online tools. Result from current study revealed that M4 has sufficient potential for

using into FPs.

Keywords: Fusion protein, IL-24, M4, Bioinformatics.


Promotion of antioxidant peptides of tomato waste seed meals by

bacillus subtilis submerged fermentation

Elham Ghanbari, Fakhri sadat Hoseini, Zahra Moosavinejad.

Microbial National Laboratory, Alzahra University, Tehran, Iran.

Abstract

The vast uses of tomato in culinary preparations and processes it into products such as juices,

sauce, ketchup, and powder cause to remain seed waste of it with high nutritive value to reach

bioactive peptides owing to they are economic, acceptable, and safe type of protein sources

among the different plants and animals proposed. In this study, we used tomato meal as by-

product of oil industry have good biological value and with a minimum processing we can reach

to peptides that are useful and healthful component with higher antioxidant activity. Ground

deoiled tomato seed meal was used for bacillus subtilis submerged fermentation in the 100 ml

cultivate medium in 250 ml flask for 72 hr incubation. Every 24 hr sampling and antioxidant

activity measured by radical scavenging activity in DPPH test and iron chelating activity in

ferrozine test on the peptides precipitated in ammonium sulfate were conducted. Data are

presented as mean ± SEM and they were analyzed by unpaired t test. Increasing radical

scavenging activity and iron chelating activity were respectively from 13.44±0.83 to 20.07±0.54

and 8.72±2.93 to 26.32±3.60 after 48 hr incubation. (p<0.05) Submerged fermentation of the

tomato seed meal by bacillus subtilis can increase antioxidant activity. Further studies are needed

to peptide sequences and structure analysis.

Keywords: Radical scavenging, DPPH test, Tomato seed meal, Submerged fermentation.

http://scholar.google.com/scholar?hl=en&as_sdt=0,5&q=radical+scavenging



https://www.google.com/search?biw=837&bih=529&q=respectively&spell=1&sa=X&ved=0ahUKEwjss9LuuMXLAhWBPxoKHZ8oAEUQvwUIGSgA



Comparison of radical scavenging activity of tomato and grape meal

peptides by bacillus subtilis submerged fermentation

Elham Ghanbari, Fakhri sadat Hoseini, Zahra Moosavinejad

Microbial National Laboratory, Alzahra University, Tehran, Iran.

Abstract:

Tomato and grape seed flours as by-product of juice and food industry represent an available,

economic, and excellent source of protein due to own biological value to reach peptides that are

bioactive, natural, and relatively free from anti nutritional factors. The seed meals of tomato and

grape after oil elimination were used for submerged fermentation in the 100 ml cultivate medium

supplementation with K2HPO4 and MgSO4 in 250 ml flask by bacillus subtilis. Peptides were

precipitated in 90% saturated ammonium sulfate and to evaluate the antioxidant activity DPPH

test was used on samples after 0 and 48 hr incubation. Data are presented as mean ± SEM and

they were analyzed by unpaired t test. Radical scavenging activity increased from

5777.44±123.57 to 7440.51±302.47 in grape peptides and 13.44±0.83 to 20.07±0.54 in tomato

peptides after 48 hr incubation. (p<0.05). Note that grape seed meal in compared with tomato

seed meal have considerable antioxidant activity and both of them antioxidant activity after

bacillus subtilis submerged fermentation can increased. Further studies are needed to structure

analysis and peptide sequences.

Keywords: Radical scavenging, Grape seed meal, DPPH test, Tomato seed meal, Submerged

fermentation.





Glutathione S-transferase protein of some cultivated wheat in Iran

and Sasan Mohsenzadeh *GhanbarzadehZohreh

Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran.

Abstract

Glutathione s-transferase is a family of multifunctional detoxification enzymes which are mainly

cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione

tripeptide. In this study, the sequence of 11 wheat cultivars of the protein gene for this enzyme

was investigated and phylogenetic analysis was drowning. These cultivars are Bosostaya,

Chamran, Roushan, Shahi, Sardari, Omid, Mahouti, Bayat, Darab, Zarrin and Alvand. The

sequences were isolated and submitted in NCBI GeneBank. Nucleotides analaysis, alignment

and draw a phylogenetic tree was performed by CAIcal Server, Multalin and CLC sequence

viewer software, respectively. The results showed that alignment between the wheat cultivars is

about 65% to 90%. The highest percentages of nucleotides in cultivars were: Sardari (T,

18.64%), Chamran (A, 20.45%), Omid (C, 28.55%), Shahi (G, 38.48%), Omid (GC, 63.72) and

Bosostaya (AT, 38.48%). GC rich proteins have more resistant to high temperature, so probably

glutathione s-transferase of Omid wheat is more resistant to high temperatures than other

cultivars. It is noteworthy that other bioinformatics data derived from these cultivars.

Keywords: Alignment, Glutathione S-transferases, Nucleotides, Phylogenetic analysis.


Studying structures and processes involved in the transfer across

nuclear pore complexes using molecular dynamics simulation

Zeinab Ghesmati1 and Sarah Mohammadinejad2

1 Department of Biological sciences, Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang, Zanjan,

Iran.

2 Department of Biological sciences, Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang, Zanjan,

Iran.

Abstract

Nuclear pore complexes (NPCs) are selectively gated pathways between nucleoplasm and

cytoplasm. Whereas small molecules can diffuse freely through NPCs, large molecules (>40

KDa) can pass only when bound to transport receptors. The NPC central channel is filled with

disordered proteins, rich in phenylalanine-glycine (FG) repeats, referred to as FG-nups. Previous

experimental studies prove that FG-nups are the main agents responsible for the selective

function of NPC. In this research, we use molecular dynamics simulation to study the mechanism

behind this selective function.We use a coarse-grained model for the FG-nups, in which each

amino acid is modeled with four spheres. Our results, show that individual FG-nups form

globular structures, whereas arrays of FG-nups tethered to a planar surface, at an FG-repeat

density found in the NPC, form brush-like structures of multi-protein bundles. More than half of

the FG-repeats are found on the surface of the bundles, offering a favorable environment for the

transmission oftransport receptors. Our results confirm the virtual-gate model for the mechanism

of selective function observed for NPCs. Also our simulations with NTF2, as a transport

receptor, show that NTF2 can pass through the NPC central channel by hydrophobic interactions

with FG-repeats, when added into the brush-like structure.

Keywords: Nuclear pore complexes, Coarse-grained model, Brush-like structure,

Transportreceptors, Virtual-gate model.


Investigating the interaction of antibacterial peptide “LLAA” with

the bacterial membrane using molecular dynamics simulation.

Goli Ghobadi1 and Sarah Mohammadinezhad 2

1 Institute for Advanced Studies in Basic Sciences (IASBS), Department of Biological Sciences, Gava Zang,

Zanjan, Iran.

2 Institute for Advanced Studies in Basic Sciences (IASBS), Department of Biological Sciences, Gava Zang,

Zanjan, Iran.

Abstract Antimicrobial peptides (AMPs) are important components of the innate immune systems of the

most organisms. AMPs are generally amphipathic and cationic and have a tendency to interact

with lipid bilayers. LLAA is a 13 residue peptide with antibacterial and anticancer properties and

this peptide is a modified analog of Aurein 1.2 peptide that has more positive charge than Aurein

and its antibacterial effect is about 3 times stronger than Aurein 1.2 peptide. In this work,

molecular dynamics simulation and GROMACS package have been used for investigation of

interaction of LLAA with modeled bacterial membranes that consist of phospholipids with the

ratio 3:1 of POPE/POPG. We have also studied of phospholipid acyl chain which show that

increasing the peptide concentration, causes of significant perturbation bacterial membrane and

decreased the stability of membrane and increases the permeability of the bacterial membrane.

Also calculating the extent of thining of membrane peptide due to interaction with the peptide

shows that increasing the in number of peptides causes more thinning of the membrane. All these

observations together show that the LLAA peptides have better antibacterial performance in the

group relative to a single peptide. Our results show that despite the high affinity of peptides

LLAA to the bacterial membrane, but over 400 ns of our simulation time, no considerable

penetration of the peptide into the membrane of bacteria is observed. This difficulty for the

penetration could be related to the small hydrophobic part of the LLAA peptide in comparison

with its polar part.

Keywords: Antibacterial peptides, Lipid bilayer, LLAA peptide, Molecular dynamics simulation,

GROMACS package.


The effects of a novel phenanthroline-imidazole derivative of

platinum complex on the structure and function of bovine liver

catalase

Rohollah Ghobadi1, Adeleh Divsalar2, Alireza Harifi Mood1, Ali Akbar Saboury3, Mahboube Eslami

Moghadam4

1 Department of Chemistry, Kharazmi University, Tehran, Iran.



4Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran.

Abstract:

Catalase is ahighly active, ubiquitous enzyme which occurs in almost allaerobically respiring

organisms and protectsthe cells from the toxic effects of hydrogen peroxide. In the present study,

the effects of a new synthesized phenanthroline-imidazole derivative of platinum complex were

investigated on the structure and function of bovine liver Catalase (BLC)using. Different

spectroscopic methods of UV–visible, fluorescence, and circular dichroism (CD) at various

temperatures of 25 and 37 °C.UV-visible spectroscopy results declared that the enzymatic

activity decreases slightly with increasing platinum compound’s concentration. Meanwhile,

raising the concentration of platinum complex lead to a significant quenching of intrinsic

fluorescence of catalase resulted changes in three-dimensional environment around the

chromophores of the enzyme structure. Analysis of fluorescence quenching data showed that

there are two binding sites on BLC for this complex and the binding constant values were

calculated 427 × 107 and 3.25 × 107 M−1, respectively at temperatures of 25 and 37 °C. Also,

circular dichroism (CD) data represented a significant decreasing in α-helix content of enzyme at

high concentrations of platinum compound. Consequently, it can be concluded that this novel

platinum complex can interact with catalase and induce minor changes in the function and major

alterations in the structure of catalase.

Keywords: Catalase, Fuorescence, Circular dichroism, Platinum complex, Quenching.


Stability of the recombinant enzyme in Lepidiumdrabaperoxidase

(LDP) against heat and hydrogen peroxide

Alireza Ghaseminasab1, Ali Riahi-Madvar2, Yaser Fattahian2

1Department of Biotechnology, Faculty of Science and Modern Technology, Graduate University of Advanced

Technology, Kerman, Iran.

2Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate

University of Advanced Technology, Kerman, Iran.

Abstract

Peroxidases, a class of enzymes in animal, plant and microorganism tissues, catalyze

oxidoreduction between H2O2 and various reductants. Peroxidases have been divided into

different superfamilies: plant peroxidases, animal peroxidases and catalases. The plant

peroxidases superfamily, which contains peroxidases from both prokaryotic and eukaryotic

origin, can be divided into three classes, based on structural similarities and certainly in a

suspected common evolutionary origin.The main purpose of this research,was investigated the

stability of the recombinant Lepidiumdraba peroxidase(LDP) against hydrogen peroxide and

heat.Therefore, after purification and refolding of the enzyme, its stability was examined against

heat in the temperature range of 35-90 °C and hydrogen peroxide in the range of 0-

14mMH2O2.The results showed that the LDP loses 50% of its activity at 67 °C (T1/2) after 10

min.whilst, the enzyme activity decreased by 40 percent at 60 °C after one hour(t1/2). The results

also showed that treatment enzyme with H2O2, lead to decrease about 50 percent of enzyme

activity in the presence of 11 Mm H2O2. Accordingto the results it may be purposed that the

enzyme has stability comparable to HRP.

Keywords: Lepidiumdrabaperoxidase, Recombinant protein, Stability.


Effect of lysine residue acetylation on the structure of apomyoglobin

Mehrnaz Azami-Movahed1, Ali Akbar Meratan2, Atiyeh Ghasemi1, Azadeh Ebrahim-Habibi3, Ali Akbar

Saboury1, Mohsen Nemat-Gorgani4


2Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.

3Endocrinology and Metabolism Research Center, Tehran University of Medical Sciences, Tehran, Iran.

4Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.

Abstract

It is well known that various chemical modifications, by bringing about significant changes in

the net charge and/or surface hydrophobicity, play important role in the structure of proteins. In

this study, effect of lysine residue acetylation, as one of the most common reversible post-

translational modifications targeting a wide range of proteins, on the structure of apomyoglobin

(apoMb) was investigated. Given that acetylation neutralizes the positive charges of basic lysine

residues, it expects that this modification would correspondingly affect the structure of the

apoMb. The extent of acetylation was verified by the fluorescamine assay and a range of

techniques including far- and near-UV CD spectroscopies, ANS and intrinsic fluorescence assays

were employed to explore structural changes of apoMb upon acetylation. Our results clearly

indicate that acetylation of lysine residues strongly destabilize the native conformation of apoMb

by altering both secondary structure and folding properties of the protein. Moreover, results

obtained by ANS fluorescence assay, demonstrated a considerable decrease in surface

hydrophobicity of the acetylated apomyoglobin compare to native form, suggesting disruption of

heme pocket upon acetylation. Our results suggest that variation in the charge distribution at the

protein surface may play a key role in the conformation stability of apoMb.

Keywords: Apomyoglobin, Lysine modification, Acetylation, Surface charge, Structural stability.


Effect of spacer length of the synthetic cationic urethane gemini

surfactants on the secondary structure of insulin

Rezvaneh Ghasemi Tabesh1, Pouneh Sadat Pourhosseini1, Ali Akbar Saboury2, and Farhood Najafi3

1 Faculty of Biological Sciences, Alzahra University, Tehran, Islamic Republic of Iran.

2 Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Islamic Republic of Iran.

3 Department of Resin and Additives, Institute for Color Science and Technology, Tehran, Islamic Republic of Iran.

Abstract

Gemini surfactants are new classes of surfactants finding their way into surfactant-based

formulations. Recently they have attracted considerable interest in the academic and industrial

communities working on surfactants. The interaction of gemini surfactants with bio-

macromolecules (proteins, genes, lipids, …) have been the subject of extensive studies because

of their applications in food and pharmaceutical industries, analytical biochemistry studies,

cosmetics, and drug delivery. In this research two kinds of cationic urethane gemini surfactants

differing in their spacer length (C2 and C4) were used and their interaction with insulin at pH 7.4

was investigated by circular dichroism spectroscopy. Far-UV CD data revealed changes in the

secondary structure of insulin as changes in the helical content as well as the β-structure of the

protein. It showed the longer the spacer, the lower the helical content. The trend of beta structure

changes was in reverse direction, however. Besides, for both surfactants the maximum helical

content was occurred at the surfactant to protein molar ratio of 3.

Keywords: Cationic gemini surfactant, Urethane, Circular dichroism spectroscopy, Insulin,

Interaction.


Superior cytotoxicity of serum albumin on microglial cells upon

hetero-seeding effect of amyloid peptide

Maryam Ferdousi1, Mehran Habibi-Rezaei1,2,Saeed Balalaie3, Sorour Ramezanpour3, Farzaneh Sabouni4,

Najmeh Poursasan5, Manijheh Sabokdast1, Ali Akbar Moosavi-Movahedi5,6

1School of Biology, College of Science, University of Tehran, Tehran, Iran. 2Nano-Biomedicine Center of Excellence, Nanoscience and Nanotechnology Research Center, University of Tehran,

Tehran, Iran. 3 Peptide Chemistry Research Center, K. N. Toosi University of Technology, Tehran, Iran. 4Department of Basic Sciences of Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran,

Iran. 5Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. 6Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.

Abstract

We demonstrate in vitro cross-seeding of bovine serum albumin (BSA) in the presence of Aβ25-35 and

their cytotoxic effects on microglial cells. To investigate the cross-seeding of BSA in the presence of

Aβ25-35 fibrils, we examined how Aβ25-35 fibrils can function as seeds to trigger and accelerate BSA

fibrillogenesis using ThT, intrinsic fluorescence, ANS fluorescence, and transmission electron

microscopy (TEM). Moreover, the effects of these fibrils on microglial viability were measured using

MTT and Annexin V/propidium iodide (PI) staining. Although Aβ25-35 is toxic against microglia, it

acted as seed and affected the aggregation pathway and accelerated the fibrillogenesis of BSA in

vitro, resulted in an enhanced cytotoxic effect in comparison with Aβ25-35 or BSA alone. These

observations thought to be helpful to understand the molecular mechanism of enhanced toxicity due

to the coexistence and cross-seeding of proteins and their effects on microglial cells that may involve

in neurodegenerative diseases such as Alzheimer’s disease (AD).

Keywords: Aβ25-35, Alzheimer’s disease, BSA, Cross-seeding, Microglia.


Prediction and evaluation of myelin oligodendrocyte glycoprotein

(MOG) antigenic epitopes

Narjes Farajzadeh-dehkordi, Mostafa Shakhsi-Niaei, Behnaz Saffar

Department of Genetics, Faculty of Sciences, Shahrekord University, Sharekord, Iran.

Abstract

Multiple sclerosis (MS) is the most common autoimmune disease involving the nervous system.

T cells reactive to the major constituents of the myelin sheath, myelin oligodendrocyte

glycoprotein (MOG). The major histocompatibility complex (MHC) class I is expressed on the

cell surface of all nucleated cells, and plays an important role in antigen presentation to

autoreactive T-cells. A neuroantigen DNA vaccine can be used for induction of tolerance of in

human. In this study, some prediction softwares such as Paproc, Netchop3.1 and Mappp were

used for prediction of proteasome cleavage sites of MOG. Generally each softwares produced

different 8-11cleaved aminoacid peptides despite some overlapping results. Therefore, to find the

best epitope, amino acid residues of 105-112, 104-111, and 243-252 which subsequently

produced by Paproc, Netchop3.1, and Mappp Softwares were checked for antigenisity by using

Predicted Antigenic Peptides web server. Results showed that antigenic amino acid residue of

243-252 which was predicted by Mappp showed the best matchable epitope with antigenisity

criteria among all predicted peptides. Altogether, prediction tools may help select more antigenic

peptides for design of DNA vaccines.

Keywords: Cleavage prediction tools, protein, DNA vaccine, MOG, MS.


Evaluation of MHC class I binding properties of designed peptides

for DNA vaccine for induction of multiple sclerosis tolerance in

human

Narjes Farajzadeh-dehkordi, Mostafa Shakhsi-Niaei, Behnaz Saffar

Department of Genetics, Faculty of Sciences, ShahrekordUniversity, Sharekord, Iran.

Abstract

One of biological functions of the immune system is the prevention of autoreactive T and B cells

activation whichare potential threatsfor autoimmune diseases like Multiple sclerosis (MS). The

major histocompatibility complex (MHC) class I is expressed on the cell surface of all nucleated

cells and plays an important role in antigen presentation to autoreactiveTcells. A neuroantigen

DNA vaccine can be used for induction of tolerance in human. In our previous study, some

prediction softwares were used for finding immunogenic epitopes by prediction of proteasomal

cleavage sites of Myelin Oligodendrocyte Glycoprotein (MOG), a related MS antigen. Therefore,

obtained antigenic amino acid residues of, 105-112,104-111 and 243-252, were analyzed for

evaluation of binding affinity of human MHC class I by using the IEDB web server. The best

results were related to MHC class I alleles of HLA-A*31:01 and HLA-A*33:01 which interact

more efficiently with epitope of KFSSLCYKQ (243-252) predicted by MAPPP software.

Altogether, prediction tools may help select better epitopes with better interaction with MHC

alleles for design of DNA vaccine.

Keywords: DNA vaccine, MHC class I, Multiple sclerosis, MOG, Tolerance.


Cloning and expression of soluble extracellular domains 1-3 of

human VEGF receptor-2 in Pichia pastoris

Zahra Fathi1, Reza Hassan Sajedi2, M. Mashhadi, Akbar Boojar1, Ehsan Dehnavi3

1Department of Cellular and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran. 2Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. 3Gene Transfer Pioneers research group, Shahid Beheshti University, Tehran, Iran.

Abstract

Vascular endothelial growth factor (VEGF) is a key regulator of pathological angiogenesis,

vascular permeability and overexpressed by most solid tumors. VEGF receptor-2 (VEGFR-2 or

KDR as it is called in human) is a specific receptor of VEGF with a high binding affinity. In this

study, a solube recombinant extracellular domain 1-3 of human VEGFR-2 (rKDR1-3) was

expressed in Pichia pastoris to inhibit the VEGF-induced angiogenesis. The 975 bp DNA

fragment, containing 948 bp extracellular domains 1-3 kdr, was designed according to the

nucleotide sequence at GenBank and protein sequence at SwissProt. The recombinant Pichia

Pink secretory expression vector (pPinkαHC/KDR1-3) was constructed and transferred into

Pichia pastoris (Pichia Pink strain 4) by electroporation. The high expression transformants were

identified through complementation of adenine auxotrophy and methanol induction. The

recombinant KDR1-3 was successfully expressed and confirmed by using SDS-PAGE and

western blot techniques. VEGF-A/KDR1-3 interaction was proved by ELISA receptor binding

assay using recombinant VEGF and bevacizumab (avastin), a anti-VEGF monoclonal antibody,

for cancer therapy. Pichia pastoris expresses soluble and highly efficient recombinant protein.

Also, it has many advantages such as protein processing, protein folding and the availability of

post-translational modifications. In conclusion, we developed a soluble extracellular domain of

KDR with high-affinity against VEGF, which could be of therapeutic value for a variety of

pathological angiogenesis. The rKDR1-3 could also be used to develop a novel monoclonal

antibody, and a fusion protein composed of the antibody and rKDR1-3 to block the

VEGF/VEGFR interaction more effectively.

Keywords: Angiogenesis, VEGF-A, VEGFR-2, Pichia pastoris.


Study of the interaction of myricetin and Morin hydrate with

bovineα-Lactalbumin

Yasir FatehiBabi and Fakhrosadat Mohammadi


Abstract

Bovine α-Lactalbumin (BLA) is an acidic Ca2+-binding protein found in milk. One of the major

roles of milk proteins is the transport of the drugs/bioactive compounds and facilitating their

functionality in delivery system. To better understanding the transport and metabolic process of

the bioactive compounds/drugs, it is essential to explore the mechanism of interactions between

these compounds and carrier proteins. Flavonoids are small natural polyphenols found in many

grapes, fruits, berries, vegetables and herbs as well as other plants. In this study fluorescence

assayshave been used to investigate the binding characteristics of Morin hydrate and Myricetin

as two bioactive flavonoids with α-Lactalbumin. The binding parameters of Myricetin and Morin

hydrate with BLA such as binding constants and the number of substantive binding sites have

been estimated from the analysis of fluorescence quenching measurements. The differences in

affinities of Myricetin and Morin hydrate for BLA were discussed based on the chemical

structure of these flavonoids and involved molecular interactions with BLA. The short Förster's

distance between donor (BLA) and acceptor (Morin hydrate and Myricetin) and also the binding

constant values demonstrated the strong interaction between these two flavonoids and BLA. The

thermodynamic parameters were obtained from the fluorescence quenching measurements in

different temperatures. It can be concluded from the sign and magnitude of ΔH and ΔS that the

final ligand–protein complexes were stabilized by hydrogenbonds. The considerable change in

microregion of the Trp residues in BLA is observed upon the binding of theMyricetin and Morin

hydrate to BLA by synchronous fluorescence.Molecular docking studies indicated that these two

compounds bind to BLA by hydrogen bonds.

Keywords: Flavonoids, α-Lactalbumin, Fluorescence quenching.


Protective effects of hydroalcohol extract of Zingiber Officinale on

the functional disorders and histological damages in Iron-induced

renal toxicity in rats

Firoozeh Gholampour1, Fatemeh Behzadii, 1 and seyed mohamad Owji2

, Shiraz University, Shiraz, Iran.of SciencesDepartment of Biology, Faculty 1

, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.of PathologyDepartment 2

Abstract

Iron overload in the body is associated with toxic effects and endanger health. Evidences have

suggested that various forms of kidney injuries may be caused by free radical formation and

subsequent oxidative stress. The roots of Zingiber officinale contain polyphenol compounds

which have a high antioxidant activity. The aim of this study was to evaluate the protective role

of hydroalcohol extract of Zingiber officinale against ferrous sulfate-induced renal toxicity in

rats. Renal damage was induced by i.p. injection of ferrous sulfate (30 mg/Kg/day) for 14 day in

male wistar rats (220-260g). In final blood samples collected for determination of the serum

creatinine, urea nitrogen and sodium (Na) concentration. Then kidney samples were removed

and preserved for histological studies and estimation of lipid peroxidation. Hydroalcohol extract

of Zingiber Officinale (400 mg/kg/day in 1 ml distilled water) was administered by gavage for 14

days. Ferrous sulfate caused deterioration of renal function, renal morphology and a significant

renal oxidative stress. Administration of hydroalcohol extract of Z. officinale significantly (p <

0.01) reversed the levels of renal functional markers and lipid peroxidation marker. All these

changes were corroborating by histological observations of kidney. This study demonstrated the

protective role of hydroalcohol extract of Z. officinale in reducing toxic effects of ferrous sulfate

in experimental male rats.

Keywords: Creatinine, Ferrous sulfate, Lipid peroxidation, Kidney, Zingiber officinale.


Human asf1a c-terminal tail phosphorylation favours formation of

stable secondary structures in this intrinsically disordered peptide

Sayed Shahryar Alavi Hejazi1

1Genomics Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan, Iran.

Abstract

When replication machinery reaches a nucleosome, the histone core must be evicted temporarily

and then be deposited onto the newly synthesised daughter strands just behind the replication

fork. In addition, as the DNA being duplicated during replication, cells need to double the

number of core histones to restore their chromatin organisation properly. The histone chaperon

Asf1a binds newly synthesised heterodimer of H3-H4 histones to provide an active histone pool

for DNA replication. In response to histone depletion for nucleosome assembly, protein kinase

TLK1 phosphorylates human Asf1a (hAsf1a) C-terminal tail, which increases the hAsf1a affinity

for H3-H4. This segment is responsible for regulation of hAsf1a activity, however the hAsf1a

tail is highly flexible and disorder analysis has showed it is unstructured. So using Amber

molecular dynamics simulation programme, the effects of phosphorylation upon hAsf1a tail

conformation have investigated. Two stretched form of hAsf1a tail, native and phosphorylated,

was constructed for 10 ns MD simulations in implicit solvent. When phosphorylated on serines

166 and 175, the flexibility of the hAsf1a tail was reduced and tended to fold and form a more

stable structure. These results suggest that phosphorylation pattern of the C-terminal tail of

hAsf1a regulates the activity of this histone chaperone by favouring formation of stable

secondary structures.

Keywords: hAsf1a, Phosphorylation, Molecular dynamics, Histone chaperone, Chromatin

replication.


Bioinformatics analysis of Aspartyl/asparaginyl β-hydroxylase

protein

Reza Azizi1, Mohammad Reza Mofid2, Ali Jahanian-Najafabadi3, Hadi Bakhtiari2, Amir Ansari2

1 Students’ Research Committee, School of Pharmacy, Isfahan University of Medical sciences, Isfahan, Iran.

2 Department of Biochemistry, School of Pharmacy, Esfahan University of Medical Sciences, Isfahan, Iran.

3 Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences,

Isfahan, Iran.

Abstract

Membrane Protein human Aspartyl/Asparaginyl beta-hydroxylase (HAAH) play an

important role in calcium homeostasis. The gene is expressed from two promoters and undergoes

extensive alternative splicing. The encoded set of proteins share varying amounts of overlap near

their N-terminal but have substantial variations in their C-terminal domains resulting in distinct

functional properties. The longest isoforms (a and f) include a C-terminal HAAH domain that

hydroxylates aspartic acid or asparagine residues in the epidermal growth factor (EGF)-like

domains of some proteins. In human tumorous cells expression of this enzyme can be elevated,

which is associated with progression of tumor. Serum level of HAAH served as indicator for

different carcinomas. In this article we study the structure and some aspects of bioinformatics in

HAAH using different bioinformatics methods and sites. The amino acid sequence of the enzyme

was taken from the NCBI site. One part of the study was carried out with bioinformatics tools

that are available on the NCBI and Expasy and was done online. Another part was performed by

Pdb Viewer-Swiss. There are several isoforms of this enzyme in different organisms, so we draw

its phylogenetic trees using the blast review software on NCBI.In addition to drawing

phylogenetic tree, we determined the amino acid sequence. Also we identified the main physico-

chemical properties of a protein, predicted primary, secondary, tertiary structure analysis, looked

for transmembrane segments and coiled-coil regions, of HAAH. Finally we used the

hydrophobicity to identify the groups with hydrophobic characterization of HAAH.

Keywords: HAAH, Tumor, Bioinformatics, Structure.


Cloning and heterologous expression of catalytic subunit of rice

(Oryza Sativa) acetohydroxy acid synthase in Escherichia coli

Ghazaleh Arabzadeh and Azar Shahpiri

Faculty of Agriculture, Isfahan University of technology, Isfahan, Iran.

Abstract

Acetohydroxyacid synthase (AHAS) EC 2.2.16, is the first enzyme that catalyses the

condensation of two molecules of pyruvate to form acetolactate in the biosynthesis of leucine,

and valine, or the condensation of pyruvate and 2-oxobutyrate to form acetohydroxybutyrate in

the biosynthesis of Isoleucin. AHAS is the target enzyme for several classes of herbicides

including sulfonylureas, imidazolinones and triazolopyrimidines that inhibit the activity of this

enzyme. AHAS holoenzymes are assembled from large catalytic subunits and small regulatory

subunits. In the absence of the small subunits, the large catalytic subunits of AHAS enzymes are

insensitive to product feedback inhibition. Higher plants have one or more AHAS isozyme

localized in the chloroplasts. The AHAS gene from Oryza Sativa, including the chloroplast

transit peptide, was purchased from NIAS cDNA library and was amplified by polymerase chain

reaction with the oligonucleotid primers containing EcoRI and HinDIII site in forward and

reverse primers respectively, and after cleavage by appropriate restriction enzyme, the PCR

product was cloned into the bacterial expression plasmid pET41a. The resulting plasmid was

used to transform an expression host Escherichia coli strain Rosetta (DE3) and Oryza Sativa

AHAS (OsAHAS) was expressed in these bacteria as a protein fused with glutathione S-

transferase (GST). The considerable amount of recombinant form of GST, GST-OsAHAS

proteins were produced from cell harboring pET41a (control) and pET41a-osAHAS plasmid

respectively after induction with Isopropyl-β-D-thiogalactoside (IPTG). The fusion product

GST-os AHAS was purified using affinity chromatography. The AHAS protein was estimated to

a molecular mass of 72 kD.

Keywords: Acetohydroxy acid synthase, Oryza sativa.


Interaction of arachidonoyl serotonin with beta-casein

nanoparticles: spectroscopy and molecular modelin studies

Maryam Atrian, AbdolKhaleg Bordbar, Mehdi Sahihi


Abstract

β-casein micelles of milk can carry hydrophobic drugs like natural nanostructures. Arachidonoyl

serotonin (AA-5-HT) which derives from tryptophan have different physical and psychological

actions. However, due to its low solubility in water, it needs biocompatible vectors for transport

in the body. In this study, β-casein’s potential in carrying ligand has been analyzed using

experimental (fluorescence spectroscopy) and computational methods. Temperature is an

important factor in analyzing β-casein’s structural stability and its complexes with other

compounds. The present study investigates the interaction of β-casein and in Arachidonoyl

serotonin different temperatures through spectroscopic methods, molecular dynamics simulations

and molecular docking. Based on fluorescence titration results and fluorescence enhancement

equations, the binding constant and the number of active binding sites of this ligand to β-casein

were calculated. Moreover, the nature of the forces involved in the interactions of this ligand and

the protein was analyzed through Van 't Hoff equation and Russ - Subramanian theory. These

analyses showed that arachidonoyl–serotonin is involved in the interactions with hydrophobic

forces and that it has one binding site. Arachidonoyl serotonin is located on the surface of this

protein. The binding constant of of arachidonoyl β-casein is proof to the higher stability of this

complex. Furthermore, results of experimental calculations (fluorescence spectroscopy)

confirming the molecular docking results. Through molecular dynamics simulation of β-casein

and its complexes arachidonoyl serotonin, RMSD, Rg, RMSF and solvent accessible surface area

were measured. Increase in RMSD, Rg, and solvent accessible surface area at the end of the

simulation for β-casein arachidonoyl serotonin complex compared to the free protein, shows an

increase in the degrees of freedom and a lack of compactness in this complex. Moreover, RMSF

in β-casein and the aforementioned complex showed less local mobility in this complex which is

a sign of its stability. These results were very much in line with experimental and molecular

docking results.

Keywords: β-casein, Arachidonoyl Serotonin, Fluorescence Spectroscopy, Docking, Molecular

Dynamics Simulation, Molecular Modelling

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjcjJKC45jLAhXiAJoKHeKaDpMQFggdMAA&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FVan_%27t_Hoff_equation&usg=AFQjCNFMTfRaY9wltOCbwlf_j9YOrqv0aw&sig2=0CoR4eVjahsvNXKdi3rP9Q


Interaction of serotonin with beta-casein nanoparticles:

spectroscopy and molecular modelin studies

Maryam Atrian, AbdolKhaleg Bordbar, Mehdi Sahihi


Abstract

β-casein micelles of milk can carry hydrophobic drugs like natural nanostructures. Serotonin (5-

HT) which derives from Tryptophan has different physical and psychological actions. However,

due to its low solubility in water, it needs biocompatible vectors for transport in the body. In this

study, β-casein’s potential in carrying ligand has been analyzed using experimental (fluorescence

spectroscopy) and computational methods. Temperature is an important factor in analyzing β-

casein’s structural stability and its complexes with other compounds. The present study

investigates the interaction of β-casein and serotonin in different temperatures through

spectroscopic methods, molecular dynamics simulations and molecular docking. Based on

fluorescence titration results and fluorescence enhancement equations, the binding constant and

the number of active binding sites of its ligand to β-casein were calculated. Moreover, the nature

of the forces involved in the interactions of this ligand and the protein was analyzed through

van't Hoff equation and russ subramanian theory. These analyses showed that serotonin is

involved in the interactions with hydrophobic forces and that it has one binding site. Molecular

docking results showed binding sites for this ligand. Serotonin is in one of β-casein’s pores.

Furthermore, results of experimental calculations (fluorescence spectroscopy) confirming the

molecular docking results. Through molecular dynamics simulation of β-casein and its complex

serotonin, RMSD, Rg, RMSF and solvent accessible surface area were measured. Decrease of

these quantities for β-casein serotonin shows the higher compactness and stability of this

complex. Moreover, RMSF in β-casein and the aforementioned complex showed less local

mobility in this complex which is a sign of its stability. These results were very much in line

with experimental and molecular docking results.

Keywords: β-casein, Serotonin, Fluorescence spectroscopy, Docking, Molecular dynamics

simulation, Molecular modelling.

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjcjJKC45jLAhXiAJoKHeKaDpMQFggdMAA&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FVan_%27t_Hoff_equation&usg=AFQjCNFMTfRaY9wltOCbwlf_j9YOrqv0aw&sig2=0CoR4eVjahsvNXKdi3rP9Q


An efficient synthesis of exenatide as an anti-diabetic drug

1, 2, Saeed Balalaie1Ramezanpour, Sorour 1, Somayeh Ahadi1Maryam Alizad

4416, Tehran, Iran.-Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 158751

Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.2

Abstract

There are so many drug as hypoglycemic drug recently. The use of peptides as natural drug is an

interesting subject in treatment of diabetes. Exenatide (marketed as Byetta, Bydureon) is a

glucagon-like peptide-1 agonist (GLP-1 agonist) medication. It could categorized based on the

group of incretin mimetics and for treatment of diabetes mellitus type 2. Exenatide has an

distinguished point as an anti-diabetic drug and it uses for the patients who the oral drug doesn't

affect the blood sugar. Exenatide is a 39-amino-acid peptide, was synthesized through Solid

Phase Peptide Synthesis (SPPS) approach and then was purified using preparative HPLC. The

structure of the product was approved using HR-MS (ESI) data. The details about the synthesis

and purification will be further discussed in the conference. The amino acid sequence for

exenatide is shown below.

Keywords: Exenatide acetate, GLP-1 agonist, Anti-diabetic peptide, Incretin.


Preparation and biodistribution assessment of 68Ga-Bleomycin as a

possible PET imaging

Saeed Kakaei1, Hamid reza Tayeri2, Elham Sattarzadeh khameneh1, Dariush Sardari2

1NSTRI, Nuclear Fuel Cycle Research Institute, P.O. Box 11365/8486, Tehran, Iran. 2Department of Nuclear Engineering, Tehran, Iran Research Branch, Islamic Azad University, Tehran, Iran.

Abstract

Bleomycin is an anti-cancer ("antineoplastic" or "cytotoxic") chemotherapy drug which is

classified as an "antitumor antibiotic. Several radiolabeled Bleomycin derivatives have been

developed for imaging and/or therapy of neoplastic tissues. The most important imaging

compounds contain indium-111,1 cobalt-57,2 technetium-99m,3 radioferric salts4 and rhodium-

105.5 The positron-emitting Ga(III) radioisotopes, 66Ga3+and 68Ga3+, have been proposed for

applications in positron emission tomography (PET) imaging. In this study, by applying a

produced 68Ge/68Ga generator, a simple technique for the synthesis and quality control of 68Ga-

Bleomycin was introduced; followed by preliminary animal studies. 68GaCl3 eluted from the

generator was studied in terms of quality control factors including radiochemical purity (assessed

by RTLC), chemical purity and radionuclide purity. This study reports the preparation and bio

distribution assessment of Gallium-Bleomycin (68Ga-BLM) complex as a radiopharmaceutical

and optimization of its labeling conditions; pH, reaction time, temperature, concentration of

Bleomycin and its bio distribution in normal mice. The bio distribution of the complex was

compared with 68Ga-Cl3 in 11 selected organs including blood, liver, lung, spleen, muscle, skin,

heart, kidney, colon, colon content, and bladder at 4 selected times of 1, 2, 4, 24 hours after

injection. The optimized pH condition was found 2 at temperature of 90ºC for reaction

temperature of 30 minutes when 1 mg of bleomycin was mixed of about 2 mCi of 68Ga-Cl3.

Radio thin layer chromatography showed an overall radiochemical purity of 90-94% at the

optimized conditions with a specific activity of about 1.5mCi/m mole and radiochemical purity

greater than 93% in 15 min.

Keywords: Bleomycin, Gallium-68, Tomography, Radiochemical, Radionuclide.


The application of HER2 protein in cancer detection using graphene

functionalized with specific DNA sequences

Abdollah Noorbakhash1 and Arezou Tabasi1

1 Department of Nanotechnology Engineering, Faculty of Advanced Science and Technology, University of Isfahan,


Abstract

Human epidermal growth factor receptor 2 (HER2) protein also known as ErbB2 (avian

erythroblastosis oncogene B) is a cancer marker. HER2 overexpression on the surface of breast

cancer cells is about 20-30%. Recent studies have shown that measurement of the amount of

HER2 protein in serum is a useful noninvasive method for the early detection of breast cancer.

The extracellular domain of the HER2 is often cleaved and released into the bloodstream.

Normal individuals have a HER2 concentration between 2 and 15 ng/ml in their blood but it’s

amount in breast cancer patient’s blood is between 15 and 75 ng/ml. So it is essential to develop

a rapid, sensitive, specific, label-free, and cost-effective diagnostic test for detection of HER2

serum level. For detecting HER2, it is possible to use electrochemical biosensors.

Electrochemical detections have some advantages including simplicity, quick response, low cost,

high reproducibility, simple of instrumentation, and sensitivity. Aptamers can be used as sensing

elements in biosensors and their properties make them play a crucial role in the development of

biosensors. In the present work, a sensitive electrochemical aptasensor was fabricated for the

determination of HER2 antigen. For this purpose, HER2 specific aptamer was immobilized on

the surface of reduced graphene oxide-chitosan nanocomposite modified-glassy carbon electrode

and is used for HER2 detection. Detection limit of the fabricated aptasensor for HER2 was

evaluated to be 0.225 ng/ml with two linear response ranges of 0.5 to 2 ng/ml and 2 to 75 ng/ml.

Keywords: HER2 antigen, Aptamer, Breast cancer, Electrochemical aptasensor, Reduced

graphene oxide.


Construction of BMP-2 agonists based on nanobody (VHH)

and Sadegh Hasannia Zahra Sahraee

Biochemistry Laboratory, Department of Biology, College of sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

In all the cases that bone regeneration is not completed and the progress cannot be done

perfectly, tissue engineering can be the best option for repairing, when the rebuilding of the bone

has been failed and has not been mended. There are three important and essential factors in the

bony and collagen tissue engineering. They include of 1- scaffold 2- biomolecules and 3- stem

cells. Biomolecules and the derived peptides are able to repair the bone and induced it, that it can

improve VHH by putting the active residual in CDR3 area. For generating of an effective

nanobody, at the first, the bioinformatic must be consideration BMP-2/ BMPR-II protein

complex with 2GOO PDB code and the related residual were determined in the interaction.

These residual in BMP-2 structure determine the sequence in the CDR3 part of nanobody. Then

the two generated VHH were linked together by a linker which includes of fibronectin. In the

other step, the said sequence "VHH" was modelled protein was simulated by the GROMACS

software in the said condition. Then the said protein was docked with BMPR-II in order to

examine the way of the said nanobody has been modelled successfully and the conclusion, come

from the dock, has predicted the good and efficient interaction whit BMPR-II.

Keywords: VHH, BMP-2, Bioinformatic, Biomolecules, Agonists.


Application of bovine serum albumin- carbon nanotubes conjugated

system for fabrication of highly sensitive arsenic aptasensor

Soroor Salehi and Abdollah Noorbakhsh

Department of Nanotechnology Engineering, Faculty of Advanced Science and Technology, University of Isfahan,


Abstract

Bovine serum albumin (BSA) is a carbohydrate-free, single-chain, highly soluble, 66.4 kDa

globular protein with a 30–35 reactive primary amino groups and contains 583 amino acids in a

single polypeptide chain. BSA is used in many biochemical applications due to its stability and

lack of interference within biochemical reactions. In addition, compared with other high

molecular weight proteins, BSA is relatively cheap and readily available and also it can be

employed for biosensor and bioreactor systems. In this work, BSA-carbon nanotube (BSA-CNT)

hybrid system was employed for fabrication of very sensitive arsenic (As (III)) impidimetric

aptasensor and signal amplification. As (III) is one of the most toxic heavy metals that is

dangerous for human health even in low concentrations. BSA was bioconjugated with the

abundant amount amino groups onto the carboxylic acid functionalized CNTs. Atomic force

microscopy (AFM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy

(EIS) was used to characterization of fabricated aptasensor. BSA-CNTs nano-bioconjugated

system shows very good ability for signal amplification.

Keywords: Bovine serum albumin- Carbon nanotube, Aptasensor, Arsenic (III), Signal

amplification, Electrochemical impedance spectroscopy.


Structural and functional characterization of reduced glycated

adduct of bovine β-casein

Tanaz Sadeghian, Zohreh Tavaf, Reza Yousefi


Abstract

As a member of intrinsically disordered protein family, the amphiphilic chaperone β-casein

prevents aggregation of whey proteins in milk. Also, β-casein is an important component of

casein micelle. In order to mimic the potent reducing environment of milk, β-casein was glycated

under reducing condition. The reduced glycated β-casein adduct was applied to both structural

and functional analyses, using different techniques. Our results suggest significant structural

alteration of β-casein upon non-enzymatic glycation. While micellization and chaperoning action

of the glucose modified protein were significantly altered, its allerginicity profile remained

largely unchanged. In addition, antioxidant activity was improved after non-enzymatic glycation

of this protein. Normally, glucose levels in breast milk are approximately one-fourth of the

mother's blood glucose level. Therefore, the effective reducing environment of human milk may

provide a suitable environment for the reduced glycation of β-casein particularly in diabetic

mothers with chronic hyperglycemia.

Keywords: β-casein, Glycation, Chaperone, Structure, Allerginicity.


Construction, expression and purification of diabody against human

vascular endothelial growth factor in bacterial system

Seyed Amir Sadeghi1, 2, Mahdi Behdani1, Fatemeh Kazemi-Lomedasht1

1 Biotechnology Research Center, Venom & Biotherapeutics Molecules Lab., Pasteur Institute of Iran, Tehran, Iran.

2 Department of science, College of biology, Tehran Science and Research branch, Islamic Azad University, Tehran, Iran.

Abstract

Antibodies and their derivative fragments have long been used as tools in a variety of

applications, in fundamental research work, biotechnology, diagnosis, and therapy. Camels

produce single heavy-chain antibodies (VHH) in addition to usual antibodies. These minimal-

sized binders are very robust and bind the antigen with high affinity in a monomeric state.

Vascular endothelial growth factor (VEGF) is one of the most important key regulators of

angiogenesis during embryogenesis, reproductive functions and skeletal growth. VEGF has also

been implicated in pathological angiogenesis associated with tumor, intraocular neovascular

disorders and other. In this study, we expressed and purified anti-VEGF Diabody. Two variable

fragments of a same camel anti-VEGF antibody were linked together by a linker to make a

diabody. Constructed diabody transferred into BL-21 E. coli cells and expression of recombinant

protein was induced by IPTG. Anti-VEGF diabody purified using nickel affinity chromatography

and confirmed by SDS-PAGE and western blot analysis. Diabodies can be produced in the low-

cost and high-yeild prokaryotic expression system, so they are suitable molecules for diagnosis

and therapeutic issues.

Keywords: Diabody, Nanobody, Vascular endothelial growth factor.


Inhibition of kanamycin-resistant bacteria by designing 10–23

deoxyribozyme targeted to kanamycin resistance mRNA

Sanaz Sadeghi, Abolghasem Esmaeili, Fateme Javadi Zarnaghi

Department of Biology, University of Isfahan, Isfahan, Iran.

Abstract

Deoxyribozymes are oligodeoxyribonucleotides that catalyze reactions such as cleaving

ribonucleotide (RNA). Deoxyribozymes have different diagnostic and therapeutic applications.

Due to DNA stability and fast and cheap synthesis, it is a good option for therapeutic

applications. 10-23 deoxyribozyme includes a cation-dependent catalytic domain of 15

nucleotides and two variable binding arms. Deoxyribozymes are used as therapeutic agents by

cutting mRNAs that lead to antibiotic resistance, cancer, neurological and cardiovascular

diseases. Fluorogenic deoxyribozyme have the ability to detect cancer cells.Materials and

Methods: Gene map of pEGFP-N1 plasmid was obtained from addgene server and the

kanamycin resistance gene sequence was determined. Then, the correct reading frame was

chosen by comparison of protein sequences of different reading frames using expasy server. The

mRNA sequence is obtained by reverse the sequence complementary. Secondary structure with

the lowest free energy was selected from the server mfold and a region without spatial exclusion

was found. Considering that 10-23 deoxyribozyme has the ability to cleave any RNA substrate

between an unpaired purine (A, G) and a paired pyrimidine (U, C), we selected a AC in the

ribosome binding site in the untranslated region with 9 bases on both sides. The absence of

similar sequences in host bacteria was checked by the NCBI server. Finally, activity and binding

of deoxyribozyme were predicted by the mfold server. Deoxyribozyme prevents the ribosome

binding and could inhibit translation of mRNA to protein. Therefore it could be used as a novel

therapeutic reagent.

Keywords: Deoxyribozyme, Ribosome binding site, Antibiotic resistance, Translation.

https://www.google.com/search?q=therapeutic+agent&spell=1&sa=X&ved=0ahUKEwitp4yVhbfKAhWFfA8KHZQ-D-AQvwUIGSgA

https://www.google.com/search?q=antibiotic+resistance&spell=1&sa=X&ved=0ahUKEwiNgLzqhLfKAhXBwQ4KHbowAJIQvwUIGSgA

https://www.google.com/search?q=fluorogenic+deoxyribozyme&spell=1&sa=X&ved=0ahUKEwjY37zJhbfKAhVBlhQKHYl5CTMQvwUIGSgA

https://www.google.com/search?q=antibiotic+resistance&spell=1&sa=X&ved=0ahUKEwiNgLzqhLfKAhXBwQ4KHbowAJIQvwUIGSgA


Investigating on the synergistic inhibitory effect of aspirin and

propolis on the glycation of human hemoglobin by fructose

Uones Sahebi1, Adele Divsalar1, Ali Akbar Saboury2


2Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.

Abstract

In the presence of sugar such as fructose, structural and functional properties of proteins are

induced by glycation. It is the main cause of damages to cellular and extracellular proteins in

diabetics. A high percent of flavonoid exist in the propolis which gifts to it lots of biological

properties such as antioxidant activity. Thus we assessed the effect of co-existence of aspirin and

propolis on the fructose induced-protein changes. Fructose was added to the purified human

hemoglobin in the presence and absence both of aspirin and ethanolic extract of propolis (EEP)

for 5 week. Then, samples were gathered and the extents of hemoglobin structural changes were

measured by destruction rate of heme group extent and fluorescamine test, both via fluorimetry.

Results from this study showed that in the presence of aspirin and propolis, heme destruction and

therefore generation of heme products, which arises from fructose binding to the hemoglobin,

was prevented. Extrinsic fluorescence study showed a significant reduction in fluorescence

emission of fluorescamine, which reflected reduction of free amine content in the glycated

hemoglobin that is resulted from fructose binding to the free amine groups, while it is inhibited

in the samples containing both of aspirin and propolis. It can be concluded that aspirin, as a

known anti-glycating drug, and propolis, as a novel anti-glycating substance, could prevented

synergically the structural changes of hemoglobin which induced in the presence of fructose.

Hence, synergistic inhibitory effect of these agents potentially is useful for decreasing

complication and destructive effects of high dosage of sugars in diabetics.

Keywords: Synergistic, Aspirin, Structure, Hemoglobin, Propolis.


Comparison on the inhibitory effects of propolis on the structural

changes of glycated human hemoglobin resulted glucose and

fructose

Unes Sahebi1, A. Divsalar1, Ali Akbar Saboury2


2 Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.

Abstract

The non-enzymatic glycation was originally considered as a specialized case of the reaction of

glucose with hemoglobin. The glycation of proteins alters both their structure and function which

have been linked to diabetic disorders. Ethanolic extract of propolis (EEP) has high percent of

flavonoids which is attributed to its biological activities. Thus, we compared the glycation of

hemoglobin in the presence of glucose and fructose in the absence and presence of and propolis

extract. The purified hemoglobin samples were incubated with glucose and fructose, separately,

in the presence and absence of EEP for 5 weeks. The extent of glycation was determined by the

means of uv-visible spectroscopy and Thioflavin T (ThT) test. Results demonstrate that

incubation of hemoglobin with glucose decreases the absorption of hemoglobin significantly in

soret band region due to destruction of heme group. The increace in flouresence emission of

ThT, which binds to amyloid fibrils was also observed, in the sample containing sugar, which

occur as a result of glycation.These changes have higher rates in the presence of fructose. In the

other hand, our results have shown that EEP can inhibit all of these alterations.In conclusion, the

higher glycating effect of fructose in comparison with glucose may be due to more potent

reducing effect of fructose. In addition, the inhibitory effect of propolis on the glycation of

hemoglobin can be resulted from its antioxidant property and decrease in oxidative stress.

Keywords: Propolis, Glycation, Glucose, Fructose, Inhibition.


Subcloning, Expression, and Activity Assay of Recombinant

Luciferin Regenerating Enzyme from Lampyris Turkestanicus

(T-LRE) in Yeast

, Saman Hosseinkhani , Farangis Ataei Fateme sahebazzamani

Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

Bioluminescence, the production of light by living organisms, have been as a powerful

technology for numerous applications in biotechnology and it is dependent on two principal

components, an enzyme luciferase and the substrate luciferin. The Luciferin-regenerating

enzyme from Iranian species of Lampyris turkestanicus (T-LRE) with theoretical weight of

33.57 kD may have role in the recycling of D-luciferin from oxyluciferin; and leads to increase

of intensity and duration of luciferase light emission. The active purification of such an enzyme

would provide great development in most of luciferase application fields. Before studies on the

T-LRE expression in E.coli revealed that expressed proteins were often as inclusion bodies.

Therefore, in this study the yeast Pichia pastoris expression system was used as a eukaryotic

cell, which possesses many capabilities of a higher eukaryotic expression system, concerning

protein folding and processing. So, suitable primers were designed according to Kex2 cleavage

site and frame of the secretion signal of vector; then, T-LRE gene resulted from PCR was sub-

cloned into the pPinkα-HC plasmids. The confirmed vectors were linearized by Sac1

endonuclease in order to integrate the expressive cassette into the genome AOX1 locus of P.

pastoris (Pichiapink); and transformation was successfully completed by electroporation and

then the target protein expressed in the transformed cells. Although, no protein was detected in

the supernatant, SDS-PAGE analysis of the soluble cell extract revealed that T-LRE protein has

remained inside the cell. This protein was purified using affinity chromatography and confirmed

by western blotting. Finally, the T-LRE activity was investigated.

Keywords: Bioluminescence, Luciferin-regenerating enzyme, Luciferase, Yeast.

Rashid

Highlight


ASA rater: A web based software for classifying surface accessibility

of protein residues from the structure

Niloofar Shirvanizadeh1and Seyed Shahriar Arab1

1 Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, IRAN.

Abstract Protein engineering have proven revolutionary to improve protein properties. For protein

manipulation many parameters needed to be consider. Surface accessibility of each residue is one

of the important parameter to consider and a proper guide for many manipulations. Mostly

hydrophilic residues are placed at the exposed parts and hydrophobic at the internal parts yet it

does not happen for all, although these parts are not favorable according to energy, but they have

some application such as protein binding or dimerization. One of the common application of

surface accessibility parameters is in thermal stabilization by the replacement of these exceptions

with appropriate amino acids of course after consideration of the other effective parameters.

ASA rater is a web based software for determining the surface accessibility. It has a user friendly

interface. User can either upload pdb file or enter the pdb ID. the threshold can be specified by

the user. At the output page the number, chain, surface accessibility, secondary structure, ACC

and ASA of each residue is specified. These characteristics help users better understanding of

their protein. Here, surface accessibility is classified in to three categories of exposed, buried and

intermediate The output table can be downloaded. ASA rater is publicly available at

http://bioinf.modares.ac.ir/software/asa_rater.

Keywords: Bioinformatics tool, Protein engineering, Accessible surface area.


Studying the effect of changing the wettability of polypropylene

films on the protein adsorption

Elham Shirani and Amir Razmjou


Abstract

Polymeric materials have an important role in human health and life. Biofilm formation is a

common feature of exposing these materials to body fluids, which causes chronic infection. In

order to prevent biofilm formation, the substratum should have protein resistance property,

whereas considering the fact that protein adsorption is known the first stage of biofilm formation.

An efficient way to prevent protein adsorption and infection is the surface modification of

materials. Hence, in this work, we desired to achieve a biomaterial that protein adsorption and

subsequent cell adhesion are minimized. Polypropylene was chemically oxidized and then was

coated with titanium dioxide nanoparticles (NPs) to obtain a hydrophilic polypropylene (PP)

surface. Superhydrophobic modification was also practiced on the PP film by incorporating of H,

1H, 2H, 2H-perfluor-ododecyltrichlorosilane (FTCS) polymer molecules. Fluoro branches of the

FTCS polymer molecules, which were attached on the 𝑇𝑖𝑂2 NPs, could inhibit intimate contact

of the surface with any biofluid including protein. The results show that the contact angle for

hydrophilic and superhydrophobic surface was 60° and 154°, respectively. For assessment of

protein adsorption on the surface, bradford assay has been employed. Bovine serum albumin

(BSA) was used as a model protein in this method. Minimized protein attachment was achieved

after surface modification of polypropylene. Finally, employing PP polymeric materials is a

promising alternative which can be used in medicine for future.

Keywords: Protein adsorption, Biofilm formation, Hydrophilicity, Superhydrophobicity,

Bradford assay.


Molecular modeling of Zika virus NS5 and evaluating its interaction

with human targets using In-silico approach

Ghazaleh Sheikhi1 and Hassan Mohabatkar1

1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan,

Iran.

Abstract

The goal of this study was to generate a three dimensional structure of Zika Virus NS5, an

emerging arbovirus of flavivirus genus, using homology and Ab-Initio modeling methods and to

predict its interactions with human proteins. 3-D structures were generated using I-Tasser web

server for homology modeling and Robetta web server for Ab-Initio modeling. Structural

analysis was performed by ERRAT and PROCHECK programs. To predict protein-protein

interactions in a sequence-based manner web servers LR_PPI and iPPI-Esml were used. The

model built by Robetta was more accurate than the other model generated by I-Tasser due to

Ramachandran plots provided by PROCHECK and overall quality factor of 98.075% given by

ERRAT programs. Interacting pairs between Zika Virus NS5 and human proteins were

determined by the high interaction score from both servers. The generated model and predicted

interacting pairs can be used in drug design and vaccine development to facilitate experimental

procedures.

Keywords: Zika Virus, NS5, 3-D structure, Modeling, Protein-protein interaction.


Extraction optimization, purification and characterization of a

protease enzyme from fruits of Withania coagulans

Saeideh shavandi1, Mehdi varidi2, Ahmad Asoodeh3

1The Ferdowsi University of Mashhad, Mashhad, Iran.

2Department of Food Science and Technology, Ferdowsi University of Mashhad, Mashhad, Iran.

3Department of Chemistry, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

Enzyme proteases are one of the most important enzymatic groups in the industry. In recent

years, extracted proteolytic enzymes from plant resources have attracted much attention because

of high activity, stability in a wide range of pH and temperature, resistance to various metal ions,

inhibitors and organic solvents. Withania coagulans is a subtropical plant with important

medicinal properties. The plant fruit is used as a milk coagulant in the east Mediterranean and

south Asia traditionally for cheese production. Withania coagulans have been investigated as a

possible source of an aspartic protease enzyme. Response surface methodology (RSM) using a

central composite design (CCD) was employed to optimize the conditions for extraction of serine

protease from fruits of Withania coagulans. The effect of independent variables, namely

temperature (30-70) sample to buffer content ratio (1/4-1/10) and buffer pH (3–8) on protease

activity, specific activity and protein content of aspartic protease from fruits of Withania

coagulans was investigated. This study showed that the optimum conditions for extracting

protease enzyme from Withania coagulans fruit are, temperature 44.5 ° C, pH 3 and sample to

buffer content ratio 1/6. Protease activity, protein concentration and specific activity in optimum

conditions were 0.609 U/ml, 0.764 mg/ml and 79.8 U/mg respectively. Then in the optimal point,

purification was performed with the method of precipitation with ammonium sulfate 0/85 % and

with the ion exchange chromatographic method (column Q-Sepharose) in following, and

components molecular weight was determined using SDS-PAGE. Electrophoresis image analysis

showed 7 bond with molecular weights between 20-70 kDa.

Keywords: Optimization, Extraction, Protease enzyme.


Designing, development and assessment a series of novel genetic

constructs for aromatic hydrocarbons bioremediation based on

investigation of bacterial dioxygenases 1, Jafar Saeedi*2, 3Mashadrizeh-, Aliakbar Haddad1Mojahed-Safoora Shahreki

1. Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi

Neyshabur, Iran.

2. Cell and Molecular Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad,

Mashhad, Iran.

3. Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

Deformation, behavior and cancerous features of the cells could be as old as human history;

however, industrialization of the societies and emergence of numerous carcinogenic compounds

such as aromatic hydrocarbons led to increase these diseases and challenged the human public

health. This type of compounds that could be through consumption of contaminated food,

drinking, smoking, occupational exposure and so on through the lungs, skin and gastrointestinal

tract can enter to the body, due toxic and mutagenic properties could induce canceric features in

a range of cells as direct or indirect. Clearing this type of pollution in the environment due to

characteristics such as solubility, non-polar and hydrophobic has always been difficult. Today,

bioremediation techniques based on the use of bacterial and non-bacterial microorganisms

greatly developed, which can provide promising solutions based on probiotics development via

genetic engineering. Bearing in mind, molecular investigation of the bacterial dioxygenases were

performed in this study for designing a series of competent genetic constructs with aromatic

capacity to hydrocarbons degradation and probiotics transforming. In this regard, the profile of

the bacterial microorganisms with the ability to digest aromatic hydrocarbons as well as

corresponding molecular mechanisms and related key enzymes were determined. Subsequently,

required sequences were retrieved from databanks such as NCBI and UniProt. Molecular

investigation of them in structures, functions and binding affinity have been taken via CD search,

Motif Scan, Blast, MEGA6, Hex and ClusPro2.0 programs. New genetic constructs have been

designed based on provision of the functional domains, and after modeling with Modeller

program, assessed and minimized via MOE. Moreover, binding affinity of the designed

constructs on aromatic compounds that are retrieved from PubChem and Colby database was

performed by using of the PatchDock web server. The results of this study while demonstrated

the various strains of the bacteria with high capacity in aromatic hydrocarbons degradation,

provided the structural and functional features of the bacteria dioxygenases as well as

dioxygenases like proteins. Moreover, provide a series of optimized genetic construct with

capacity to transforming probiotic strains that ought to examine in experimental condition.

Keywords: Cancer, Aromatic hydrocarbons, Bioremediation, Probiotics.


Enhancing extraction efficiency of heterologously expressed

recombinant prostate stem cell antigen in Ecoli

Mahboube Shahrabi-Farahani1, Mohammad M Farajollahi1, Neda Saraygord-Afshari1

1Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences,

Tehran, Iran.

Abstract

Prostate stem-cell antigen (PSCA), a cell-membrane glycoprotein, has shown to be

overexpressed in several major cancers, including prostate, bladder and pancreatic neoplasms.

Highly specific expression pattern of PSCA in the most prevalent cancers leads to drastic

medical applications of this biomarker. In order to apply PSCA in medical and biological

investigations, many researchers have tried to produce this valuable biomarker via recombinant-

protein technology. Considering the hydrophobic nature of PSCA, extraction yield of this

membrane protein by heterologous expression is a subject matter. Therefore, in the present study

PSCA gene was cloned in pET-28a(+) vector, which was expressed in BL21(DE3) Ecoli strain

as a His-taged protein. Yields of recombinant-PSCA exaction were then evaluated for different

ultrasound exposure time (30s, 5 and 10) in different lysis buffer solutions. All the solutions

were composed of 0.05% 2-mercaptoethanol, 1 mM PMSF and 50 mM Tris but varied in

detergent type and/or concentration. TritonX-100 and SDS were the two detergents which were

examined here. After extraction, total protein content was subjected to electrophoretic separation

followed by a blotting procedure using anti-His-HRP-conjugates. Comparison of the blotting

patterns confirmed that the PSCA extraction yield was obviously increased in the presences of

high concentration of SDS (5%) in the lysis solution. Likewise, prolonged ultrasound exposure

(10) yielded a higher-level of PSCA in each extraction procedure. In conclusion we approved

that the nature of PSCA as a glycosylphosphatidylinositol-anchored membrane glycoprotein

demands more rigorous extraction conditions to extract it from the cell membrane and keep it in

the soluble phase.

Keywords: Prostate stem cell antigen, Extraction, Sonication, Detergent.


The properties of biosurfactant produced by Lactobacillus

rhamnosus ATCC 7469

Maliheh Shokouhfard1, Rouha Kasra-Kermanshahi1, Mohammad Mehdi Feizabadi 2, Shahram

Teimourian 3

1 Department of Microbiology, Faculty of Biological sciences, Alzahra University, Tehran, Iran.

2 Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.

3 Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran.

Abstract

lactobacilli, which constitute an important part of natural microbiota, are recognized as potential

interfering bacteria by producing various antimicrobial agents such as organic acids, hydrogen

peroxide, bacteriocins, and adhesion inhibitors, such as biosurfactants. Biosurfactants, a group of

surface active molecules synthesized by microorganisms, have recently become an important

product of biotechnology for medical applications. The Lactobacillus rhamnosus ATCC 7469

was selected as a probiotic strain to produce biosurfactant. In this study, the Drop-collapse

method and FTIR assay was used for the determination of biosurfactant. In Drop-collapse

method, biosurfactant was able to decrease the surface tension between water and hydrophobic

surfaces. The FTIR analysis showed biosurfactant appears to have more protein than

polysaccharide and phosphate. Anti-adhesive activities was determined using co- incubation

method on the Serratia marcescens strains. This biosurfactant in 2.5 mg/ml concentration

showed antiadhesive activity. The results obtained suggest the possible use of this biosurfactant

as an anti-adhesive agent in the medical field for applications against micro-organisms

responsible for the infections.

Keywords: Lactobacilli, Biosurfactant, FTIR, Anti-adhesive.

http://jlc.jst.go.jp/DN/JST.JSTAGE/jgam/59.425?from=Google


Investigate the mechanism of the BAX, a pro-apoptotic protein,

activation through SMBA1, an anti-cancer treatment: a molecular

modeling and molecular dynamics study

Yaser Shabanpour, Parviz Abdolmaleki, Esmaeil Behmard

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran.

Abstract

Bax is a central death regulator that lead the cell toward apoptosis. Serine 184 (S184) of Bax is a

momentous functional switch controlling for its pro-apoptotic activity. Experimental methodes

had shown that SMBA1, a small molecule from NCI library and Bax agonist, induces

conformational changes in Bax by blocking S184 phosphorylation, facilitating Bax insertion into

mitochondrial membranes and forming Bax oligomers. The latter leads to cytochrome c release

and apoptosis in human lung cancer cells. At first was used AutoDock 4.2 to find the best

conformation of protein- ligand complex, from docking was obtained 30 results with different

energy binding score and different conformation that was selected the best one for molecular

dynamic simulation study, one that had minimum energy binding score, for this docking we

considered 8 residues as flexible residues around the serine 184 pocket Such as Asp 98, Asp 102,

ASn 106, Arg 109, Phe 176, Val 180, Ala 183, Ile 187and serine 184 itself. Molecular dynamic

simulation during the simulation time, 110 nanosecond, shown that SMBA1 creates

conformational change in BAX protein, was obtained rmsd graph, rmsf Graphs, distance Graphs

between residues, hydrogen bond charts and Salt bridge charts for BAX protein in water box and

then for BAX-ligand complex in water box. This result was compared and was found out

conformatinal changes that occurred.

Keywords: BAX, Pro-apoptotic protein, SMBA1, Molecular modeling, Anti-cancer treatment.


Effect of mare (Equus caballus) caseins and whey proteins on breast

cancer cells

Malihe Shariatikia and Mandana Behbahani

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.

Abstract

Breast cancer is the most common cancer in women and the leading cause of cancer death in

middle-aged women. There are many therapeutic ways for breast cancer, including surgery,

radiation therapy and hormone therapy. Anticancer drugs often cause severe side effects so

further investigations is required to search for potential drugs. In the present study anti-tumor

effects of mare caseins and whey proteins on MCF7 cell line (human breast cancer cell) were

investigated in vitro. Mare milk samples were collected and caseins and whey proteins were

obtained after precipitation of caseins at pH 4.6 with 1 N HCl and centrifugation. The anticancer

activity of caseins and whey proteins was evaluated, using MTT assay. Breast cancer cells

(MCF-7) were cultured in RPMI-1640 medium containing 10% fetal calf serums. Results

showed that mare caseins have 75% cytotoxicity and whey proteins had no effect on cancer cells.

In conclusion, all the data indicated that mare milk is potential drug candidates for inducing

apoptosis in human breast cancer cells.

Keywords: Mare milk, Caseins, Whey proteins, Anticancer, MTT assay.


Endolysins as new class of antimicrobial agents against

pathogenic bacteria

Khashayar Shahin, Majid Bouzari


Abstract

Bacteriophage endolysins (peptidoglycan hydrolases) are enzymes coded and used by

bacteriophages at the end of their replication cycle(specially lytic cycle) to degrade the murine

structure of the bacterial host from within, resulting in cell lysis and release of progeny

virions. The absence of an outer membrane (Lipopolysaccharide) in the gram-positive

bacterial cell wall make it possible for endolysins to access the peptidoglycan and destroy them

when applied externally as well as internally. This potential making endolysins interesting as

novel antimicrobial candidates, particularly in light of increasing in antibiotic resistance in

pathogenic bacteria in recent decades. It is now widely recognized that alternative bactericidal

agents for the prevention and treatment of bacterial infections are urgently required. Besides the

use of native and engineered endolysins for controlling of pathogen bacteria in medical manner,

this also can be used as biocontrol agent to prevent of food spoilage in different stage of food

production procedures. This review summarizes the basic structure and functions of different

groups of endolysins and presents the most recent application of native and engineered ones to

treat multi drug resistance gram-positive bacterial species and also their new application in food

safety.

Keywords: Endolysin, Bacteriophage, Antibiotic resistance bacteria.


Study on the interaction of novel cationic platinum complexes with

human serum albumin

1, Reza Yousefi2Masoud Nabavizadeh, Seyed 1, Mehrnaz Jamshidi1Mohammad Bagher Shahsavani

1Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.

2Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran.

Abstract

Human serum albumin (HSA) predominantly functions as a transport carrier for a vast variety of

natural ligands and pharmaceutical drugs. In the present study, three structurally related cationic

Pt (II) complexes ([Pt(ppy)(dppe)]CF3CO2: 1, Pt(bhq)(dppe)]CF3CO2: 2, and

[Pt(bhq)(dppf)]CF3CO2: 3) were used to assess their interaction with HSA using different

biophysical methods. The spectroscopic results suggest that upon binding to HSA, the Pt(II)

complexes could efficiently induce structural alteration of this protein. The complexes can bind

to HSA with the binding affinities of the following order: 3 > 2 > 1. Also, thermodynamic

parameters of binding between these complexes and HSA indicated the existence of entropy-

driven spontaneous interaction which mostly dominated with the hydrophobic forces. In

addition, molecular docking revealed the involvement of π–π stacking and hydrophobic

interaction between these complexes and HSA. Moreover, CD results exhibited that 1 & 2 could

induce the secondary structural alteration of this protein to larger extent than 3. Complex 3 with

the highest binding affinity for HSA indicates lowest denaturing effect on this protein. The low

denaturation properties of 3 appear important in the terms of lower susceptibility of this platinum

complex for possible development of harmful side effects.

Keywords: Cationic Pt(II) complexes, Human serum albumin, Structural alteration,

Fluorescence, Docking simulation.


Spectroscopic and dynamic properties of arachidonoyl serotonin- β-

Lactoglobulin complex: A molecular modeling and chemometric

study

Samira Gholami, AbdolKhalegh Bordbar, Nadia Akvan


Abstract

UV– -lactoglobulin (BLG) and arachidonoyl serotonin (AA-5HT) in

BLG complex were examined and analyzed using chemometrics method. Analysis of the spectral

data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS)

algorithm resulted to the pure concentration calculation and spectral profiles resolution of the

, 1-, (4.532±0.007)×104 M1-chemical constituents and the values of (6.433±0.019)×104 M

as estimated equilibrium constants at 288, 1-and (2.977±0.013)×104 M 1-(3.364±0.010)×104 M

293, 298 and 303 K, respectively. The number of chemical constituents involved in the

interaction, was extracted by PCA method were free and bound BLG. The spontaneity of the

binding process and critical role of hydrogen bonding and Van der Waals interactions as main

driving forces in stabilizing protein-ligand complex have been designated by negative values of

Gibbs free energy, entropy and enthalpy changes of AA-5HT binding. Molecular docking study

showed that AA-5HT binds to Val(41), Leu(39), Leu(54), Ile (71), Phe (82), Asn(90), Val(92),

Phe(105), Met(107), Glu(108) with the free binding energy of –37.478 kJ/mol. Computational

studies predicted that, in spite of serotonin (5HT) which anchors to the outer surface of the BLG

by hydrogen bonds, AA-5HT is situated in the calyx pose and stayed there during the entire time

of simulation with no any major secondary and tertiary protein structural changes which pointed

that BLG could be considered as a suitable carrier for AA-5H.

Keywords: Arachidonoyl Serotonine (AA-5HT), Binding modes, UV–Vis absorption,

Multivariate curve resolution-alternating least squares (MCR-ALS), Molecular docking,

Molecular dynamics simulation.


Purified milk fractions and bioactive peptides, unknown source of

health for Iranian people

Delfan-, Abbas SoleimaniMohammad Rabbani Khorasgani

Department of Biology, Faculty of Science, University of Isfahan, Hezar Jerib Street , Isfahan Islamic Republic of

IRAN.

Abstract

Milk is the first source of food for infant mammals before they are able to eat other types of

food. Use of food supplements, milk derivatives and amino acid and peptides supplements are

increasing rapidly in many countries .Furthermore milk and some fermented products of milk

like yogurt consist of various amino acids and peptides molecules such as alpha-lactalbumin that

could be use in relaxation products, lactoferrin in blends, ß-lactoglobulin in products for high

blood pressure, cGMP in appetite regulation and IgG supplement to fight pathogenic bacteria or

infections resistant to antibiotics. In other hands some pure amino acids like Arginine is essential

for growth of muscles and these supplements can be use directly in some sport groups diets. Also

the main structural proteins in milk, Whey and Caseines, can be use in raw material as a food

supplement. Unfortunately, only some raw material like Caseines and Whey proteins is

remarkable to Iranian markets and the potential of these bioactive peptides of milk are unknown

yet. However and in conclusion, in this short study we argued about the potential of these

derivatives and amino acids for marketing in Iran.

Keywords: Milk, Bioactive peptides, Health, Marketing, Iran.

https://en.wikipedia.org/wiki/Nutrition

https://en.wikipedia.org/wiki/Digestion


Design of ubiquitin conjugated peptide of toxoplasma gondii SAG1

antigen for presentation on MHC class I

Soudabeh Soltani1, Behnaz Saffar1, Mostafa Shakhsi Niaii1, Karim Mahnam2

1Department of Genetic, College of Sciences, Shahrekord University, Shahrekord, Iran.

2Department of Biochemistry, College of Sciences, Shahrekord University, Sharekord, Iran.

Abstract

Toxoplasmosis, a zoonotic transmitable disease among different host species, can infect all warm

blooded mammals as well as birds worldwide. An acute infection with this parasite in the early

stage of pregnancy can cause prenatal malformations and abortion in hosts. The major

histocompatibility (MHC) class I antigen presentation pathway plays an important role in

alerting the immune system responses to intracellulary infected cells. MHC class I molecules are

expressed on the cell surface of all nucleated cells and present peptide fragments derived from

intracellular proteins. Ubiquitin, a 76-amino-acid peptide is used to enhance DNA vaccine

responses to antigens in the adjuvant setting. Conjugating ubiquitin to a DNA construct was

intended to enhance the proteasome dependent degradation of endogenously synthesized

antigens, which would also result in an increased cell-mediated response against the conjugated

antigens in vivo. In the present study, some prediction softwares such as Vaxijen, PropredI,

Paproc, Syfpeithi, Netctl, Netmhc were used to prediction of proteasome cleavage sites, and

antigenicity of SAG1 antigen. Comparing results of Paproc, Netctl and PropredI softwares

(detection proteosome digestion site)with results of Vaxijen, Syfpeithi, Netmhc softwares(

prediction immunogenicity )led to identification of different epitopes (amino acid residues of: 8-

15, 65-72, 169-185, 101-109, 199-206, 270-278). Bioinformatics analysis showed that this

region has proper epitope characterization therefore this analysis can be useful for producing

recombinant DNA vaccine design.

Keywords: Toxoplasmosis, Epitope prediction, Ubiquitin.


T-cell epitope prediction of different antigen for developing

Toxoplasma gondii vaccines

, Mohammad Reza 2Karim Mahnam, 1, Mostafa Shakhsi Niaii1, Behnaz Saffar1Soudabeh Soltani3Mahzunie

1 Department of Genetic, College of Sciences, University of Shahrekord, Sharekord, Iran.

2 Department of Biochemistry, College of Sciences, University of Shahrekord, Sharekord, Iran.

3 Department of Immunology, College of Veterinary Medicine, University of Shahrekord, Sharekord, Iran.

Abstract

Toxoplasma gondiiis is an obligate intracellular protozoan parasite responsible for toxoplasmosis

in warm-blooded animals, including man. Although it is generally clinically asymptomatic in

healthy individuals, toxoplasmosis may cause severe complications in pregnant women and

immunocompromised patients. The development of subunit vaccines thus constitutes an

alternative way to achieve effective protection of humans against congenital infection and to

prevent infection of immunosuppressed individuals. In immunocompetent hosts, a robust T cell

response controls parasite growth via the protective cytokine gamma interferon, although

parasites can persist within cysts in the brain and muscle for the lifetime of the infected host. The

crucial role of T cells in controlling T. gondiiinfection is highlighted by the susceptibility of

patients with T cell deficiencies to toxoplasmosis. In the present study, a wide range of on-line

prediction software (such as Vaxijen, Epijen, Ctlpred, Tappred, Iedb) was used to predict T-cells

epitopes, secondary structure and antigenicity SAG1, ROP2, MIC4, GRA7 antigens. The

bioinformatics approach used in the present study was validated by comparing its results with

eight available experimental epitope predictions. Bioinformatics analysis identified T-cell

epitopes at AA residues SAG1 (288-297,155-163), ROP2 (457-465,424-432), MIC4 (467-

475,279-287), GRA7 (208-217,189-197). Finally, all of T-cell predicted epitopes, showed

antigenicity ability except 424-432 (ROP2) and 189-197 (GRA7) residuals. Bioinformatics

analysis showed that this region has proper epitope characterization and so may be useful for

producing recombinant DNA vaccine for Toxoplasma gondii.

Keywords: Toxoplasmosis, Epitope prediction, T-cell epitope.


Kinetics of xantho-oligosaccharide production by xanthan

degrading enzymes from Paenibacillus sp. strain AS7

Maede Sarvi, Mohammad Reza Soudi, Seyed Zahra Mousavi-nejad, Simin Ashraf

Departments of Microbiology and Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.

Abstract

Xantho-oligosaccharides are products of enzymatic reactions by xanthan degrading bacteria.

Much like as many other oligosaccharides, they have a good potential to be used in many

applications such as prebiotic, antimicrobial and antiviral developments. In this study, the

bacterium was cultivated in liquid medium in presence of xanthan. The supernatant of the culture

was sampled at intervals and mixed with 0.5% (w/v) xanthan in 0.03 molar phosphate buffer (pH

6) and incubated for 4h. Thin layer chromatography showed the production of all of the

monosaccharide residues in addition to two different oligosaccharides. The results revealed the

release of the metabolites 12 hours after inoculation. The oligosaccharides were mainly produced

within 24 hours. DNS assay showed that the culture produced the greatest concentration of

reducing sugars at 18h (0.54 mg/ml). According to the results, the related enzymatic activity of

the strain increased to the maximum value in 18-24h while the maximum cell growth was

observed much later, during the time 36h to 48h.

Keywords: Oligosaccharide, Paenibacillus, Xanthan, Xanthan dingrading enzymes.


A thermodynamics study on the interaction of Allura Red AC with

calf thymus DNA

Nasrin Sohrabi1, Nahid Rasouli2, Sahar Alamatsaz3

1,2 Department of Chemistry, Payame Noor University, PO. Box 19395-3697, Tehran, Iran.

3 Department of Chemistry, Payame Noor University, Isfahan, Iran.

Abstract In the present study, the aggregation behavior of a food colorant such as Allura Red AC is

investigated in 5 mM aqueous phosphate buffer of pH 7.0 at 25.0 °C at various concentrations

and ionic strengths using optical absorption spectroscopy. The results suggest that Allura Red

AC do not aggregate in the experimental concentration range. Also, the interaction of Allura Red

AC with ct-DNA is studied by optical absorption, fluorescence spectroscopy, thermal

Denaturation and viscosity measurements. The Allura Red AC bind to ct-DNA via van der

Waals mode as illustrated by hypochromism in the UV-vis absorption band of Allura Red AC

with addition of ct-DNA.The binding constants are determined by analysis of the optical

absorption spectra of the Allura Red AC at various temperatures. The fluorescence intensity ofct-

DNA-ethidium bromide complex decrease withincreasing of concentration of Allura Red

AC.The viscosity studies showed no considerable changes in the viscosity of ct-DNA with the

increasing of the concentration of Allura Red AC. The thermodynamic parameters are also

calculated by van't Hoff equation. The enthalpy and entropy values of the reaction are both

negative and showed that the reaction is enthalpy-favored and entropy-disfavored.

Keyword: Calf thymus DNA, Allura Red AC, UV-vis spectroscopy, Thermal denaturation,

Fluorescence spectroscopy.


Molecular cloning of a Bacillus licheniformis BR1390 α-amylase

gene and biochemical characterization of the recombinant enzyme

Fatemeh Sabzalizadeh and Hamid Reza Karbalaei-Heidari

Molecular Biology Laboratory (MBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.

Abstract

Bacillus licheniformis α-amylase (BLA) is an important industrial enzyme which is used to make

corn syrup from starch. In this study, an α-amylase gene fragment with 1536 bp was amplified

using strain BR1390 genome as template by PCR and then cloned into pET 24b (+) expression

vector. Sequencing of the construct, pET24-Amy, showed that the new amylase gene has a

mutation at the position of 33th amino acid in compare to BLA Uniprot P06278. Which actually

is the 4th aa in the mature form of enzyme. Optimum extracellular expression of the recombinant

amylase in Escherichia coli BL21 (DE3) cells using the native signal peptide was obtained after

induction by 0.1 mM IPTG as inducer and 24 h incubation at 30 oC and 220 rpm. The enzyme

was purified by using DEAE-sepharose anion exchange and Ni-NTA affinity column. The

recombinant amylase showed optimum activity in the pH range of 4.0-8.0 and temperature of 90

°C. Study on the effect of 5 mM EDTA on the recombinant amylase activity revealed that the

optimum temperature was decreased to 55 oC. Positive effect of calcium in thermal stability of

the enzyme had the similar behavior of previous reported amylase from Bacillus licheniformis.

Keywords: Amylase, Calcium effect, Overexpression, Thermal stability.


Investigation on the effect of food colorant Allura Red AC on the

bovine serum albumin by various spectroscopic techniques

3Zahra Arabpour, 2, Nahid Rasouli1Nasrin Sohrabi

, Iran., Tehran3697-Department of Chemistry, Payame Noor University, PO. Box 19395 1,2

, Iran.Department of Chemistry, Payame Noor University, Isfahan 3

Abstract

In the present study, the aggregation behavior of a food colorant such as Allura Red AC is

investigated at various concentrations and ionic strengths in 5 mM aqueous phosphate buffer of

pH 7.0 at 25.0 °C by optical absorption spectroscopy. The results showed that Allura Red AC do

not aggregate in the experimental concentration range. Then, the interaction of Allura Red AC

with Bovine Serum Albumin (BSA) is studied by optical absorption, fluorescence spectroscopy

and viscosity measurements. The Allura Red AC bind to Bovine Serum Albumin (BSA) via

hydrophobic mode as illustrated by hypochromism in the UV-vis absorption band of Allura Red

AC with addition of Bovine Serum Albumin (BSA) and also the decreasing of fluorescence in

the presence of different concentrations of Allura Red AC. The binding constants are determined

by analysis of the optical absorption spectra of the Allura Red AC at various temperatures. The

viscosity studies showed no considerable changes in the viscosity of Bovine Serum Albumin

with the increasing of Allura Red AC concentration. The thermodynamic parameters are also

calculated by van't Hoff equation and the results indicate that the process is entropy-driven and

suggest that the main driving forces are hydrophobic interactions.

Keywords: Bovine serum albumin, Allura Red AC, UV-vis spectroscopy, Viscosity.


Efficient synthesis of argirelin acetate as anti-wrinkle peptide

Ali Nikbakht1,2, Hossein Zahedian1, Sorour Ramezanpour1, Saeed Balalaie1,2

1 Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran.

2 Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Abstract

Peptides are among the most powerful and interesting skin care ingredients being used in

successful anti-aging and anti-wrinkle products to date. Peptides are frequently created by the

digestion of proteins in the body and are readily and rapidly absorbed by the bloodstream. For

this reason, peptides that are synthesized from plants are non-toxic, safe and particularly

effective ingredients for skin care products. Argirelin acetate is an acetyl hexapeptide that works

to relax certain types of facial wrinkles. Acetyl Hexapepitde-3 Argireline and Acetyl Glutamyl

Heptapeptide-1, Snap 8, when topically applied, treat the same type of wrinkles as Botox,

botulinum toxin injections. Argireline decreases wrinkles on the face initiated by the contraction

of muscles of facial expression, especially in the forehead and round the eyes. Argireline is a

safer, lower, and milder alternate to Botulinum Toxin, topically aiming at the identical wrinkle

formation mechanism in a very distinct way. Ac-Glu-Glu-Met-Gln-Arg-Arg-NH2. We report

herein the synthesis of API argirelin acetate through the solid phase peptide strategy and using

the fmoc-protected amino acids. The safe used resin was 2-chlorotrityl chloride and TBTU was

used as coupling reagent.The crude product was purified using preparative HPLC and finally the

structure was confirmed using HRMS (ESI) data. The details about the synthesis approach and

other details will discuss in the conference.

Keywords: Solid phase peptide strategy, Argiriline, Anti-aging, Anti-wrinkle.


Thermostable alginate lyase from Pseudomonas aeruginosa strain

293

Maryam Zali1, Parinaz Ghadam1*, Ahya Abdi Ali2 and Sara Gharavi1

1- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.

2- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.

Abstract

Mucoid strains of Pseudomonas aeruginosa produce alginate which is a viscous

exopolysaccharide and express alginata lyase activity which can degrade this polymer. These

bacteria are important pathogens in cystic fibrosis (CF) patients commonly colonizing the

respiratory tract and the persistence of these bacteria to treatment by antibiotics, make this

pathogen the major cause of mortality in these patients. One attempt to alleviate the infection is

the destruction of the bacterial biofilm by alginate lyase enzyme. This enzyme is a member of

the polysaccharide lyases that have been isolated from various sources including marine algae,

molluscs and a wide range of microorganisms. Alginate lyases , poly(β-D-1 ,4-mannuronide)

lyase (EC 4.2.2.3) and poly(α-L-I,4-guluronide) lyase (EC 4.2.2.11), cleave the 1-4 glycosidic

linkage in alginate by β-elimination reaction. Alginate is a linear polymer of α-L-guluronate

and β-D-mannuronate arranged in homo- and hetero- polymeric blocks. In this study, alginate

lyase produced by Pseudomonas aeruginosa strain 293(from Rajai hospital in Tehran) was

partially purified and the thermal stability was determined. For this purpose, bacteria were

cultured in the liquid medium YTG (yeast extract, tryptone, glucose) and alginate lyase was

extracted by heat shock method. Enzyme activity was assayed by the thiobarbituric acid (TBA)

method. The enzyme lost just 20% of its activity after 5 hours incubation at 80 ° C. This

indicates that the enzyme has a high thermal stability and it may have many applications in

industry and medicine.

Keywords: Pseudomonas aeruginosa, Alginate lyase, Thermal stability, Thiobarbituric acid.


PH stability of alginate lyase from pseudomonas aeruginosa strain

293

Maryam Zali1, Parinaz Ghadam1, Ahya Abdi Ali2, Sara Gharavi1

1 Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.

2 Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.

Abstract

Pseudomonas aeruginosa is a Gram-negative opportunistic bacterial pathogen that secretes a

capsule-like polysaccharide called alginate that is a linear, acetylated polymer consisting of β (1-

4)-linked D-mannuronate and L-guluronate residues and a key component of mucoid biofilm

matrix. This biofilm is important for the evasion of host defenses and antibacterial therapies,

especially during chronic pulmonary disease of patients with cystic fibrosis. Most proteins for

alginate biosynthesis are encoded by the 12-gene algD operon. Interestingly, this operon also

encodes AlgL, a lyase that degrades alginate and in particular, it enhances phagocytosis and

killing of P. aeruginosa by human immune cells. Alginate lyases (also called alginases) have a

preference for either L-guluronic or D-mannuronic acid residues and have been characterized in

a variety of bacteria including marine organisms, Bacillus circulans, and Pseudomonas species,

including P. aeruginosa. Alginases cleave the 4-0-linked glycosidic bonds between uronate

residues by an eliminative mechanism, resulting in a molecule containing an unsaturated uronic

acid residue at the non-reducing end. In this research, alginate lyase produced by Pseudomonas

aeruginosa strain 293 (from Rajai Hospital in Tehran) was partially purified and the pH stability

characterized. Bacteria were cultured in YTG (yeast extract, tryptone, glucose) liquid medium

and alginate lyase was extracted by heat shock method. The enzyme was then placed in different

pH (2, 4.5, 7.5, 12) of wide range buffer for a 6 hour period and enzyme activity was assayed by

the thiobarbituric acid (TBA) method. This demonstrated that enzyme lost just 50% of its

activity after incubation in alkaline and acidic pH and can therefore be used at extreme pH.

Keywords: Pseudomonas aeruginosa, Alginate lyase, PH stability, Thiobarbituric acid.


Memory prison of protein

Gholamhossein Riazi1, Shahryar Pooyan, Nima Allahyari

Neuroorganic Lab, Department of Biochemistry, Institute of Biochemistry and Biophysics (I.B.B),

University of Tehran, Tehran, Iran.

Abstract

The mechanism of information custody in biological specious in perhaps the most

complex subject among life’s processes to study such mechanism has been tested since

several centuries ago. Based on fractal theory, the human memory of mimics small

molecules such of proteins, complex globular structure of proteins in protect candidate for

keeping information so called memory. Primary sequence and geometry of third and

fourth structure would be involved in memory of biological organisms. Naturally more

complexity drives the protein to more ability for prisoning information inside.

Microtubules proteins which in a polymer of thousands of tubulin monomer, with

hydrophobic pocket changing hydrophobic pocket structure has been shown to the very

stable while microtubule protein, as to as vesicle transporter at the time.

Keywords: Memory, Microtubules, Complexity, Fractal theory.


Effects of Silver Nanoparticles on Protein Pattern and Antioxidant

Enzymes Activities of Canola (Brassica napus L.) Under In vitro

Conditions Roya Razavizadeh

Department of Biology, Payame Noor University, PO BOX 19395 Tehran, Iran

Abstract

The effect of Silver Nanoparticles was investigated on protein pattern changes, silver

accumulation and alterations in antioxidant capacity in canola (Brassica napus L.) cultivar

Ocapy under in vitro conditions. The grown seedlings on MS medium were subjected to MS

medium containing 0, 0.5, 1, 1.5 and 2 ppm concentrations of silver nanoparticles for four

weeks. Application of different concentrations of nanosilver had no significant effect on the total

soluble protein in shoot but had decreased protein content in 1.5 ppm concentration in root. The

study of shoot and root protein patterns using one dimension gel electrophoresis (SDS-PAGE)

and consequence analysis of bands by ImageJ program showed some remarkable changes.

Relative expression of three proteins in shoot and five proteins in root were changed in response

to nanosilver treatment. Silver accumulation was only detected in shoot tissue. There were some

changes in antioxidant enzymes activities. The reduced sugars were increased in 1.5 ppm of

nanosilver comparing with the control plants in shoot. It seems that the nanosilver at 1.5 ppm

concentration is the best treatment of nanosilver as an ethylene action inhibitor under in vitro

condition for B. napus L. cultivar Ocapy in this study.

Keywords: antioxidant enzymes, Brassica napus, nanosilver, protein pattern


Spectroscopy study on interaction of amaranth with bovine serum

albumin (BSA): a thermodynamic approach

3Nafiseh Rezvani, 2, Nahid Rasouli1Nasrin Sohrabi

3697, Tehran, Iran.-Department of Chemistry, Payame Noor University, PO. Box 19395 1, 2

Department of Chemistry, Payame Noor University, Isfahan, Iran. 3

Abstract

In the present study, at first aggregation behavior of a food colorant such as amaranth is

investigated in 5 mM aqueous phosphate buffer of pH 7.0 at 25.0 °C at various concentrations

and ionic strengths using optical absorption spectroscopy. The results suggest that amaranth do

not aggregate in the experimental concentration range. Also, the interaction of amaranth with

bovine serum albumin (BSA) is studied in 5 mM aqueous phosphate buffer of pH 7.0 by optical

absorption, fluorescence spectroscopy and viscosity measurements. The amaranth bind to (BSA

via hydrophobic mode as illustrated by hypochromism in the UV-vis absorption band of

amaranth with addition of BSA and also the decreasing of fluorescence in the presence of

different concentrations of amaranth. The binding constants are determined by analysis of the

optical absorption spectra of the amaranth. The viscosity studies showed no considerable

changes in the viscosity of BSA with the increasing of the concentration of amaranth. The

thermodynamic parameters are also calculated by van't Hoff equation. The results indicate that

the process is entropy-driven and suggest that the main driving forces are hydrophobic

interactions.

Keywords: Amaranth dye, Bovine serum albumin (BSA), UV-vis Spectroscopy, Fluorescence,

Viscosity.


Development a broad-spectrum immunotoxins based on in-silico

ligands assay

Mohammad Rastegar Moghadam Baghestani 1, Aliakbar Haddad-Mashadrizeh2, Javad Baharara 3

1 Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur,

Iran.

2 Cell and Molecular Biotechnology Research Group, Institute of Biotechnology and Department of Biology, Faculty

of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

3 Department of Biology, Mashhad branch, Islamic Azad University.

Abstract

Prostate cancer, after the cardiovascular disease and lung malignancies is the third major cause of

death in the men of society. Therefore, wide strategies for diagnostic and treatment of this

disease such as immunotoxin therapy have been developed. Accordingly, development a series

of broad-spectrum immunotoxins could be valuable for targeting several cancerous tissues and or

metastatic cells, which in turn is required to detecting broad-spectrum antigens. In this regard,

cell surface specific antigens were gathered; in-silico expression assays of them were then

performed by proteinatlas into the breast, cervix, colon, skin, brain, head and neck, liver, lymph

nodes, lung, uterus, ovary, pancreatic, prostate, kidney, gallbladder, stomach, testicular, thyroid,

and urinary tract cancerous tissues. Subsequently, common antigens have been selected, and then

corresponding nucleotide and protein sequences retrieved from related databank. Moreover, 3D

structures of these antigens have been determined. On the other hand, ligands assays performed

via string program and validated by cluspro based on scoring and binding affinity. The results of

this study led to reveal 15 cell surface prostate-specific antigens. Among these antigens, PAGE3

and KDM5D showed the highest expression on the cancerous cell surface of prostate and other

tissues which are surveyed in this study. Interestingly, the expression of these antigens on the

surface of normal cells was negative. Moreover, HPA062248, HPA049086 with high binding

affinity, short in length and limited in post-translational modification candidate as the best

ligands for broad-spectrum immunotoxins development, with 20 targets of cancer cells.

Keywords: Cancer, Prostate, Immunotoxins, Antigen, Ligand.


Structural alterations in hemoglobin by glycation; prevention by

ferulic acid and p-coumaric acid.

Esmat Rahmanifar1 and Mehran Miroliaei2

1Department of Biology, College of Sciences, Institute of Nourdanesh, Isfahan, Iran. 2Cell, Developmental and Molecular Biology Division, Department of Biology, College of Sciences, Isfahan

University, Isfahan, Iran.

Abstract

Protein glycation is a non-enzymatic reaction between reducing sugars and free amino groups of

proteins. This reaction finally produces advanced glycation end-products (AGEs). The

accumulation of AGEs in body leads to structural and functional modifications of tissue proteins.

Since oxidative reactions participate in the process of AGEs formation, so antioxidants may

prevent this event. Therefore, we studied effects of ferulic acid and p-Coumaric acid in human

hemoglobin/fructose system. The formation of AGEs, level of glycation and conformational

alterations were assessed by various spectroscopic techniques including uv-vis, circular

dichroism and fluorescence spectroscopy. Alterations in the secondary structure of hemoglobin

was observed upon glycation, which was mitigated by applying the ferulic acid and p-Coumaric

acid. Accordingly, these compounds may have potential of block the refolding of hemoglobin.

Our results showed that ferulic acid and p-Coumaric acid may have beneficial roles in the

prevention of glycation-associated diseases.

Keywords: Protein glycation, Hemoglobin, Fructose, Antioxidants.


Protein glycation and anti-AGE agents; possible role in treatment of

glycation-associated diseases.

Esmat Rahmanifar1and Mehran Miroliaei2

1Department of Biology, College of Sciences, Institute of Nourdanesh, Isfahan, Iran. 2Cell, Developmental and Molecular Biology Division, Department of Biology, College of Sciences, Isfahan

University, Isfahan, Iran.

Abstract

Protein glycation is a non-enzymatic browning reaction between reducing sugars and free amino

groups of proteins. This reaction finally produces advanced glycation end-products (AGEs). The accumulation of AGEs in body leads to structural and functional modifications of tissue

proteins. There is emerging evidence that protein glycation is implicated in the aging process,

pathogenesis of the complications of diabetes (retinopathy, neuropathy, nephropathy and

atherosclerosis) and Alzheimer’s disease. It has been proposed that discovery of inhibitors of

glycation cascade should offer a promising therapeutic approach for the prevention of diabetic or

other pathogenic complications. There have been many reports on the inhibitory activities of

some phenolic compounds in plant against glycation of proteins. Therefore, we studied

therapeutic potential of curcumin and chlorogenic acid in human hemoglobin/fructose system.

The formation of AGEs, level of glycation and conformational alterations were assessed by

various spectroscopic techniques including uv-vis, circular dichroism and fluorescence

spectroscopy. Alteration in the secondary structure of hemoglobin was observed upon glycation,

which was mitigated by applying the curcumin and chlorogenic acid. Higher amount of α-helix

in the presence of these compounds could be ascribe to their anti-glycation effects. Our results

showed that curcumin and chlorogenic acid may have therapeutic potential in treatment of

glycation-associated diseases.

Keywords: Protein glycation, Hemoglobin, Anti-AGE agents.


A simple bioluminescence method for determination of benserazide

by inhibitory effect on aequorin in biological sample

Hossein Rahmani and Reza H. Sajedi

Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

The increasing development of diagnostic systems in drug monitoring require to design new

approach to create. Aequorin as a bioluminescence protein due to ease of use, non-toxic and high

capability of detecting has long been interest of researchers. Bioluminescence properties of

photoproteins are strongly dependent on conformation and stability of their substrate, namely

coelentrazine, in the binding pocket. Slight change in the binding pocket and microenvironment

of coelentrazine leads to alteration of protein-substrate interactions and strongly influence the

bioluminescence properties. This method has been considered recently to measure the analytes is

the assessment of the inhibitory effect of analyte on phtoprotein. Therefore, it can be used to

detect and measure compounds with structural similarity to coelentrazine. Benserazide (BA) is a

drug used indirectly for clinical treatment of Parkinson’s disease. This analyte can significantly

reduce bioluminescence of aequorin in a concentration-dependent mode. Linear calibration curve

were obtained in a range of about 0.1 to 10 μM with a detection limit down to 10 nM.

Furthermore, we demonstrate the application of the approach in human serum samples, which

suggests its great potential for diagnostic purposes.

Keywords: Aequorin, Benserazide, Biolumencence inhibition assay, Drug monitoring.

https://en.wikipedia.org/wiki/Aequorin


Cognition enhancing and neuromodulatory propensity of

satureiahortensis extract against lysozyme induced cognitive

impairments in rat hippocampus.

Hassan Ramshini1 and Nayyereh Kovsari2

1Biology Department, Payam Noor University, 19395-4697 Tehran, I.R. of Iran.

2Mobinihospital, Sabzevar University of Medical Sciences, Sabzevar, Iran.

Abstract

Alzheimer's disease is the most common form of dementia among the elderly and is

characterized by massive neuronal loss and progressive cognitive impairment. Beta amyloid

hypothesis is the main theoretical research frame work for Alzheimer's disease which states that

extracellular aggregation of beta amyloid results in synaptic loss and cell apoptosis. Although

intensive research was done for its diagnostics and/or treatment, a drug that inhibits amyloid β

aggregation and ameliorates the disorder has not been approved to date. One important approach

in the development of therapeutics is the use of herbal extracts which are rich in aromatic

molecules. At the present study, we induce amyloid aggregation in hen egg white lysozyme

(HEWL), and the therapeutic efficacy of Satureiahortensis extract on amyloid aggregation

inhibition, spatial learning and memory of rats was investigated. 24 male wistar rates (250-280

gr) were divided into 4 groups (n=4): control, received scopolamine, received lysozyme amyloid

aggregates and received lysozyme aggregates formed in presence of Satureiahortensis extract.

The Morris Water maze was used for studying the spatial learning memory. The results showed

that the hippocampal injection of HEWL aggregates damaged the spatial memory rates but

amyloid aggregates formed in presence of Satureiahortensis, there was no significant effect on

spatial memory in rat. These observations suggest that aromatic molecules of Satureiahortensis

extract are capable directly insert into amyloidogenic core of early aggregates and inhibit

amyloid fibril formation. Second, showed the importance of using model proteins as a valid tool

to investigate the pathogenesis of Alzheimer’s disease.

Keywords: Hen egg white lysozyme, Amyloid aggregation, Satureiahortensis extract, Alzheimer,

Spatial memory.

http://www.ncbi.nlm.nih.gov/pubmed/26677075




Protective effect of 1, 3, 5 tri fluoro phenyl benzene against lysozyme

oligomerization and amyloid-mediated cell death in PC12 cells.

Hassan Ramshini and Najmeh Annabestani

Biology Department, Payam Noor University, 19395-4697 Tehran, I.R of Iran.

Abstract

Alzheimer’s disease (AD) is a progressive neurodegenerative brain disorder that affects millions

among the aging population.The progressive production and subsequent accumulation of the

βamyloid peptides (Aβ) in the brain play a central role and thus Methods to prevent Aβ

aggregation have been proposed for treatment of AD. Recent studies have suggested that

interactions between aromatic small molecules may play an important role in amyloid

aggregation inhibition. At the present study, we have evaluated a tri phenyl benzene as a

aromatic small molecule to reduce hen egg white lysozyme (HEWL) aggregation.HEWL was

chosen for induction amyloid aggregation and effect of the compound was assayed via various

techniques including: Thioflavin T (ThT) and Congo red absorption and atomic force

microscopy. Our studies showed that the compound dose-dependently inhibit HEWL lysozyme

aggregation processes. This compound, not only inhibited the formation of aggregated structures

by HEWL but also the cytotoxic activity of HEWL aggregates toward cultured cells. The results

of this study provide further experimental support for the paradigm of amyloid inhibition by

heteroaromatic interaction and point to tri indole derivatives as a simple molecular platform for

the development of novel fibrillization inhibitors.

Keywords: lysozyme, Amyloid aggregation, Drug design.




Structural study of wnt-pathway inhibitors, Mesd and dkk1 on

LRP6, potentials for anti-cancer peptide design

Najme Dehghan–Bonadaki and Majid Taghdir

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.

Abstract

Signaling pathways are the most overriding part of cellular communications and life

development is coupled to increment of these pathways. The significance of their role in

embryonic events and adult tissues homeostasis is exhaustively obvious and in human diseases,

particularly cancers, some of these pathways are aberrantly active. Interestingly, in triple

negative breast cancer (TNBC), a highly aggressive subtype of breast carcinoma, Wnt/β catenin

signaling is aberrantly activated because of overexpression of crucial co-receptor of the

pathway”LRP6”. The pathway is conserved and highly regulated with lots of mechanisms.

DKK1, sFrp and Wif1 are the most structurally known inhibitor of the path. On the other hand,

Mesd, an essential chaperon for proper folding of BP domains of LRP6, is a universal inhibitor

and shows anti-cancer effect. Mesd and DKK1 bind to lrp6 and inhibit the pathway. But the

mechanism of their inhibition is not fully understood. Here, we used a series blind and site-

directed docking and long term molecular dynamic simulation to create some of Mesd and

DKK1 complexes with LRP6 to get a clearer picture about their interaction mode and binding

sites on LRP6. The results show that some binding regions on LRP6 are overlapping and

common for Mesd and DKK1. Additionally, the pattern of interaction and mechanism of action

seems similar from RMSD, RMSF and gyration plots, extracted from MD trajectory. Free Gibbs

energy calculation give meaningful results about mechanism of action of these inhibitors. This

finding is matched to some experimental assays. Interestingly affinity of Mesd to domain 12 of

LRP6 is more than domain 34 and this is vice versa for DKK1. These results proposed new

insight to design of novel anti-cancer proteins or peptides based on Mesd and DKK1.

Keywords: Breast cancer, Anti-cancer, Docking simulation.


Lactopeptides are natural antibiotics can be replace with artificial

antibiotics

Saleeme khajepour and Ali Niazi

Departement of Biotechnology, Shiraz University, Shiraz, Iran.

Abstract Animal milks have good nutritive value, in addition to their antigenotoxic and anticytotoxic

effects. milk also offers several unique health benefits attributed to the presence of high

concentration of insulin/insulin like protein, immunoglobulin, lactoferrin, lactoperoxidase and

peptidoglycan recognition protein. The disease spectrum is broad and includes acute disease,

such as erysipelas, sepsis, pneumonia, and numerous other infections, having a direct association

to a given pathogen, as well as chronic diseases, where microbes often cause a long-standing

inflammatory state. In many respects, we have reached a point for certain infections where no

therapeutic agents are longer available. As a result of these accelerating problems with multidrug

resistance, there is a large current interest in antimicrobial peptides (AMPs). AMPs are key

components of the innate immune system, where they constitute a first line of defense against

invading pathogens. Although AMPs affect bacteria in many different ways, including inhibition

of cell wall, DNA, RNA, and protein synthesis, and inhibition of enzymatic activity, the main

mode of action of AMPs is the disruption of bacterial membranes. Some of the important milks

AMPs are lactoferrin, lactoferampin, lactoferricin,… each of them besides work as antibiotics do

some other important reaction in different situations and we can replace them with these

dangerous and artificial antibiotics, todays are common.

Keywords: Lactopeptide, Antimicrobial peptides, Antibiotics.


Investigation of the antifouling and protein adsorption properties of

polyethersulfonemembranes by titaniadioxide nanoparticles coating

Mahsa Khalili1, Parisa Moazzam2, Amir Razmjou1, Rasoul Shafiei3

1Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, P.O. Box

73441-81746, Isfahan Iran.

2Department of Nanotechnology, Faculty of Advanced Science and Technology, University of Isfahan, Isfahan, Iran.

3Department of Biology, Faculty of Sciences, University of Isfahan, Iran.

Abstract

Although polymeric membrane has superior properties, its applications in biomedical and

industrial fields are very limited. Biofouling is a major concern in membrane which is created

from particular interactions between membrane and untreated water content. Here, for the first

time we showed that a carful superhydrophilic modification of polyethersulfone (PES)

membrane can address those drawbacks which have hindered their utility. Development of

nanocomposite membrane is a suitable strategy to reduce protein adsorption and biofouling

formation. The PES membrane surfaces were characterized by SEM, EDAX, AFM, contact

angel (CA) goniometry, surface free energy (SFE) measurement, Bradford and microtiter plate

assays and also flow cytometry analyses. Results showed that CA and SFE changed

from57°and30° to 0°in 25 seconds and 43 to 44mN/m, respectively. The stable and durable

modification led to a substantial reduction in static BSA protein absorption. The effect of such a

treatment on the biofilm formation was analyzed by using two different bacteria. The microtiter

plate assay and flow cytometry analysis showed that the superhydrophilic modification could

substantially reduce the bacterial adhesion and then biofouling formation. Hence, combination of

chemical and mechanical modification due to a significant effect on surface pore size, bacterial

attachment and protein adsorption resistance as well as hydrophilicity.

Keywords: Polymeric membrane, Polyethersulfone, Biofouling, Biofilm formation.


Interaction of human serum albumin with the resveratrol in the

presence of nanoparticles and EMF (up to 1 MHz)

Nooshin Khaghani1

, Azar Fani2, Jamshidkhan Chamani1

1 Department of Biochemistry and Biophysics, Mashhad Branch, Islamic Azad University, Mashhad, Iran.

2 Assistant Professor of Radiation Oncology, Cancer Research Center Mashhad University of Medical Sciences,

Mashhad, Iran.

Abstract

Human serum albumin (HSA) as a kind of main carrier protein is the most abundant in human

blood plasma and provide about 80% of osmotic compression of blood. HSA has a high affinity

to an extraordinarily divers range of materials such as drugs, fatty acids. Metabolites and metal

ions, so it is transporter for the materials. Resveratrol (RES) is a dietary polyphenolic, non-

flavonoid antioxidant derived from grapes, peanuts, barriers, and other plant sources. Resveratrol

has various health benefits, such as cardiovascular and cancer prevetive properties, and it induces

apoptosis by up- regulating pro-apoptotic genes while simultaneously down- regulating anti-

apoptotic genes. Possibility that RF (Radio Frequency) radiation may cause changes in protein

conformation and hence in biological properties has been revealed. In our work, the binding of

resveratrol to plasma protein, human serum albumin (HSA) in the presence of EMF and

nanoparticles, have been investigated systematically by fluorescence quenching technique, UV-

Vis absorption spectroscopy, circular dichroism (CD) spectroscopy and FRET. The fluorescence

data showed that the binding of resveratrol to HSA is a static quenching procedure. The CD

spectroscopy indicates that the secondary structures of the protein is changed in the presence of

resveratrol with nanoparticles and EMF. The result of fluorescence spectra UV-Vis absorption

spectra and FT-IR spectra showed that the conformation of human serum albumin has been

changed in the presence of resveratrol and EMF. The Stern-Volmer curve of the fluorescence

quenching of HSA by resveratrol indicated that the quenching mechanism between resveratrol

and HSA was mainly static quenching.

Keywords: Human serum albumin, Resveratrol, Electro magnetic field, FTIR, UV-Vis, Circular

dichroism.


Interaction between silver nanoparticles and human serum albumin

revealed by fluorescence spectroscopy in the presence of resveratrol

Nooshin Khaghani1, Azar Fani2

, Jamshidkhan Chamani1

1 Department of Biochemistry and Biophysics, Mashhad Branch, Islamic Azad University, Mashhad, Iran.

2 Assistant Professor of Radiation Oncology, Cancer Research Center Mashhad University of Medical Sciences,

Mashhad Iran.

Abstract

The interaction between silver nanoparticles (SNPs) with three different sizes and human serum

albumin (HSA) was studied by fluorescence spectroscopy in this work. Human serum albumin

(HSA) is a principal carrier protein in serum known to bind an extensive variety of endogenous

compounds with dissociation binding constants (KD) in the range of 10-3 to 10-8 mol 1-1.

Resveratrol (3, 5, 4-trihydroxystilbene) is a natural polyphenolic compound produced in plants

(e.g., grapes, mulberries, peanuts) in response to damage and fungal attack. Resveratrol exists as

trans and cis isomers. Most of its biological activities are attributed to the trans isomer.

Nanoparticles are used in a large variety of scientific and industrial applications and their

chemical behavior has begun to be well studied on the nanoscale. The interaction between

nanoparticles and human serum albumin was investigated at physiological pH in an aqueous

solution using fluorescence spectroscopy. The analysis of fluorescence spectrum and

fluorescence intensity indicates that SNPs have a strong ability to quench the intrinsic

fluorescence of HSA by static quenching mechanisms. Resonance light scattering (RLS) spectra

showed the formation of a complex between HSA and SNP in presence of resveratrol. The

analysis results suggested that the electrostatic interactions played key roles in the reaction

process. The CD spectra proved secondary structure alteration of HSA in the presence of

resveratrol.

Keywords: Silver nanoparticles, HSA, Resveratrol, Fluorescence spectroscopy.


Comparison of phytase production in submerged and solid state

fermentation of a strain of Aspergillus niger and investigation of 3

various solid media containing wheat bran as the basic substrate

Atefeh Hamzeh1 Jamshid Fooladi 1, Fakhri Sadat Hosseini 2

1 Laboratory of Industrial Microbiology, Faculty of Biology, Alzahra University, Tehran, Iran.

2 Faculty of Biology, Alzahra University, Tehran, Iran.

Abstract

Phytases are enzymes that catalyze hydrolysis of inorganic phosphate from phytic acid. Simple

stomached animal have any or little amount of this enzyme. So phosphate will be added to their

feed dietary; but additional phosphate and undigested phytate will excrete to environment and

lead to phosphate pollution and eutrophication. Therefore using phytase in simple stomached

dietary can improve their growth and reduce environmental pollution (Broz et al.1994; Cromwll

et al.1995). Solid state fermentation can use agricultural wastes as substrate; hence enzyme

production with this method is more cost–effective. In this study, solid state fermentation of

Aspergillus niger for phytase production was carried out with 3 different media in 250 ml

Erlenmeyer flasks: 1-wheat bran + glucose +dextrin (Bhavsar et al.2010) 2-wheat bran, 3-wheat

bran + malt extract 1 %. Flasks were incubated in 30 OC for 96 hours. Enzyme assay was carried

out with Phosphomolybdenum blue method (Engelen et al. 1994). Furthermore we compared

enzyme production of submerged and solid state fermentation. Among different solid media, the

maximum and minimum enzyme activity was observed in the second and the first media

respectively. In the first media, glucose has inhibitory effect on phytase production, because of

its influence on gene level. Batal and Karem reported similar results in 2002. It seems that due to

the presence of malt extract in the third media, phytate concentration increases and eliminates

phytase production. But obviously the solid state fermentation had higher enzyme activity than

submerged fermentation.

Keywords: Phytase, Aspergillus niger, Solid state fermentation, Wheat bran.


Hydrolysis of collagen-containing wastes as a renewable nitrogen

source

2, Mohammadhadi Jazini1Mojtaba Hasiri

Iran. Department of Chemical Engineering, Isfahan University of Technology, Isfahan,1

Department of Chemical Engineering, Isfahan University of Technology, Isfahan, Iran.2

Abstract

According to the rapid population growth in recent years, the demand for livestock meat

consumption increased.Massive production of meat has been resulted in huge amount of animal

tissue wastes. These wastes cannot be disposed in the environment because of extremely bad

smell and high organic carbon content. Hence, they must be somehow treated to be ready to

release to the environment. Tissues from intestine of cows are one of the main solid wastes

produced by slaughterhouses. This tissue consists of different kinds of proteins, lipids and

carbohydrates which are arranged in a multi-layer structure. One of the layers is used as natural

skid in sausage industry. The others are wasted. This kind of waste consists of protein, mainly

collagen. Hydrolysis of this protein could provide a renewable source of nitrogen. This organic

nitrogen source could be used in microbiology for formulation of media. Besides, it can be used

in the production of chelated minerals in animal nutrition. The hydrolysis of collagen is difficult

because of its recalcitrant structure. Hence, in this study different methods for hydrolysisof

collagen were presented and theiradvantages and disadvantages were discussed. These methods

include acidic, basic, thermal, microbial and enzymatic hydrolysis. The hydrolysis methods then

were compared in terms of their potential to be implemented in relevant industries.

Keywords: Hydrolysis, Protein, Collagen, Animal tissue, Collagen-containing waste.


In silico evaluation of binding affinity of zanamivir, peramivir, and

laninamivir octanoate drugs compared with oseltamivir to the

neuraminidase in influenza A (H1N1)

Seyed Ali Hosseinian1 and Seyedeh Samira Hosseinzadeh2

1Department of Biology, Science and Research Branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran.

2Department of biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

The 2009 pandemic swine origin influenza A H1N1 virus (pH1N1) has reminded the world of

the threat of pandemic influenza, and resulted in 140 confirmed deaths in Iranian population in

this year. The influenza neuraminidase (NA) enzyme is the most successful drug target against

the seasonal and pandemic flu. Treatment of influenza with the neuraminidase inhibitors (NAIs)

oseltamivir phosphate (Tamiflu®), zanamivir (Relenza®), laninamivir octanoate (Inavir®), and

peramivir (Rapiacta®) has become common among Japanese primary care providers. In this

study, first the structures of receptor and ligands from PDB were received. The neuraminidase

(NA) selection and determination of ligand binding site through Discovery Studio3.0 Client,

docking and data analyzing by AutoDock Tools 4.2.6 (AutoDock Vina), the study of

conformations and bindings through Pymol and the comparison and valuation of the data using

SPSS, were accomplished. The data from the calculations in 27 conformations for each of

ligands in 3 repeat, for following values: binding energy, RMSD, hydrogen bonds, and VDW

and electrostatic interactions; demonstrates more binding affinity of Zanamivir, Peramivir, and

Laninamivir Octanoate drugs, respectively, compared with Oseltamivir. Due to the increasing

resistance to Oseltamivir in influenza A (H1N1) virus and considering the results of the

calculation of the interaction of receptor-ligand, it seems that these novel neuraminidase

inhibitors, especially Zanamivir, can be good alternatives to Oseltamivir in the treatment of

influenza A (H1N1).

Keywords: H1N1, Novel NAIs, Oseltamivir, AutoDock Vina.

https://en.wikipedia.org/wiki/Neuraminidase_inhibitor


The simulation and evaluation of fever temperature effects on the

active site of neuraminidase protein receptor in influenza A (H1N1)

virus in the in silico

Mohammad Fatehi Abdolabadi, Vahid Mirzabayati, Seyed Ali Hosseinian

Department of Biology, Science and Research Branch, Islamic Azad University, Neyshabur, Khorasan Razavi, Iran.

Abstract

Influenza is an important cause of morbidity and mortality. The treatment of influenza with

neuraminidase (NA) inhibitors has been very common. Fever is listed as a predominant symptom

for influenza on the centers for disease control and prevention (CDC) website. First, the

structure of chain A of protein NA with ID: 3ti6 was received from PDB. Then the identification

of the active site amino acids (AAs) including: ARG118, GLU119, ASP151, ARG152, ARG292,

and ARG371 was accomplished through DiscoveryStudio3.0Client. The simulation of protein

modes were performed using GROMACS5.07, containing gromos96 43a1 force field. That was

done for two different modes: 1- Normal body temperature, 37°C (310°K), in 1000ps of time,

and 2- Fever temperature, 39°C (312°K), in 1000ps of time. The mentioned data was fed in

NVT→NPT→MD simulation steps, respectively. The alignment and analysis of protein modes

was done by Pymol.

The analyzed results in pymol showed: 1- the change of the direction of AAs conformations of

ARG118, ARG152, ARG292, and ARG371 moving toward the inside of the active site and 2-

the deletion of intra-AAs hydrogen bonds of ARG118, GLU119, ASP151, and ARG152. Our

results suggest that in fever temperature, the AAs conformation of active site causes the decrease

of protein's cave space, so it is expected that it results in the decrease of drug's penetration into

the active site. Due to the deletion of hydrogen bonds in this temperature and regarding the little

simulation time it is expected that the protein conformation cannot be stable in the active site. As

a general conclusion, this study can explain that fever temperature may result in the destruction

of the structure and the function of virus NA protein.

Keywords: H1N1, Fever, Neuraminidase, Binding site,

GROMACS5.07.


Investigation of binding interactions of apigenin and morin hydrate

with beta-lactoglobulin

MohammadiFakhrosadat andMasoomeh Hoseini


Abstract

β -Lactoglobulin is the major whey protein of cow and sheeps milk, and is also present in many

other mammalian species; a notable exception being humans. This protein can bind many

hydrophobic molecules, suggesting a role in their transport. β -Lactoglobulin is a small protein,

soluble in dilute salt solution as befits a globulin, with 162 amino acid residues. In this study, we

investigated the binding interactions of apigenin and morin hydrate with the milk protein β-

Lactoglobulin. Apigenin (4′, 5, 7-trihydroxyflavone), found in many plants, is a natural product

belonging to the flavone class that is the aglycone of several naturally occurring glycosides. It is

a yellow crystalline solid that has been used to dye wool. Morin Hydrate (3, 5, 7, 2′, 4′-

pentahydroxyflavone) is a yellow chemical compound that can be isolated from osage orange,

old fustic and from leaves of common guava. In a preclinical in vitro study. In this study,

spectroscopic techniques such as UV–Vis absorption, steady-state fluorescence and synchronous

fluorescence have been used. The fluorescence titration experiments showed that these two

compounds have quenching effect on the fluorescence intensity of β-Lactoglobulin. The binding

parameters including number of binding sites and binding constant have been calculated based

on the fluorescence quenching data. The short Förster's distance between donor (BLG) and

acceptor (Apigenin and Morin Hydrate) and also the binding constant values demonstrated the

strong interaction between these two flavonoids and BLG. The synchronous fluorescence results

indicated that binding of these two compounds may not cause considerable alterations in the

conformation of β-Lactoglobulin.

Keywords: β-Lactoglobulin, Apigenin, Morin hydrate, Fluorescence quenching, Synchronous

fluorescence.


Exploring the thermal stability and activity of proteinase K in the

presence of spermidin by biophysical techniques and molecular

dynamic simulations

Mansoore Hosseini Koupaei1, Behzad Shareg 2 , Ali Akbar Saboury2,3, Aboulfazl Semnani4 , Fateme

Davar5 , Fateme Reisi1

1Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box.115, Iran.


3 Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.

4 Department of Chemistry, Faculty of Science, University of Shahrekord, Shahrekord, Iran.

5 Department of Chemistry, Isfahan University of Technology, Isfahan, Iran.

Abstract

Polyamines such as spermidine are ubiquitous to all living organisms, can have interactions with proteins.

The aim of the present study was to investigate how spermidine could influence the thermal stability and

activity of proteinase K as a model enzyme. Here UV Visible spectroscopy, fluorescence spectroscopy

and molecular dynamic (MD) simulation techniques have been employed to understand the stability and

activity changes of proteinase K. The thermal stability results showed that by increasing the

concentrations of polyamine, the thermal stability of enzyme increased. We report that polyamine

enhance the enzyme activity of proteinase K using para nitrophenyl acetate (pNA) as a synthetic substrate

of proteinase K in 50 mM Tris-HCl with pH8. The intrinsic fluorescence of proteinase K was decreased in

the presence of polyamine due to excited- state proton transfer. Molecular docking also indicated that the

hydrogen bonds and hydrophobic interactions dominated in the binding site of polyamine on proteinase

K.

Keywords: Poly amine, Activity, Molecular dynamic, Proteinase K


Investigation of the effect of spermine on the interaction between

ADA and its substrate using computational methods

Seyedeh zohreh Hosseini1, Marzieh Dehghan-Shasaltaneh2, Seyedeh Zahra Moosavi-Nejad1

1Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.

2Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran, Iran.

Abstract

Adenosine deaminase (ADA) is an aminohydrolase which shares in the purine metabolism. It

degrades either adenosine or 2’-deoxyadenosine producing inosine or 2’-deoxyinosine,

respectively. ADA plays important roles in proliferation, maturation, function and development

of the immune system. Its activity may be changed by variety of components including synthetic

or natural products. Spermine is a natural metabolite and a member of polyamines family which

exists in all cells and tissues. This compound affects the cell proliferation and enzyme regulation.

To regulate the function and stabilize its structure, it interacts with negative charge of the

macromolecules such as DNA, proteins and enzymes. In this study, the effect of spermine on the

interaction between ADA and its substrate has been investigated using docking studies. So first

of all, adenosine as a substrate was docked with adenosine deaminase. Then, the enzyme was

docked with adenosine in the presence and absence of spermine. All processes were performed

using autodock vina. Ligplot and VMD were used to evaluate hydrogen and vdw bonds between

all components. The results showed adding spermine to enzyme leads to occur three hydrogen

and 27 vdw bonds, while adenosine did not perform any hydrogen bonds with ADA. We can

conclude polyamine makes to stabilize enzyme structure and it held positive effect on the

interaction between substrate and enzyme, because polyamine and substrate were interacted to

the different sites of adenosine deaminase. As a consequence, effector role of spermine plays an

important role in the interaction between substrate and enzyme.

Keywords: Adenosine deaminase, Spermine, Vina, Hydrogen bond.


Study of laccase activity of Bacillus spores by zymogeraphy

Afrouzossadat Hosseini-Abari, Giti Emtiazi, Maryam Fanaei

Department of Biology, University of Isfahan, Isfahan, Iran.

Abstract

Bacillus spores are resistance to lethal extreme conditions so they are suitable particles for use in

industry and elimination of hazardous material from environment. They have several enzymatic

activities that the most of them are because of the crystalline CotA protein. Since spores help

bacteria to survive at high temperatures or extreme pH values, spore-associated enzymes might

also resist in such conditions which it would be advantageous for industrial applications. In the

present study, laccase activity in the spores of new marine bacillus isolated from Persian Gulf

was confirmed by SDS-PAGE and Native- PAGE. Native-PAGE analysis was performed by

using a 10% gradient gel (Bio-Rad) under nondenaturing conditions )i.e., SDS and 2-

mercaptoethanol were omitted in the sample buffer and the samples were not boiled). The

Native- PAGE gels containing the same samples were stained with catechol as a substrate. The

catechol staining was performed by incubating the gel in a solution containing 75mM catechol in

pH 5 at 40˚C. Zymogram analysis and comparison of Native-PAGE and SDS-PAGE indicated

that the molecular weight of the spore coat laccase is 65 KDa. By using this novel zymogram

staining technique, it was possible to identify and distinguish laccase from other proteins.

Keywords: Laccase, Bacillus spores, Zymogeraphy.


Study of expression and activation of engineered coagulation factor

IX with propeptid of protrombin

Motahareh Hassankhani1, Jafar Vatandoost2, Ali Akbar Jannatabadi3

1 Msc student, Deparment of biotechnology Azad University, Sabzevar, Iran.

2 Assistant professor, Department of Biology. Hakim Sabzevari University, Sabzevar Iran.

3 Assistant professor, Deparment of biotechnology, Azad University, Sabzevar Iran.

Abstract:

Factor IX and other vitamin K-dependent blood coagulation factors require gamma

carboxylation of Gla domin for its biological function that catalyzed by gamma carboxylase

enzyme. Propeptide of vitamin K-dependent proteins is first recognition site of gamma

carboxylase and a reduced affinity allowing greater substrate turnover and result in high gamma

carboxylation. Since the gamma carboxylase enzyme has least affinity for prothrombin, it was

hypothesized that exchanging the propeptide of factor IX with prothrombin would enhance

gamma carboxylation. A chimeric cDNA consisting of the human prothrombin pre-propeptide

followed by mature human factor IX was generated and transfected into S2 cells. The expression

and activity of the normal and chimeric recombinant factor IX were investigated by ELISA and

APTT after various times of transfection. The results showed that the concentrations and activity

of factor IX and so gamma carboxylation in chimeric factor IX more than normal factor IX.

Keywords: Coagulation factor IX, Gamma carboxylase, Propeptid, Prothrombin.


Identification of biologically active recombinant human

erythropoietin (rHuEPO) glycoforms

Somaye Chayani1, Hooman Kaghzian2, Mansure Ghezlue3, Farzad Mokhtari4

1Department of Biotechnology, Faculty of Advanced sciences & Technology, Pharmacutical Siences Branch,

Islamic Azad University, Tehran-Iran (IAUPS). 2Research and Production Complex of Pasteur Institute of Iran. 3Group of biophysics, faculties of science, Science and Research Branch of Islamic Azad University. 4Tehran university institute for biochemistry and biophysics research, Tehran, Iran.

Abstract

The human Erythropoietin (EPO) is a glycoprotein growth factor (30 kD) which originally

secreted from kidney due to hypoxia conditions. EPO has an important role on red blood cells

population and had a positive effect on erythropoiesis. Nowadays recombinant EPO (rHuEPO)

considered as therapeutic biological drugs for severe anemia. Oligosaccharide moiety of rHuEPO

made more than 40 percent of its molecular mass. rHuEPO could be glycosylated at three N-

linked glycosylation sites (asparagine 24, 38 or 83) and one C-linked site (serine 126). Many

evidences has been elucidated the role of glycosylation containing sialic acid at the end of

antennaon rHuEPO biological activity. Therefore, specific isoforms with determined sialic acid

selected as a proper drug with high biopotency. In this study, we identified the glycosylated

isoform of rHuEPO with most biological activity. rHuEPO provided from Pasteur institute of

Iran. The rHuEPO had been expressed in CHO cell line and purified by various chromatography

techniques. The erythropoiesis assay in rabbit showed the biological activity of samples. Due to,

capillary zone electrophoresis (CZE), we identified that only one percent increasing in

concentration of 13 sialylated glycan branch forms could promote rHuEPO biological activity

more than two-fold. In conclusion we can propose that any modification in production process

which causes increasing in 13 sialylated glycan-branchwould have favorable responses to

rHuEPO biological activity.

Keyword: Erythropoietin, Glycoforms, Biologically active molecue.


Thermodynamic stability of β-lactoglobulin in the presence of

cetylpyridinumbromide: UV-Vis spectroscopy andmdocking studies

and Mehdi Sahihi Zahra ChavoshpourNatanzi

Department of chemistry, University of Isfahan, Isfahan 81746-73441, Iran.

Abstract

In this work, the stability of β-lactoglobulin (BLG), variant A in the presence of cationic

surfactant cetylpyridinum bromide (CPB) in a temperature range from 298-338 K was studied

using UV-Vis spectroscopy. The results of UV-Vis show that denaturation process of BLG at

difference concentrations of CPB is cooperative. All of denaturation curves, assumes a linear

concentration dependence of the pre-and-post transition base lines and gave the most realistic

values for ∆GD (H2O). The results show that the minimum value of ∆GD (H2O) occurs at 328 K

(16.740 kJ.mol-1). Also, cooperative structure changes of protein due to its interaction with

surfactant was confirmed by fluorescence spectroscopy. Thermodynamic analysis by Gibbs-

Helmholtz equation found ∆HD (H2O) and ∆SD (H2O) were 86.025 kJ.mol-1 and 212.24 J.mol-1. k-

1,respectively. Molecular docking results suggest that, CPB binds on the surface of BLG with the

binding energy of -5.52 kcal.mol-1. Analysis of the molecular docking results represents that

Tyr(102) interacts with CPB by one hydrogen bond interaction.

Keywords:β-lactoglobulin, Cetylpyridinum bromide,Denaturation, UV-Vis spectroscopy,

Molecular docking.


Investigating Interaction of DNA and protein immobilized gold

nano particles with nitrocellulose membranes

Atefeh Javani and Fatemeh Javadi-Zarnaghi


Abstract

In recent years the use of nanoparticles, particularly gold nanoparticles by having the

physicochemical properties has improved for diagnostic and therapeutic applications. Among

these are noted the use of nanoparticles functionalized with proteins and nucleic acids. The

conjugates based on their applications, are fixed on different membrane. One of the surfaces is

nitrocellulose membranes, the binding biomolecules such as nucleic acids or proteins on

nitrocellulose membranes is of particular importance, since the nitrocellulose membranes are

hydrophobic property, thereby to improve the interaction of biomolecule-nanoparticle with

nitrocellulose membranes must be optimized with a variety of test conditions. Including

conditions that must be examined include: the conditions of buffer and its pH, temperature,

concentration of biomolecule-nanoparticle to attach to the substrate, the humidity, the time

required for better connectivity and more. In this study we try to do multiple tests to optimize

conditions for better connection biomolecule-nanoparticle access.

Keyword: Nanoparticles functionalized with biomolecules (DNA-Protein), Nitrocellulose

membrane, Interaction.


Prediction 3D structure of IGFBP3 using homology modeling and

molecular dynamic

3, Karim Mahnam2, Mohammad reza Mofid 1iElham Jafar

1 Department of Medicinal Chemistry and Bioinformatics Research Center, School of Pharmacy and Pharmaceutical

Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.

2 Department of Clinical Biochemistry and Bioinformatics Research Center, School of Pharmacy and

Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Iran

3 Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, I.R. Iran.

Abstract

Three helix bundle small polypeptide hormone, Insulin growth factor (IGF1) is one of key

regulator in cell proliferation, differentiation and death. In normal and neoplastic cells, growth

and differentiation effects of IGF1 are performed through interaction with the insulin-like growth

factor 1 receptor (IGF1R). Around 99% of IGF1 bound to IGF binding proteins (IGFBPs), with

most bound to IGF binding protein 3 (IGFBP3). IGFBP3 regulate its availability for receptor and

increase the half-lives of circulating of IGF1. IGFBPs families are six soluble proteins with 219–

292 residues. IGFBP3 (291 aa) applied therapeutically in a complex with IGF1 as iPlex. IGFBP3

plays a role in cancer reduction, by both IGF1 dependent and independent mechanisms.

According to multifaceted role of IGFBP3 in body, as well as, the lack of 3D-Structure of this

protein, structure of this protein was predicted using of homology modeling (modeler, phyre 2

and Gromaxs softwares) in this study. IGFBP3 considered 3 domains (N-terminal with high

affinity to IGF1, linker-domain with protease, glycosylation, phosphorylation site and C-terminal

domain with thyroglobulin motive has affinity to acid labile subunit (ALS). Protein-Protein-

Interaction of key residue of the best designed model with IGF1 was performed by haddock

software. Results showed that final obtained 3D model of phyre 2 was satisfactory after MD.

HADDOCK clustered 159 structures in 15 clusters. Obtained results of haddock revealed that

helix 1 of IGF1 including; GLu3 and (Gly7–Cys18 residues) are important region for binding to

Ser 121 and (38-44 residues) of N-domain of designed IGFBP3.

Keywords: Homology modeling, Molecular dynamics, IGFBP3, Protein-protein-interaction.


An investigation on the interaction of antibacterial peptides "aurein

1.2" with the bacterial membrane using molecular dynamics

simulation

Marziye Jazini and Sarah Mohammadi nejad

Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.

Abstract

Short cationic antimicrobial peptides (AMPs) are produced by almost all living organisms in a

defense strategy against invading pathogens. These peptides stop bacteria activity by disturbing

their membrane and rapidly kill pathogens. Aurein 1.2 is a short peptide (13 residues) shows a

broad spectrum of antibacterial activity. In this study, some of the structural and functional

properties of Aurein 1.2 in solution as well as in interaction with membrane are studied using

molecular dynamics simulations. For modeling membrane of bacteria, lipid compositions of

POPE/POPG (3:1 ratio) have been used. Our results show that, Aurein 1.2 tends to penetrate into

the membrane in an inclined orientation and by their C-terminal face to the membrane.

Calculating the distance between the center of mass of peptide with the center of mass of the

membrane and the distance between both peptide terminals with membrane center of mass

confirms these results. Also the number of water molecules penetrated into the membrane show

that Aureins 1.2 penetrates easier into the membrane of bacteria than a single Aurein 1.2. The

thinning of the membrane is examined because of penetration of peptides and pore formation. It

is observed that phosphates also penetrate to the membrane besides peptide. In the other hand,

hydrophilic side of Aurein faces to the inside of membrane. These observations lead to the

conclusion that toroidal pore mechanism can for the action of this peptide.

Keywords: Aurein1.2, Atomic-scale molecular dynamics, Antibacterial activity mechanism,

Bacterial membrane.


Luciferase mutation at K329 position by SDM for proteolytic

stability

Samane Jarchi, Roghaye Hamidi, Farangis Ataei, Saman Hosseinkhani

Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.

Abstract

Firefly luciferase from Photinus pyralis is a single polypeptide chain (62 kDa), responsible for

emission of yellow-green light; known to be most efficient bioluminescence system that make it

an excellent tool for reporter in nano-system biology and medicine. However, it is very sensitive

to proteolytic degradation, which reduces its intracellular half-life, leads to loss in sensitivity and

precision in analytic applications. In order to generate more stable luciferase against protease

digestion, we substituted a tryptic site, Lysine 329, with other amino acid, Isoleucine; K329I. The

aim if this study is the expression and purification of this mutant and comparison of its stability

against trypsin serine protease digestion with wild type luciferase. The quik-change site-directed

mutagenesis method is performed. After confirmed by sequencing, this mutant enzyme, K329I,

under different conditions such as temperature, time and concentration of lactose was

successfully expressed and then by Ni-NTA sepharose column chromatography purified.

Proteolysis conditions of this mutant and native enzymes are being investigated.

Keywords: Luciferase, Mutation, K329 I, Proteolysis, Trypsin.

Rashid

Highlight


Determination of 3-D structure of human HMGB4 protein using

MODELLER software

Safa Lotfi and Mojtaba Mortazavi

Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate

University of Advanced Technology, Kerman, Iran.

Abstract

HMGB proteins are the most abundant group of non-histone HMG proteins. This family consists

of four members including HMGB1, HMGB2, HMGB3 and recently discovered HMGB4.

HMGB1-3 proteins are transcriptional activators which possess two DNA-binding domains

named HMG-box A and B respectively. In contrast to the other members of HMGB family,

HMGB4 functions as a potent transcriptional repressor. This protein is strongly and

preferentially expressed in the testis. HMGB proteins are known to reinforce the cytotoxic

properties of platinum-based anticancer drugs like cisplatin. It seems the hypersensitivity of

testicular germ cell tumors to cisplatin stems from high expression of HMGB4 in these cells. To

date, the 3-D structure of HMGB4 protein was not determined in any mammalian species. In this

study, 3-D structure of human HMGB4 was determined using MODELLER software (version

9.15). Prediction of 3-D structure of proteins by MODELLER software consists of several steps

including finding the PDB structures related to the target protein, selecting the best template,

aligning target and template sequences, building and evaluating the models. 2yrq which is

corresponding to human HMGB1 PDB structure was selected as a template for HMGB4

modelling. In overall, five models were built by MODELLER software and the best model was

selected according to DOPE score. The results demonstrate although HMGB4 like HMGB1 has

two HMG-box domains for DNA-binding, the overall structure of two proteins shows distinct

differences. The results obtained from the project will be helpful to understand the structure-

function relationship of the protein and to design new anticancer drugs.

Keywords: HMGB proteins, HMGB4, HMG-box domain, MODELLER software, Protein 3-D

structure.


Antiadhesive activity of a biosurfactant isolated by Lactobacillus

acidophilus onSerratiamarcescens strains

Maliheh Shokouhfard1, Rouha Kasra-Kermanshahi1, Mohammad Mehdi Feizabadi2,

ShahramTeimourian3

1 Department of Microbiology, Faculty of Biological sciences, Alzahra University, Tehran, Iran.

2 Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.

3 Department of Medical Genetics, Iran University of Medical Sciences, Tehran, Iran.

Abstract

Serratiamarcescens usually cause secondary infections like urinary, respiratory, wound, septic

arthritis. The ability to adhere to medical devices and host epithelial surfaces to form biofilm is

an important feature in the pathogenesis of S. marcescens. Lactobacillus acidophilus ATCC

4356, was selected as a probiotic strain to produce biosurfactant. The SDS-PAGE methodand

FTIR assay was used for the determination of biosurfactant. Antiadhesive activities was

determined by pre-coating and co- incubating methods. The FTIR analysis and SDS-PAGE of

derived biosurfactant revealed one band with approximate size of 10 kDa. Due to the release of

such biosurfactants, L. acidophilus was able to interfere with the adhesion and biofilm formation

of the Serratiamarcescens strains. This biosurfactant in 2.5 mg/ml concentration showed

antiadhesive activity against of S. marcescensstrains. Our results showed that this biosurfactant

can be used as a preventive strategy to interrupt the onset of pathogenic biofilm growth on

catheters and other medical insertional materials.

Keywords: Serratiamarcescens, Biofilm formation, Biosurfactant, SDS-PAGE.

http://link.springer.com/article/10.1007/s00253-009-1987-7

http://link.springer.com/article/10.1007/s00253-009-1987-7


Fermentative production of lysine by Corynebacterium glutamicum

from different nitrogen sources

Hanieh Ebrahimi1, Jamshid Fooladi1, Majid Mamhad Heravi2


2 Faculty of Science, Department of Chemistry, Alzahra University, Tehran, Iran.

Abstract

Amino acids are the basic building blocks of proteins. Among the 20 Proteinogenic L-amino

acids, L-lysine has been recognized as one of the most deficient essential amino acids which are

nutritionally necessary for humans and animals. It has also got various pharmaceutical

applications in the formulation of diets with balanced amino acids concentration and in amino

acids infusions. In this research, production of lysine by Corynebacterium glutamicum (ATCC

13032) from different nitrogen sources including: ammonium nitrate, ammonium sulphate,

ammonium chloride, ammonium dihydrogen phosphate and urea on lysine accumulation were

investigated. For this purpose, beet molasses was selected as a constant carbon source. The

production of L-lysine was examined qualitatively using Thin Layer Chromatography (TLC).

The results of fermentation experiments showed that ammonium sulphate was the best nitrogen

source for lysine production and for other substrates the yield of lysine was lower.

Keywords: Lysine, Fermentation, Corynebacterium glutamicum, TLC, Ammonium sulphate.


Optimization of different carbon sources for production of L-lysine

by Corynebacterium glutamicum

Hanieh Ebrahimi1, Jamshid Fooladi1, Majid Mamhad Heravi2


2 Faculty of Science, Department of Chemistry, Alzahra University, Tehran, Iran.

Abstract

Amino acids are the basic bioelements of proteins. Out of the 20 standard L-amino acids, L-

lysine is one of the 9 amino acids which are essential for human and animal nutrition. L-lysine is

useful as medicalment, chemical agent, food material and feed additive. In this research,

Corynebacterium glutamicum (ATCC13032) were used as a biocatalyst of lysine production.

The effect of different carbon sources including: glucose, sucrose, beet molasses, malt extract

and whey on lysine production were investigated.For this purpose, ammonium sulphate was

selected as a constant nitrogen source. The production of L-lysin was examined qualitatively

using Thin Layer Chromatography (TLC). The results of fermentation experiments showed that

beet molasses and malt extract have the maximum yield of lysine production while other carbon

sources consist of lower yield of lysine.

Keywords: Lysine, Fermentation, Corynebacterium glutamicum, TLC.


In silico comparison of structural features of envelope protein of

zika virus with the homologous proteins of two close viruses

Samira Ebrahimi and Hassan Mohabatkar


Abstract

This days, world has been facing valid separation of Zika virus outside its geographical zone.

Investigations prove a relationship between Zika virus and microcephaly in newborn babies.

Working on important proteins of this virus could be useful for struggling against this virus. In

the present investigation, computational study of envelope protein of Zika virus (ZIKV) was

performed and the results were compared with envelope protein of two close related viruses,

Dengue virus (DENV), and Spondweni virus (SPOV). In the present study important structural

properties of envelope protein of Zika virus were predicted. Prediction was performed by means

of bioinformatics tools such as T-COFFEE, PseAAC, Virus-PLoc, Signal-3L, GOR IV,

MemBrain, DiANNA, BCPREDS, MHCPred, and GlycoEP. Similarities and differences

between these envelope proteins were predicted and discussed.

Keywords: Zika virus, Flavivirus, Envelope protein, Bioinformatics, Microcephaly, Zoonosis.


Activation of EF-hand II of photoproteinaequorin by replacement of

its calcium-binding loop

Mahsa Ebrahimi1, Reza Hassan Sajedi2, Khosro Khalifeh 1, Bijan Ranjbar3

1Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.

2Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.

3Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.

Abstract

Aequorin, a calcium-binding photoprotein, was originally isolated from the jellyfish

Aequoreavictoria that emits light in the presence of Ca2+, decomposing into apoaequorin,

coelenteramide and CO2. This protein has four EF-hand motifs which consist of a helix–loop–

helix structure with a high affinity for calcium ions and are critical for calcium sensitivity and

triggering bioluminescence activity. This protein contains four EF-hand structural domains I, II,

III, and IV from the N to C terminus that tree of them (I, III, IV) bind to calcium. In this study,

we designed a new structure of aequorin by replacing loopII with loop III. This substitution was

purposed in order to investigate the calcium dependent behaviors of this modified protein then

was modeled and energy minimization performed by MODELLER. In this work, the encoding

gene of the photoprotein was synthesized into pUC57 and inserted into the EcoRI/XhoIsite of the

pET28a vector . Protein expression was carried out successfully in E. coli BL21 (DE3). Activity

determination revealed that, the expressed protein is active and its calcium dependent features

changed compared to native aequorin.

Keywords: Aequorin, EF-hand, Calcium-binding, Replacement.


Bioinformatics design of deoxyribozyme 10-23 targeted to beta-

lactamase mRNA for inhibition of ampicillin-resistant bacteria

Nasrin al-Sadat Ahmadi1, Abolghasem Esmaeili 2, Fatemeh Javadi-Zarnaghi3

1MSc student; Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of

Isfahan; Isfahan; Iran. 2 PhD, Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of Isfahan;

Isfahan; Iran.

PhD, Cellular and Molecular Biology Division; Department of Biology; Faculty of Sciences, University of Isfahan;

Isfahan; Iran.

Abstract

Deoxyribozymes (DZ) can play a role as gene expression inhibitors at the mRNA level. Among

them 10-23 deoxyribozymes have a significant potential in treatment of diseases. Designed DZ

includes a catalytic core made of 15 deoxyribonucleotides and two diagnostic arms consist of 9

nucleotides for binding to target RNA and hydrolyzing it. The catalytic feature of this

deoxyribozyme cause cutting of RNA between an unpaired purine (A) and a pyrimidine pair. For

this purpose the first sequence of plasmid with beta –lactamase genewas taken through the

www.addgene.com database. The secondary structure of the ampicillin resistance gene was also

taken via Mfold software. Then intended gene region which is situated in target zone was found.

In another hand ORF sequence was taken from expasy server and due to the protein sequence

related to intend region of the gene, the ORF with the most related sequence similarity was

chosen. Subsequently the complete DNA sequence was taken from expasy and the DZ was

designed based on the reverse complement sequence of mRNA. Results show that the designed

DZ targets the mRNAs involved in several diseases pathways.Their enhanced biological

stability, small size; negligible side-effects in vivo caused by high specificity and lack of

immunogenicity, have paved the way for DZs to enter clinical trials.

Keywords: Deoxyribozyme 10-23, Gene expression, Ampicillin-resistant bacteria.


Prediction of the mode of interaction between monoterpenes and the

nitroreductase from Enterobacter cloacae by docking simulation

Zeynab Ahmadianpour

Department of Biochemistry, sanandaj Branch, Islamic Azad University, Sanadaj, Iran.

Abstract

Monoterpenes from the essential oils of several plants have been shown to enhance the

bactericidal activities of nitrofurantoin and furazolidone against the bacteria of

Enterobacteriaceae family. In this study, computer-aided molecular mode ling and docking

techniques have been employed to simulate the theoretical mode of interaction between

monoterpenes and Enterobacter cloacae nitroreductase. Enhancement of nitro drug potency in

the presence of mono terpenes may be the result of modulation of nitroreductase activity.

Binding nitroreductase with monoterpenes may decrease the efficient conversion of toxic

reactive intermediates to final products lacking bactericidal activity.

Keywords: Enterobacter cloacae, Docking simulation, Nitroreductase, Molaecular modeling.


Molecular modeling, docking and molecular dynamics simulation

approaches to assessment binding of coumarin to β-casein

Zahra Adibipour, Abdol-KhaleghBordbar, Mehdi Sahihi, Najme Fani


Abstract

Low solubility of hydrophobic drugs is a major problem in pharmaceutics industry. In the

present work, a comprehensive computational study has been done on the interaction of

coumarin as a hydrophobic drug with bovine β-casein protein (βCN) as a nano-carrier by using

molecular modeling, molecular docking and molecular dynamics (MD) simulation procedures.

This study revealed the possible application of this nano particle as an efficient and

biocompatible drug carrier of coumarin. First, 3D structure of βCN was modeled using I-

TASSER server, and then to accomplish more stable and better structure of the model obtained

from I-TASSER, a 50 ns MD simulation using GROMACS 4.5.4 software package was

performed on the βCN structure. Using the obtained structure from MD simulation for βCN a

molecular docking calculation was performed to find the binding site of βCN for coumarin.

Docking results showed that coumarin binds to the hydrophobic core of βCN and is in contact

with Leu 103, Pro 101, Pro 100, Phe 102, Phe 48, Ile 45, Pro 168, Glu 51, Glu 46 and Lys 47

residues. Moreover, coumarin is able to form a hydrogen bond interaction with Phe 102 amino

acid residue. Finally, another MD simulation on the ligand-protein complex was done to examine

the effect of coumarin on the conformation of βCN protein. MD simulation results showed that

coumarin can interact with βCN through van der Waals and hydrogen bond interactions without

affecting the secondary structure of this protein.

Keywords: β-casein, Coumarin, Molecular modeling, Molecular docking, Molecular dynamic

simulation.


Exploring binding properties of coumarin with Bovine β-Casein:

multispectroscopic and chemometrics studies

Zahra Adibipour, Abdol-KhaleghBordbar, Mehdi Sahihi, Najme Fani


Abstract

Several studies have been done through encapsulation of hydrophobic drugs in protein

nanoparticles to increase their aqueous solubility.Coumarin is a compound that belongs to benzo-

α-pyrone group and reveals high antibacterial effect. β-casein (βCN) is a protein which is found

in bovine milk and can be used as natural nano-delivery vehicles for hydrophobic drugs. In the

present study, we load βCN with coumarin and then explored the binding properties of coumarin

to βCN by using absorption and fluorescence spectroscopies and chemometrics analysis. The

spectrofluorometric titration experiment was run at four different temperatures from 293K to

308K and at two excitation wavelengths of 280nm and 295nm. The results show the quenching

effect of coumarin on fluorescence spectrum of βCN. The binding and Stern-Volmer constant

values at the excitation wavelentgth of 295nm were in the order of 104M-1 magnitude and

decreased with temperature which indicates high strength of binding and static quenching

mechanism for Tryptophan residue of βCN. Also data analysis represented the formation of 1:1

complex, negative values of entropy and enthalpy changes and the essential role of hydrogen

bonding and van der Waals interactions in binding of coumarin to βCN. The Förster’s distance

value (4.078nm) represents the static quenching mechanism of βCN by coumarin and significant

binding affinity. A positive deviation from linearity was observed for Stern-Volmer plot at the

excitation wavelength of 280nm, which demonstrate the dynamic quenching mechanism for

tyrosine and phenylalanine residues. Chemometrics analysis of UV-Vis spectroscopic titration

data showed the presence of three different species in the solution with the binding affinity of

105M-1 order of magnitude and the formation of 1:1 complex of coumarin with βCN.

Keywords: β-casein, Coumarin, Spectrofluorometric, Chemometrics.


Measurement of dioxin contamination in water samples by a

bioluminescence method

SeyedePegah Azarchehry1, Farangis Ataei1, Saman Hosseinkhani2

1Biochemestry department of TarbiatModares University, Tehran. 2 Biochemistry department of TarbiatModares University, Tehran. The head of bioluminescence Laboratory.

Abstract Dioxins have harmful effect in environment. Dioxins include the group of molecules which have

same structure and same function in different organisms. The measurement of Dioxin‘s

concentration was obligated by World Health Organization (WHO). Dioxins has been produced

during the production of certain chlorinated phenols and their derivatives, and as a result of high

temperature pyrolysis and combustion of organic compoundsContaining halogens. This

compounds are very resistance in the environment. Because of its high lipophilicity and water

insolubility, dioxin concentrates in sediments and is incorporated into food chains.The traditional

method for measuring the concentration of dioxins in samples was gas chromatography-high

resolution mass spectrometry. Although it was very accurate technique, it is costly and of

limitation in number of tests done in a distinctive period of time.Cell based screening methods

such allow high throughput screening and are cheaper than last methods.In this study, according

to importance of water quality, we have tried to screen dioxins-like compounds in water samples

using bioluminescence method, extraction and clean up the dioxins with silica chromatography

column were set, and detection and measurement the concentration of dioxins in different water

samples by cells will be reported.

Keywords: Dioxins, Biosensor, Bioluminescence, Water sample, Contamination detection.

Rashid

Highlight


Role of the pre- molten globule structure in amyloid fibril formation

Ali Es-haghi1, Azadeh Ebrahim-Habibi2, Mohsen Nemat-Gorgani3

1Faculty of Science, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran.

2Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran

University of Medical Sciences, Tehran, Iran.

3Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.

Abstract

The major factor that caused extensive research on the protein fibrillation is their crucial roles in

important diseases known as the amyloidosis diseases. Neurodegenerative diseases, including

Alzheimer's, Parkinson's, diabetes and Huntington are the most important types of this disease.

Understanding the mechanisms of fibril formation and ways of treatment can be useful in

reducing this type of disorder. In this project, the fibrillation of carbonic anhydrase protein was

investigated as a model. Carbonic anhydrase creates two stable intermediated known as pre-

molten and molten globule, in different pH solution. This protein at pH between pH 3-4 molten

globule structures was formed while the pre- molten form took place under pH 3. In our tests at

pH 3.5 when the protein in molten globule structures only the amorphous aggregates were

formed. Instead, at pH 2.4 in pre- molten globule structure amyloid fibrils formed in the protein.

There some reports, indicated the protein from pre- molten globule structure go toward amyloid

assembly. Even intrinsically unstructured proteins such as alpha-Synuclein first took a structure

similar to pre- molten globule and then made amyloid fibrils. It seems pre- molten globule

structure have the major role in promoting to amyloid fibrils. Perhaps drugs that prevent the

formation of pre- molten globule structure have an important role in inhibiting amyloid fibrils.

Keywords: Pre-molten globule, Carbonic anhydrase, Amyloid fibril.


Nano-liposomal lipid peroxidation as a consequence of the diabetic

albumin glycation

Maha Asadi1, Hamzeh Maleki1, Mehran Habibi-Rezaei1, 2

1College of Science, University of Tehran.

2Nano-biomedicin Center of Excellence.

Abstract

Glycation is a non-enzymatic reaction between reducing sugar and bio-macromolecules. This

reaction leads to distruction or activity defection in biomolecules and produces glycation end

products (AGE) and reactive oxygen species (ROS). Albumin that is a more important serum

protein, glycated by high glucose in diabetic condition and raises AGE and ROS in blood. In this

study, the effect of diabetic protein glycation on membrane lipid peroxidation is reported using

constructed nono-liposomes. Liposomes prepared using lecitin and cholesterol then incubated in

the presence of the bovine serum albumin (BSA) in diabetic condition for 40 days. The lipid

peroxidation (LPO) induced by diabetic protein glycation is monitored by AGE and ROS using

intrinsic AGE dependent auto-fluorescence and malondialdehid (MDA) measurement,

respectively. The amount MDA was increased as increasing the time of incubation of liposomes

under diabetic glycation of albumin by carbohydrate, however, a rate increase was observed at

after 20th day. The protein glycation produces AGE and ROS. The ROS generation and LPO are

highlighted as a causative mechanism in diseases such as cardiovascular, neuropathies,

nephropathies, retinopathies etc.

Keywords: Nano-liposomes, Peroxidation, Glycation, Reactive oxygen radicals, Diabets.


Gold nanoparticles-capped mesoporous silica for enzyme responsive

controlled release of doxorubicin in cancer therapy

Parvaneh Eskandari1, Ali Akbar Saboury1, Mehdi Khoobi2

1Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran. 2Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.

Abstract

Mesoporous silica nanoparticles (MSN), as prominent candidates for next generation therapeutic

carriers, have a great deal of attention because contain parallel pores with two unique openings

that anticancer drug load in this pores. Therefore, this characterization makes it as an ideal

delivery system that can controlled release simultaneously, in which, the pores can be closed

using a cap and opened with internally or externally stimuli. Matrix metalloproteases (MMPs)

are a family of extracellular proteolytic enzymes that are overexpression in cancerous tissues.

We studied the stimuli-responsive release profiles of doxorubicin loaded gold nanoparticles-

capped MSNs delivery systems by using peptide cleavable linker that sensitive to overexpressed

matrix metalloproteinase in extracellular of cancer cells.In this nanosystem high dose of

doxorubicin deliver to cancer cells without effect on healthy tissues.

Keywords: MMP-cleavable peptides, Mesoporous silica, Responsive systems, Doxorubicin.


Isolation of ACE-inhibitory peptide produced by enzymatic activity

of goat milk whey proteins

Mehrnaz Esmaeilpour1, Mahmood Aminlari 2, Mohammad Reza Ehsani 3, Shahram

Shekarforoush 4, Ebrahim Hoseini 3

1 Department of Food Science and Technology, Fasa Branch, Islamic Azad University, Fasa, Iran. 2 Department of Biochemistry, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. 3Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran,

Iran.

4 Department of Food Hygiene and Public Health, School of veterinary Medicine, Shiraz University, Shiraz, Iran.

Abstract

In this study, goat milk whey proteins was hydrolyzed by trypsin, ficin and a combination of the

two to isolate angiotensin I-converting enzyme (ACE) inhibitory peptides. The hydrolysates

were fractionated using ultrafiltration membranes. The hydrolysate obtained by trypsin with

molecular weight <3 kDa exhibited the highest ACE-inhibitory activity that purified with reverse

phase high performance liquid chromatography (RP-HPLC). Among the fractions, fraction 2 had

the highest ACE inhibitory activity (IC50: 160 µg/ml). The results of this study indicate that

peptides produced by trypsin and ficin treatment could be considered as natural antihypertensive

agents alternatives to chemical counterparts used in food and pharmaceutical industries.

Keywords: Goat milk whey proteins, Bioactive peptide, ACE inhibitory activity, Ficin, Trypsin.


The presence of JC virus VP1 capsid of genotype 2B in rheumatoid

arthritis patients in Isfahan, Iran

Sayyedeh Rahmaneh Atyabi1and Majid Bouzari1

1Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.

Abstract

Opportunistic JC virus (JCV) infection is an asymptomatic latent infection that in

immunosuppressed individuals (patients undergo immunosuppressive treatment) such as

rheumatoid arthritis cases may lead to progressive multifocal leukoencephalopathy (PML). This

disorder causes demyelination of the white matter of brain. VP1 capsid of genotype 2B is an

aggressive form of the virus specially can be excreted from urine. In this study 43 patients with

rheumatoid arthritis and 100 healthy individuals were tested for the presence of JCV in urine.

PCR with specific primers were performed on urine pellet for detection of VP1 gene. All of the

positive PCR products of both patients and healthy individuals were sequenced. Fisher's exact

test was used for statistical analyses, then DNA and translated DNA sequences detected in this

study and the same from different countries obtained from GenBank with phylogenetic tree

constructed. JCV was detected in 18.60%, and 7% of rheumatoid arthritis patients and healthy

individuals respectively. Genotypes 1, 3 and 4 were detected in 2(25%), 5(62. 5%) and 1(12.5%)

of the rheumatoid arthritis patients and genotype 1 was found in 2(28.57%) and genotype 3 was

found in 5(71.42%) of healthy individuals respectively. The frequency of infection in the urine of

rheumatoid arthritis patients was higher. This may increase the risk of PML in them. On the

other hand only genotypes 1, 3 and 4 were detected that compare to genotype 2B are less

aggressive and so less chance of causing PML.

Keywords: JC virus, Progressive multifocal leukoencephalopathy, VP1, Rheumatoid arthritis,

Isfahan.


In Silico analysis of single nucleotide polymorphisms (SNPs) and

screening of mutations affecting protein stability and function of

KRAS protein

Fatemeh Arabi Jeshvaghaniand Mohamad Reza Ganjalikhany


Abstract The human KRAS gene is the member of the RAS family of oncogenes with cytogenetic location

of 12p12.1 that encodes KRAS protein, a small GTP-binding protein which plays a critical role

in RAS/RAF/MEK/ERK pathway in fundamental cellular processes such as proliferation,

differentiation, apoptosis, and survival. Single nucleotide polymorphisms (SNPs) can influence

protein function, structure and stability. In this analysis we use five in silico SNP prediction

algorithms, SIFT, PolyPhen, nsSNPAnalyzer, SNPs&GO and PROVEAN to identify functional

SNPs in coding regions of KRAS gene and predicts the effect of these variants on KRAS

function and stability. This study is the first extensive in silico analysis of the highly

polymorphic KRAS gene. Polymorphism data for the KRAS gene were retrieved from NCBI

database of SNPs (dbSNP) then used as inputs in SIFT (Sorting Intolerant from Tolerant) and

PolyPhen (Polymorphism phenotyping) algorithms and the other tools that predict the potential

impact of amino acid substitutions on protein function and structure. The dbSNP-NCBI database

revealed a total of 2717 SNP for human KRAS gene which comprised of 73 missense SNPs. We

selected the missens SNPs for our further investigations. It has been predicted that 45 missens

SNPs (61.64%) are deleterious by SIFT analysis, 43 missens SNPs (58.9%) are predicted to be

possibly damaging to KRAS function according to our Polyphen-2 results. nsSNPAnalyzer,

SNPs&GO and PROVEAN show the diseases and natural SNPs in KRAS gene separately with

their related specific scores. We find GLY12ASP, GLY13ASP, GLY60ARG and VAL14ILE as

the most deleterious mutation by these tools. Then these four mutations were analyzed by Align-

GVGD that combines the biophysical characteristics such as side chain composition, polarity and

volume of amino acids and protein multiple sequence alignments (Grantham Variation (GV) and

Grantham Deviation (GD) scores) to predict where amino acid substitutions fall in a spectrum of

deleterious to neutral. Biophysical analysis indicates a clear insight of stability loss due to these

mutation in KRAS protein. As there are numerous SNPs in KRAS gene our computational

analysis can be effective for further study in linkage and association of genetic studies to

understand the changes affect protein functions and stability for diagnosis KRAS related disease,

design and development of new drugs particularly the inhibitors of RAS/RAF/MEK/ERK

pathway.

Keywords: Single nucleotide polymorphism (SNP), In silico analysis, KRAS protein, Stability.


Computational molecular docking studies of bioactive peptides from

milk proteins as angiogenesis converting enzyme inhibitors with

antihypertensive effects

Fatemeh Arabi Jeshvaghani1 and Mohamad Reza Ganjalikhany

Department of Biology, Faculty of science, University of Isfahan, Isfahan, Iran.

Abstract

Milk represents a unique source of nutrients and biologically active proteins and peptides that

secreted into milk and released by proteolytic action. There are many milk protein-derived ACE

inhibitory peptides with antihypertensive activity to avoid undesirable side effects of synthetic

drugs. Hypertension is the most common worldwide risk factor for stroke, kidney disease and

several cardiovascular disorders. The renin-angiotensin system (RAS) activation plays a key role

in hypertension. Inhibition of RAS with angiotensin converting enzyme (ACE) inhibitors by

blocking the enzyme that catalyses the conversion of angiotensin I to angiotensin II can lead to

reduce blood pressure by blood vessels dilation. The aim of this study is to analyse the potential

ACE inhibitory action of four bioactive peptides in milk by computational docking studies and

campary with synthetic ACE inhibitor drug. Molecular docking study of benazepril (FDA

approved ACE inhibitor drug) and APTLtetrapeptides, IPP and VPP tripeptides and YP

dipeptides with ACE (PDB ID: 1O86) has been done using Autodock 4.2.6. The results have

indicated that among these bioactive peptides in milk IPP showed higher binding affinity

compared to others with the lowest binding energy (-6.65kcal/mol) and the high potential effect

for hypertension treatment. While, the lowest binding energy was observed in YP (-

5.28kcal/mol). The binding energy of benazepril to ACE was -8.75kcal/mol. Our findings clearly

demonstrate the potency of milk bioactive peptides for discovery and development of new ACE

inhibitors from natural sources with less toxicity and more selectivity than chemical inhibitor and

prove that dietary foods like milk can be effective for treatment of hypertension and other

cardiovascular disorders.

Keywords: Molecular docking, Bioactive peptides, Milk, Angiotensin converting enzyme,

Hypertension.


Molecular docking and quantitative structure--activity

relationships(QSAR) studies of herbal compounds in Iris

pseudopumila (Iridaceae)asacetylcholinesterase inhibitorsin

alzheimer's disease treatment

Fatemeh Arabi Jeshvaghani1, Mohamad Reza Ganjalikhany2


Abstract

Alzheimer's disease (AD) a progressive neurological disorder is the most common cause of

dementia. Acetylcholinesterase inhibitors can be applied in neurodegenerative disorders

treatment like alzheimer's disease by inhibition of acetylcholinesterase (AChE) enzyme that is

encoded by the ACHE gene on chromosome 7 which catalysis the hydrolysis of neurotransmitter

ACh into acetate and choline in conducting tissue specially in motor neurons. Natural herbal

products that have been used traditionally as nutrition or medicine may also act as AChE

inhibitors.Iris pseudopumila (Iridaceae)flowers and rhizomes extract consist of two non-

alkaloidal compounds including isoorientin and isovitexin that can have significant AChE

inhibitory effect. The aim of this study is to analyse the potential AChE inhibitory action of

natural compunds in Iris pseudopumila by computational docking studies. Molecular docking

study of Donepezil and PyridostigmineAChE chemical inhibitor drugs and Isoorientin and

isovitexin with AChE (PDB ID:4PQE) has been done using Autodock 4.2.6.QSAR studies have

been implemented to predict the biological properties of the bioactive compounds. The

molecular descriptors such as molecular weight, hydrogen donor, acceptors, LogP, Total

Polar Surface Area (TSPA), were obtained using FAF drugs ADME/Tox filtering . The

results have indicated that among these two compounds in Iris, isovitexin showed higher binding

affinity compared to another with the lowest binding energy (-6.49kcal/mol) and the high

potential effect for AD treatment that is more than Pyridostigmine inhibition effect. Donepezil

showed the lowest binding energy (-8.25kcal/mol). Our findings clearly demonstrate thepotency

of these herbal compounds for discovery and development of new AChE inhibitors with less

toxicity and more selectivity than chemical inhibitors and prove that natural herbal compounds

like Iris pseudopumila can be effective for treatment of Alzheimer's disease and other

nurological disorders.

Keywords: Molecular Docking, QSAR studies, Alzheimer's disease, Acetylcholinesterase

Inhibitor, Iris pseudopumila.


Study of the binding of warfarin drug to β- lactoglobulin by UV-

visible and isothermal titration calorimetry techniques

Afshari Sahar, Zeyni – Esfahani Asghar, Rastegari Aliasghar

Department of Molecular and Cell Biochemistry, Islamic Azad University, Falavarjan, Esfahan, Iran

Abstract

β- lactoglobulin is one of the lipocalin family's members and the major protein of cow's milk.

It comprised two disulphide bridges and one free Cys121. The biological function of β-

lactoglobulin remains unknown yet but it was suggested that this protein has a potential role in

fatty acid transportation through digestive tract. Thus, it can be used as a transporter for

hydrophobic molecules for controlled delivery applications. Warfarin is a hydrophobic molecule

and an anticoagulant preventing the clot formation in blood vessels. In this study, the interaction

of warfarin with β-lactoglobulin was investigated by the ultraviolet-visible (UV –Vis) and

circular dichroism (CD) spectroscopy. The results of UV-vis titration in different temperatures

(25, 30, 35, 40℃ ) showed that the warfarin/ β-lactoglobulin interaction was exothermic and

spontaneous. The binding constant was 103M-1. The protein was more stable at low temperatures

and the results of CD Spectroscopy did not demonstrate any significant structural changes for

warfarine binding to β-lactoglobulin.

Keywords: β-lactoglobulin, interaction, Hydrophobic, warfarin, UV–Vis spectroscopy, Circular

dichroism.


Fabrication of gold nanorod assemblies on BSA amyloid fibril

scaffolds

YasinAkhtari1, Mina Sadat Eghbal2, Tahereh Tohidi Moghadam3, Bijan Ranjbar2, 3

1 Department of Biomedical Engineering, Faculty of High Technology, TarbiatModares University, Tehran, Iran.

2 Department of Biophysics, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.

3 Department of Nanobiotechnology, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.

Abstract

Today, gold nanorods have attracted significant attention due to their optical, thermal and

catalytic properties, promising variety of applications in conjugation with proteins and

nucleic acid. This effort has focused on simultaneous exploitation of dual properties presented by

hybrid scaffolds of nano and bio counterparts, leading to fabrication of interesting biotemplates.

Gold nanorods (GNRs) were interacted with bovine serum albumin (BSA) amyloid fibrils to

design a nanowires-like scaffold. To obtain amyloid fibril structures of BSA, different

concentrations of protein were dissolved in 0.1 M phosphate buffer (pH 8.9). Samples were

incubated at 62 ˚C, with continuous stirring for 12 hours. GNRs were synthesized via seed

mediated growth protocol and characterized by TEM and UV-Vis spectroscopy. Monitoring of

the amyloid fibril formation by Thioflavin T (ThT), far and near-ultraviolet Circular Dichroism

(CD) spectropolarimetry indicated conformational changes in BSA and transformation into

amyloid fibril structures. SEM images of the nanostructures treated with BSA amyloid fibrils

also depicted ordered aggregates of GNRs on the biotemplate. Results of this investigation

highlighted possibility of fabricating directed nanostructured assemblies on amyloid fibril based

scaffolds, as a novel candidate for future biomedical and biosensing applications in tissue

engineering and hybrid drug delivery systems.

Keywords: Gold nanorods, Nanostructures, Biotemplate, Amyloid fibrils.


The effect of modified tryptophan residues on kinetic,

thermodynamic and structure of mashroomtyrosinase

Saeed Emami1and Nematollah Gheibi2

1Department of Biology, Faculty of Basic Sciences, Islamic Azad UniversityScience and Research Branch, Tehran,

Iran.

2 Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.

Abstract

MashroomTyrosinase (MT) is a metalloenzyme and is a good model in mechanistic point of

view for the study of tyrosinase as the key enzyme in melanogenesis. To recognizing mechanism

of MT’s activity its inhibition, activation, mutation and modification are important methods of

investigations. Here, the chemical modification of MT tryptophan residues have been done by N-

bromosuccinimide (NBS) and the activity, stability and structure of native and modified enzyme

were comprised. Chemical modification of MT tryptophan residues induced by enzyme

incubation with different concentrations of NBS. The relative activity of native and modified MT

were investigated through catecholase reaction of enzyme by L-Dopa as substrate.

Thermodynamic parameters including: ∆G25°C and Tm obtained from thermal denaturation of the

native and modified enzyme. The circular dichroism and intrinsic fluorescence techniques have

been used for study of secondary and tertiary structure of MT respectively. The relative activity

reduced from 100% for native to 10%, 7.9% and 6.4% for modified MT with different 2, 10 and

20 mM concentrations of NBS, respectively. Thermal stability of modified enzyme were

emphasized by decreasing in Tm and ∆G25°C values.In accordance with kinetic and

thermodynamic studies the lower stability of modified MT was observed from the changes of its

secondary and tertiary structures. Chemical modification of tryptophan residues with NBS

reduces activity and stability of MT in line with its structural changes. So this study emphasized

to the crucial role of tryptophan residues in the structure-function relationship of the enzyme.

Keywords: Chemical Modification, MashroomTyrosinase, N-Bromosuccinimide, Kinetic,

Structure.


Covalent immobilization of glucoamylase on superparamagnetic

nanocomposites4 O3graphene oxide Fe

Mahkame Amirbande and Asghar Taheri-Kafrani

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan.

Abstract Recently, highly soluble enzymes in physiological environment and hydrophilic has been

noticable. Graphene oxide is a nontoxic material and selective modulator for enzyme activity and

is also a thermostable molecule that is important in large-scale nanostructure sheet applicatoins.

Nanostructures of hybrid graphene oxide-Fe3O4-cyanuric chloride (GO-MNP-CC) have

adjustable surface chemistry that is an excellent candidate for covalence immobilization

enzyme.Glucoamylase is used in industrial food products and other applications. The interaction

of GO-MNP-CC with a bioactive molecule, such as a glucoamylase enzyme, hasn't been

explored. The results of this study indicated that the reusability and stability of immobilized

enzyme have been obviously improved compared to the free enzyme. The optimum condition of

immobilized glucoamylase determine at pH 6.5 and 60oC. The apparent Km and Vmax for free

and immobilized glucoamylase were also determined. These properties make them a good

candidate to improve the practicality and further the development of the capacity enzyme

attachment. Thus, magnetic nanoparticles GO–Fe3O4 can be used in various applications with an

industrial purpose. The structure properties of the immobilized glucoamylase and support were

characterized by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy

(XPS), Fourier-transform infrared spectra (FTIR), thermo-gravimetric analysis (TGA) and

vibrating sample magnetometer (VSM) analysis.

Keywords: Graphene oxide, GO-Fe3O4, Cyanoric chloride, Glucoamylase, Enzyme

immobilization.


Functionalized superparamagnetic chitosan nanoparticles in enzyme

engineering: A highly dispersive, stable and robust biocatalyst

Mahkame Amirbande, Asghar Taheri-Kafrani

Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan.

Abstract

Glucoamylase (EC 3.2.1.3) from Aspergillus Niger was immobilized on chitosan

superparamagnetic nanoparticles (SPCh-CC) by covalent binding after activation with cyanuric

chloride to produce glucose from starch. The important parameters such as temperature, pH,

reaction time, enzyme concentration and other parameters have been studied and optimum values

were detected. The activity recovery of immobilized glucoamylase was over than 80% and this

result showed that immobilization processcouldn’t significantly inhibit enzyme-substrate

interaction and thus the enzymatic activity. The Michaelis-Menton constant (Km) and vmax values

were improved and this suggested that SPCh-CC nanocarriers can be an ideal choice for

immobilization of glucoamylase. The structure properties of the synthesized SPCh-CC and

immobilized glucoamylase, was characterized using TEM, XRD, and FT-IR analyses.

Keywords: Chitosan nanoparticles, Glucoamylase, Cyanuric chloride, Enzyme immobilization,

Robust biocatalyst, Enzyme activity.


Investigation on physicochemical properties of [Ni (FIP) 2] (OAC)2

complex and its interaction with ct-DNA and Its effect on ct-DNA

stability

Alireza Amini Khozani and Nasrin Sohrabi

Department of Chemistry, Payame Noor University, PO. Box 19395-3697, Tehran, Iran.

Abstract

Deoxyribonucleic acid (DNA) is an important genetic substance in the organism, which carries

most of hereditary information and facilitates the biological synthesis of proteins and enzymes

through replication and transcription of this information. It is one of the most important

biological molecules targeted by natural and synthetic compounds. Investigation on the

interactions of small molecules with DNA has been an intensive topic over the past years in the

scope of life science, chemistry, clinic medicine and genetics. These studies are beneficial for

screening new and more efficient drugs targeting to DNA, investigating the structure and

biological function of DNA, and elucidating the damage mechanism of DNA. In this study, the

physicochemical properties of [Ni(FIP)2](OAC)2complex and its interaction with calf thymus

DNA at different temperature were investigated using UV/Vis and fluorescence spectroscopies,

viscosity and denaturation methods. The results show that the shape and position of the bonds

did not change significantly. So, this complex has suitable stability and doesn’t show any

aggregate and the interaction with calf thymus DNA is endothermic and the driving force is

entropy and the binding mode of [Ni(FIP)2](OAC)2 complex to calf thymus DNA is electrostatic

mode.

Keywords: Calf thymus DNA, [Ni (FIP)2](OAC)2, UV/Vis spectra, Denaturation, Fluorescence

emission.


An in-silico investigation on the structure and function of the

Phenanthrene degradative bacteria enzymes, an introduction to

development of anti-cancer probiotics Elnaz Enferadi-Moghadam1 and Aliakbar Haddad-Mashadrizeh 2, 3

1Department of Biology, Science and Research Branch, Islamic Azad University, Khorasan Razavi, Neyshabur,Iran.

2Cell and Molecular Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of

Mashhad,Iran.

3Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

Abstract

Gut flora, as an organ with extensive known and unknown capabilities, containing different

kinds of bacteria with various properties. Some of these bacteria recognized as probiotics which

in turn have beneficial effects on the health via digestion facilitation and or production some

complex compounds such as vitamins and antibiotics. In this regard, the performance of these

bacteria in prevention and treatment of a range of diseases have been revealed. So, absorption

and digestion the aromatic hydrocarbons (AH), which are in food, could be a promising strategy

for the prevention of a wide range of diseases such as cancer via equipping the probiotics to the

corresponding genes of AH catabolism or dairy enrichment with related enzymes. Bearing in

mind, profiling and characterization the competent corresponding enzymes of AH metabolism

would be providing approaches for cancer prevention, which are considered in this study through

Phenanthrene. For this purpose, a profile of bacterial enzymes with capacity in Phenanthrene

degradation has been gathered and then corresponding nucleotide and protein sequence were

retrieved from related databases such as NCBI and UniProt. CD Search, motif Scan,

InterProScan, Blast, MEGA6, Hex and ClusPro2.0 were then used for molecular analysis of the

selected sequences. Structural modeling carried out via Modeller program and assessment by

MOE. Moreover, thermal stability of the selected domains performed via Gromacs program. The

results of this study whilst presents a profile of the bacterial enzymes involved in Phenanthrene

degradation, provided a series of efficient of domains with high binding affinity to Phenanthrene

as well as other HA other hydrocarbons with temperature stability in some cases. Overall, these

results led to provide a series of data for designing new genetic construct for probiotic

development as well as chimeric enzymes production for AH, especially Phenanthrene,

catabolism.

Keywords: Aromatic hydrocarbons, Phenanthrene, Cancer, Probiotics.


The effect of time and temperature incubation on bacterial phytase

activity

SarehAnvari1, Jamshid Fooladi1, Parichehr Hanachi1

1Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.

Abstract

Phytase [myo-inositol hexakisphosphate hydrolase] initiates the step-wise removal of phosphate

from phytate [myo-inositol hexakis phosphate]. Phytate is the major storage form of

phosphorous in cereals, legumes, oil seeds, and nuts. This enzyme has been used widely in

animal feeding to improve phosphorus nutrition, and reduce phosphorus pollution of animal

waste. The bacterial phytase isolated from soil, and grew on PSM (Phytase Specific Medium).

To investigate the effect of incubation conditions on phytase activity, sodium phytate as substrate

incubated with extracellular phytase at various periods of time (10, 20,30,40,50 and 60 min) and

temperatures (4, 25,37,42,56 °C). The activity of phytase was assayed by measuring increased

rate of inorganic orthophosphate (Pi) using ammonium heptamolybdate. The reaction mixture

consisted of 500 µl acetate buffer (0.2 M, pH 5.5 containing 2.5 mM sodium phytate), and 500 µl

of the supernatant. After incubation, the reaction was stopped by adding 500 µl of 15%

trichloroacetic acid (TCA). Assay mixture mixed with 1000 µl of ammonium heptamolybdate

reagent. The amount of released free phosphate was determined spectrophotometrically at 750

nm. Results showed the optimum time for incubation was 30 minutes. It possessed a temperature

optimum of 42 °C. Soil and water micro-organisms are capable of hydrolyzingphytic acid.

Utilizing of these micro-organisms in animal feed helps to decrease environmental pollution, and

raise the uptake of mineral materials.

Keywords: Phytase, Phytate, Incubation conditions, Animal feed.


Thermal stability of lactoperoxidase stabilized on modified magnetic

nanoparticle

Narges Babadaie Samani1, Hashem Nayeri1, Gholamreza Amiri2

1Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran.

2Falavarjan Branch, Islamic Azad University, Isfahan, Iran.

Abstract Immobilized enzymes are drawing significant attention for potential commercial applications as

biocatalysts by reducing operational expenses and by increasing process utilization of the

enzymes. Typically, immobilized enzymes have greater thermal stability and are more resistant

to denaturation that the soluble native form of the enzyme. Magnetic nanoparticles provide

advantages as the supporting material for immobilized enzymes, and magnetic modified

nanoparticles have more ability instead of not modified one such as: higher surface area that

allows for greater enzyme loading, lower mass transfer resistance, less fouling effect, and

selective, nonchemical separation from the reaction mixture by an applied a magnetic field. In

this study at the first, we synthesized Fe3O4 and then was coverage by SiO2 by co-precipitation

and sol-gel respectively. Lactopeoxidase in an optimum situation was immobilized on to Fe3O4@

SiO2 NPs, after that its thermal stability was studied in different temperatures (40-100) at various

times (5min-1h). The results of this study showed that in all temperatures (40-100) and times

(5min-1h) activity of free and immobilized enzyme were decreased, but in all situations activity

of immobilized enzyme was more than free enzyme. According to the results of this study it can

be concluded that stabilized of lactoperoxidase on Fe3O4@ SiO2 NPs can be increase its thermal

stability and preparation of this enzyme for industry.

Keywords: Fe3O4@ SiO2 NPs, Lactoperoxidase, Enzyme immobilization, Thermal stability.


Effect of over-expressing Apaf-1 on apoptosis induction

Maisam Bakhshoudeh, Farangis Ataei, Saman Hosseinkhani

Department of Biochemistry, Faculty of biological sciences, TarbiatModares University, Tehran, Iran.

Abstract

Cancer is the second main cause of death in Iranian women. Out of different kinds, breast cancer

is the most dominant. The rate of apoptosis decreases significantly in breast cancer leading to

metastasis stage of cancer. Apoptotic protease activating factor 1 (Apaf-1) and cytochrome c are

key players in formation of apoptosome, which subsequently activates the cascades of caspase

activities. In most malignant cells, rate of expression of Apaf-1 is low compared to normal cells,

which results in lower rate of apoptosis. In addition, in recent studies it was determined that in

presence of “p53 associated Parkin-like cytoplasmic protein” (PARC/CUL9), cytochrome c is

targeted for ubiquitination, while there is low Apaf-1 availability. This, results in decreased rate

of apoptosis. In this study, we have demonstrated that exogenous expression of Apaf-1 in MCF-7

cell line caused higher caspase 3/7 activity compared to untreated MCF-7 cells after induction of

apoptosis by doxorubicin. As it was expected, since the MCF-10A cell line has higher levels of

Apaf-1 in comparison to MCF-7 cell line, a greater caspase 3/7 activity was observed.Therefore,

it seems that Apaf-1 levels and apoptosis rate are in positive correlation. More conclusive results

will need to be gathered to further prove this claim.

Keywords: Apoptosis, Apaf-1, Breast cancer, Doxorubicin.

Rashid

Highlight


Studying the presence of hemolysin BL and NHE subunit genes in

Iranian native Bacillus strains with probiotic potential by PCR

NastaranBahrami Gahrooei1, Mohsen Golnari Maranni2, Mohammad Ali Asadollahi2, SeyedSafa

Ali Fatemi3

1Microbiology group, NourDanesh non-profit higher education institute of Meymeh, Isfahan, Iran.

2 Biotechnology Department, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.

3Systeme Biology Group, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.

Abstract

A tripartite hemolytic heat-labile enterotoxin designated HBL is responsible for the diarrheal

food poisoning syndrome caused by some strains of Bacillus spp. HBL is the product of an

operon containing hblA, hblD, and hblC, which encode the binding subunit (B) and the L1 and

L2 lytic components, respectively. Additionally, a non-hemolytic enterotoxin (NHE) operon has

recently been characterized. NHE also consists of three proteinaceous subunits including nheA,

nheB and nheC, two lytic factors and a binding factor. Consumption of enterotoxigenicBacillus

spp. at high cell densities results in symptoms of diarrhea, with possible vomiting from a

separate heat-stable emetic toxin. In the present study, we investigated the presence of HBL &

NHE subunit genes in Bacillus isolates by PCR. Thirty-nine Bacillus strains were isolated from a

variety of dairy products, soil samples, vinegar, livestock excreta and poultry excreta samples.

Isolates were identified by biochemical and molecular methods. These Bacillus strains were

screened for probiotic characteristics and finally 16 strains were selected to investigate the

presence of HBL & NHE subunit genes. These strains belong to the B. subtilis, B. licheniformis,

B. toyonensis, B. pumilus, B. coagulans B. amiloliquifaciens, B. endophitycusand B.

siamensisspecies. The results showed that among the 16 strains, seven contained HBL & NHE

subunit genes. This study suggested that HBL & NHE subunit genes could be detected among

Bacillus spp. outside the Bacillus cereus group.

Keywords: Enterotoxin, Hemolysin BL, Non-hemolytic enterotoxin, Bacillus, Probiotic.


Inhibition of angiogenesis signaling pathways by synergic

administration of VEGF antibody along with endostatin derived

peptide in the human umbilical vein endothelial cells

Hossein Bayat1, Reza H. Sajedi1, Kamran Mansouri2, Seyed Mohsen Asghari3

1Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran. 3Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran.

Abstract

Angiogenesis is one of the most important stages in tumor growth, though it is a very suitable

target for drug designing. Inhibition of tyrosine kinase receptors like VEGFR-1 and VEGFR-2

by recruiting a monoclonal antibody called bevacizumab (Avastin) and removing its VEGF

ligand (a kind of mitogen for endothelial cells and necessary for angiogenesis process), leads to

angiogenesis inhibition. On the other side, endostatin derived peptide is able to inhibit

endothelial cell growth through an especial integrin receptor. The main goal of this research is

investigating the synergic effect of VEGF antibody (as a specific inhibitor), and endostatin

derived peptide (as a general inhibitor), in order to achieve efficient angiogenesis inhibition and

reduce the dosage of drug administration. The proliferation assay on Human Umbilical Vein

Endothelial Cells (HUVEC) showed the best synergic effect in 400 ng/ml of peptide along with

400 µg/ml of Avastin with 95% inhibition, while single administration of peptide in 400 ng/ml

concentration and anti-VEGF antibody in 400 µg/ml concentration, led to 62% and 48%

angiogenesis inhibition, respectively. The estimation of cytosolic Ca2+ by fluorescence Ca2+

indicator, Fura-2 and tube formation assay confirmed MTT data. Therefore, we concluded that

synergic administration of these two drugs effectively inhibits the endothelial cell growth.

Keywords: Cancer, Angiogenesis, Avastin, Endostatin, Synergic effect.


Evaluation of antioxidant activity in peptides of fermented soybean

meal by Lactobacillus rhamnosus

Maryam Bigdeli, Fakhri-Sadat Hosseini, Mohammad Reza Soudi, Zahra Moosavi-nejad

Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.

Abstract

Soybean meal is a byproduct of vegetable oil industry that can use for livestock feeding. Solid-

state fermentation (SSF) has received great attention because this bioprocess has potential to

successfully convert inexpensive agro industrial residues, as well as plants, in a great variety of

valuable compounds, such as bioactive peptides .The aim of this study was the production of

antioxidant peptides from fermented soybean meal by Lactobacillus rhamnosus. Lactobacillus

rhamnosus was used to produce antioxidant peptides at 30 °C under appropriate humidity during

different incubation time from 24 hours to 72 hours .Antioxidant activity was studied by DPPH

(2, 2-diphenyl-1-picrylhydrazyl) radical scavenging .The result indicated more than 91 % radical

scavenging property in fermented soybean meal .

Keywords: Antioxidant activity, Antioxidant peptides, Lactobacillus rhamnosus, Soybean meal,

Soli state fermentation.


Production of antioxidant peptides from soybean meal by Bacillus

subtilis

Maryam Bigdeli1, Fakhri-Sadat Hosseini1, Mohammad Reza Soudi2, Zahra Moosavi-nejad3

1 Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran.

2Department of Microbiolgy, Faculty of Biological Science, Alzahra University, Tehran, Iran.

3 Department of Biochemistry, Faculty of Biological Science, Alzahra University, Tehran, Iran.

Abstract

Oxidative stress has been assumed as one of the most important reasons for increasing

occurrence of different diseases such as cancer, diabetes, hypertension, and asthma. Antioxidant

peptides are produced from different dietary proteins which provide defense against oxidative

stress. Soybean meal is a byproduct of vegetable oil Industry. Solid state fermentation of soybean

meal by Bacillus subtilis subsp. subtilis was used to produce antioxidant peptides at 30 °C under

appropriate humidity within 72 h incubation time. Antioxidant activity was measured by radical

scavenging test using DPPH (2, 2-diphenyl-1-picrylhydrazyl). The results indicated greater than

82% radical scavenging property in fermented soybean meal.

Keywords: Antioxidant peptides, Soybean meal, Bacillus subtilis, Scavenging activity, Solid

state fermentation.


Theoretical design of a new vaccine for multiple sclerosis (MS)

Karim Mahnam1, Nasrin Payab1, Mohsen Mobine Dehkordi2, Mostafa Shakhsi-Niaei2

1. Biology Department, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.

2. Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran.

Abstract

Multiple sclerosis (MA) is an autoimmune demyelinating disease targeting the human central

nervous system. It is believed that the activation of T cells reacting with the CNS antigens is the

first autoimmune event in MS. MOG and MBP are the myelin sheath proteins and highly

pathogenic antigen epitopes involved in immune response. Today, more researchers are looking

for drugs with high specificity to function on the immune system. Tolerogenic vaccines are a

new class of drugs that reduce the immune response to the MS antigens by presenting the

associated antigens. This study aims to model a fusion protein vaccine using the combination of

MOG(1-20) and MBP(147-166) linked to interlukine-16 and examine its antigenic properties. For this

propose at first model MOG(1-20) linked to MBP(147-166) was made by modeler 10 and. The best

obtained model connected to C-terminal domain of IL-16 and was used for 10 ns molecular

dynamics simulation via Gromacs 5 package. Also free MOG and MBP antigens were simulated

separately for 10 ns. The results revealed that the solvent accessible surface areas of MOG and

MBP epitopes are almost the same in both free and in fusion protein. Then we can conclude that

this fusion protein preserve antigenic property of MOG and MBP epitopes.

Keywords: Multiple sclerosis, Vaccine, Fusion protein, Protein engineering, Molecular dynamics

simulation.


The effect of temperature on the formation rate of liposome of

DSPC and CHOL by coarse-grained molecular dynamics

simulations studies

and Majid Taghdir parchekanichoozaki Jalil

Faculty of Biological Science, TarbiatModares University, Jalal Ale Ahmad Highway, P.O.Box: 14115-111, Tehran,

Iran

.

Abstract

In general, the importance of liposomes in medical and pharmaceutical can be divided into two

areas of treatment and diagnosis of diseases. The application of liposomes as a tool, a model or a

reagent in basic research such as cell interactions, cognitive processes is notable. The stability of

liposomes containing pharmaceuticals are also very important and heavily influenced by the type

of their phospholipids and the general composition of phospholipids that are more unsaturated.

Based on thermodynamic concepts and chemical-physical properties of phospholipids these

molecules in aqueous media tend to that form vesicle structures. In this study coarse-grained

simulations were done at different temperatures to simulate the liposome DSPC and CHOL. The

structure analysis showed that the liposomes is formed as well as.The further analysis showed

that temperature has an important effect on the formation rate of liposomes.These results showed

that the formation of the liposome in higher rate is happen in higher temperature. These findings

revealed that the temperature tune the balance of van der waals and electrostatic interactions in

the formation of liposome.

Keywords: Self-assembled liposome, Liposome stability, Temperature effect, Coarse-grained

simulations.


Purification of sugar beet pulp induced pectinase from P. indica by

chitosan-PVA magnetic beads

ParisaFathi Rezaei1, Somayeh Kiani1, Saleh Shahaabivand1, Gholamreza Mahdavinia2

1Department of Biology, Faculty of Science, University of Maragheh, Maragheh, Iran. 2Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.

Abstract

Pectinases or pectinolytic enzymes are one of the upcoming commercial enzymes that are

produced by higher plants and microorganisms such as fungi, bacteria, yeasts. These enzymes

have a wide range of industrial applications including fruit processing, tea and coffee

fermentation, in paper and textile, waste water treatment and plant oil extraction. Pectins are

complex polysaccharides which present in cell wall of plants and degraded by pectinase to

simple substances such as galacturonic acid. Because of the vast industrial applications of

pectinases, all over the world many groups are searching to find new efficient methods for

purification and immobilization of pectinase. In line with other attempts, here the efficiency of

chitosan-PVA magnetic beads for purification of P. indicaproduced pectinase was evaluated.

Sugar beet pulp (SBP) as a by-product of sugar factory was used to induce production of

pectinase by P. indicain submerged fermentation. For this reason, P. indica was cultured on

Kaefer medium supplemented with SBP. The slurry was filtered by centrifugation at 10,000 rpm

at 4 ºC for 15 min. Then the supernatant was incubated with chitosan-PVA magnetic beads at 4

ºC overnight with continues shaking. The enzyme was desorbed from magnetic beads by 0.5 mM

CaCl2 (PH= 5.9). The protein content of samples was determined by Bradford assay. Based on

the results, the protein content of the solutions treated with chitosan-PVA magnetic beads was

increased significantly. In conclusion, chitosan-PVA magnetic beads could be a good candidate

to purify pectinase, but further optimization is required.

Keywords: Piriformosporaindica, Pectinase, Pectin, Sugar beet pulp, Chitosan-PVA magnetic

bead.


Investigating the role of DADLE on 6-OHDA-induced cell toxicity in

human neuroblastoma cells SH-SY5Y as an in vitro model of

Parkinson’s disease

Elham Pooresmaeili-Babaki, Saeed Smaeili-Mahani, Mehdi Abbasnejad

Department of Biology, Faculty of Sciences, ShahidBahonar University of Kerman, Kerman, Iran.

Abstract

Parkinson’s disease is a common neurodegenerative disorder characterized by the loss of

dopaminergic neurons in the substantia nigra pars compacta and the accumulation of

proteinacousintraneuronal inclusions known as Lewy bodies. Pharmacologic treatment of PD can

be divided into symptomatic and neuroprotective therapies. DADLE ([D-Ala2, D-Leu5]-

Enkephalin) is a syntheticopioid peptide with analgesic properties. It prevents and reverses

methamphetamine (METH)-induced damage of dopaminergic terminals of brain. It prevents

naltrexone-sensitive PC12 cell apoptosis in serum deprivation conditions. Thus, it might play an

essential role in the survival of neurons and organs.Therefore, the present study was designed to

investigate the effects of DADLE on 6-OHDA-induced SH-SY5Y cells toxicity as an in vitro

model of Parkinson disease. To induce cell toxicity, the SH-SY5Y cells were treated with 150

µM 6-OHDA. In treatment groups, different doses of DADLE (1, 5, 10 and 50 μM) were used to

investigate its possible protective mechanisms. Cell toxicity was determined by MTT assay.The

results suggested that DADLE doesn't have any neuroprotective effects against 6-OHDA-

induced apoptosis in dopaminergic cells.

Keywords: DADLE, MTT assay, 6-OHDA, SH-SY5Y cell.

https://en.wikipedia.org/wiki/Chemical_synthesis

https://en.wikipedia.org/wiki/Chemical_synthesis

https://en.wikipedia.org/wiki/Analgesic


Interactions of β-lactoglobulin with Lovastatin

Asghar Ali Asghar, Rategari Isfahani -Zeini, NajafabadiFerdos-Pouresmaeili

Department of Molecular and Cell Biochemistry, Islamic Azad University, Flavarjan, Iran.

Abstract

The major protein in bovine milk whey, 𝛽-Lactoglobulin (𝛽-LG), has several binding sites for

ligands. The biological function of 𝛽 − 𝐿𝐺 is not clear, but its potential role in carrying fatty

acids through the digestive tract has been suggested. 𝛽-LG has been found in complexes with

lipids such as butyric and oleic acids and has a high affinity for a wide variety of compounds.

Lovastatin (Lvt), is an important anticholesterolemic drug which inhibits the conversionof HMG-

CoA to mevalonate in the biosynthesis of cholesterol. In this study, the interaction of Lvt with 𝛽-

LG was investigated using circular dichroism (CD) and UV–vis spectroscopic. The results of

UV–visshowedincrease in absorbance during its interaction with Lvt and this ligand interacts

with 𝛽 -LG forming equimolar complexes. The binding and thermodynamicparameters were

calculated. Hydrophobic interactions were proved to play significant role in theinteraction of Lvt

with 𝛽-LG. According to far- and near-UVCD results, this ligandhas no apparent influence on 𝛽-

LG secondary structure, however they partially destabilize its tertiary structure.

Keywords: β-lactoglobulin, Lovastatin, Circular dichroism, UV-vis spectroscopy.


Efficient synthesis and purification of buserelin acetate

Somayeh Ahadi1, Samane Poursan1, Saeed Balalaie1,2

1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Abstract

Buserelin Acetate (Brand name: Suprefact®) is a potent luteinizing hormone releasing hormone

(LHRH) and (GnRH) agonist analogue, that is categorized as antineoplastic drugs. It is used for

men, to lower levels of testosterone which is the palliative treatment of advanced (metastatic)

prostate cancer. Buserelin acetate works by blocking the production of testosterone that reduces

the growth and reproduction of prostate cancer cells. In women, it lowers levels of estrogens and

progesterone and has been studied as a treatment in estrogen receptor positive breast cancer.

Buserelin acetate is administered by subcutaneous injection or as a nasal solution. Herein, we

report an efficient novel approach based on the use of suitable protected amino acid and the type

of deprotection methods to access the pure product. The synthesis was done based on SPPS

method and Fmoc protected amino acids. The structure of buserelin acetate was confirmed based

on HRMS (ESI) data.

Keywords: Buserelin acetate, LHRH analogue, FH, FSH.


A thermodynamic approach of the interaction between human

serum albumin and a new synthesized platinum complex

Atefeh Poursoleiman1, Adeleh Divsalar2, Ali Akbar Saboury1, MahboubeEslami Moghadam3



3Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran.

Abstract

Human serum albumin (HSA) can interact, reversibly or irreversibly with macromolecules such

as proteins, drugs, smaller organic compounds and inorganic ions. Platinum-based drugs are

frequently used in the clinical practice to treatment of various cancers. Because of some serious

side effects in these complexes, we are looking for other platinum complexes with lower toxicity.

In this study, we investigated the binding properties of a new platinum complex (Pt (NH3)2) Gly-

Amyl) as an anti-cancer compound to HSA under simulative physiological conditions via

spectroscopic techniques of fluorescence and circular dichroism (CD). Results of fluorescence

study showed that the considerable quenching in intrinsic fluorescence of HSA upon binding of

this complex. The values of binding constant (Ka) and the corresponding numbers of binding

sites (n) measured according quenching methods, respectively. In addition, far-UV-CD results

show that this complex did not induce any significant changes in the secondary structure of HSA.

These findings provide a molecular-level understanding of complex-HSA binding interactions,

which can be used as a useful guideline for further drug design.

Keywords: Anti-tumor component, Platinum complex, Human serum albumin, Fluorescence.


Computational analysis of miR-423 mediated drug response in

breast cancer

Nadia pourmoshir and SadeqVallian

Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR Iran.

Abstract

MiRNAs play a significant role in pharmacogenomics by down-regulating genes that are

important for drug function. These interactions can be described as triplet sets consisting of a

miRNA, a target gene and a drug associated with the gene. In the present study we aim to

investigate the association of miR423 expression and cyclophosphamide function by combining

data on miRNA targeting and protein-drug interactions. In this study, miR-423 targeting

information was derived from miRanda database and information of cyclophosphamide and

cdkn1a were obtained from drug bank and PDB databases, respectively. Then, cdkn1a-

cyclophosphamide interactions were annotated by PharmGKB database. Finally, all the data

were investigated and validated by Pharmaco-miR database. The data showed that miR-423

could inhibit CDKN1A expression, which functions as a master downstream effector of tumor

suppressors. Together, a miRNA, a target gene and a drug that interacts with the product of the

target gene, form a miRNA pharmacogenomics set.

Keywords: MiR-423, Drug response, Breast cancer.


Evaluation of dioxin contaminations in fish oil samples by

bioluminescence method

ElnazTajabadiEbrahimi, Saman Hosseinkhani, Farangis Ataei, ElhamTahmasbi

Department of Biochemistry, Faculty of Biological Sciences, TarbiatModares University, Tehran, Iran.

Abstract

In determination of contaminants (dioxins, polychlorinated biphenyls, polyaromatic

hydrocarbons), cell-based assays are useful methods for screening purposes: they are mainly

characterized by high sample throughput and lower costs than Mass Spectrometry (MS)-based

methods. Cell-based assays are highly sensitive for the determination of dioxins. Fish oil has

been identified as one of the most important contributors to the levels of polychlorinated

biphenyls (PCBs) in food and feed products. In this study dioxins are extracted from fish oil by

an extraction solution of 97% Hexane and 3% Diethyl ether. An ultrasonic process is used to

ensure intimate contact of the matrix with the extraction solution. Then, the extracted sample is

passed on an activated silica gel column, resulting in the purification of dioxin, which can be

exposed on dioxin responsive-chemically activated luciferase gene expression cells. The cells are

incubated for 24 hour at 37⁰C with 5% CO2. After incubation, the cells are lysed with lysis

reagent and luciferase activity is measured. Upon exposure to dioxin-like compounds, the cells

express luciferase in a dose-dependent manner. The measured luminescence resulting from

exposure to a chemical or chemical mixture is converted into a bioassay toxic equivalency value

by the direct comparison of the response for a given sample to a dose-response curve obtained

with 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin).

Keywords: Dioxin, DR-CALUX, Fish oil, Bioluminescence.

Rashid

Highlight


Characterization of electrospun gelatin nanofibers crosslinked with

tannic acid

Elham Tavassoli-Kafrani1, Sayed Amir Hossein Goli1, Milad Fathi1, Asghar Taheri-Kafrani2

1Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan

84156-83111, Iran.

2Department of Chemistry, Laboratory of Biophysical Chemistry, University of Isfahan, Isfahan 81746-73441, I.R.

Iran.

Abstract

This work was aimed to prepare crosslinked electrospun gelatin nanofibers. As a natural phenolic

compound, tannic acid was used to crosslink gelatin and subsequently electrospinning was

fabricated using acetic acid/ water mixture (60:40) as solvent. The properties of gelatin solution

were characterized measuring electrical conductivity, viscosity, and surface tension. The

prepared gelatin fibers were analyzed by SEM, DSC, and FTIR tests. Electrical conductivity and

viscosities of crosslinked gelatin solutions were both higher than that of non-crosslinked gelatin

solution and surface tension showed no major difference. Using SEM, crosslinked gelatin was

determined to maintain fiber morphology. However, the fiber mean diameter showed an increase

in crosslinked samples in comparison to non-crosslinked gelatin nanofibers. FTIR spectra

revealed that tannic acid probably interacted with C-N-C groups of gelatin molecules and DSC

analyses proved that crosslinking led to an increase in thermal stability of gelatin nanofibers.

Keywords: Electrospinning, Gelatin, Tannic acid, Crosslinking.


Kinetics and spectrofluorimeteric the studies of catalase in presence

of spermidine

Fateme Tavakoli Chalespari and Behzad Shareghi

Department of biology, Faculty of science, University of shahrekord, P. O. Box 115, Iran.

Abstract

Catalase (CAT) is one of the most important enzymes of antioxidantdefense systems, which

could protect cell againstoxidative stresses induced by reactive oxygen species. Catalase is an

oligomeric enzyme (MW=240000Da) with four identical subunits.In this study, the effects of

different concentrations of spermidine was investigated on the catalytic activity of catalase by

using spectrophotometer (UV-Visible) at pH=7.4 and 370C. Moreover, we used fluorescence

spectroscopic method for investigating the changes in tertiary structure of enzyme at different

temperatures based on the changes in intrinsic emission. The kinetic parameters of the enzyme

activity showed that the increased concentrations of spermidine lead to decrease in the enzyme

activity as a non-competitive inhibitor. In addition, fluorescence data represented the decreasing

in intrinsic emission of enzyme with increase inspermidine concentrations, which indicates that

changeshave been done at three dimensional environments around the enzyme chromophores.

These results demonstrated that fluorescence quenching of spermidine occur through a static

mechanism. The thermodynamic data suggested that electrostatic interactions were the

predominant intermolecular forces in the binding reaction.

Keywords: Catalase, Spectrophotometer, Spectrofluorimeter, Spermidine.


Effect of TiO2 nanoparticle on structural stability and activity of

catalase

Fateme Tavakoli Chalespari and Behzad Shareghi

Department of biology, Faculty of science, University of shahrekord, P. O. Box 115, Iran.

Abstract

Catalase, is an important antioxidant enzyme that has numerous industrial and medical

applications. TiO2 nanoparticles, the most widely used metal oxide nanoparticles, have been

increasingly employed in a variety of industrial applications. These lead to increasing human

exposure and to affecting human health and the environment. As a result the study of interaction

between enzyme and nanoparticles is important. In this experimental study, the alterations in

catalase activity were measured in the absence and the presence of different concentrations of

TiO2 nanoparticle by using spectrophotometer (UV-Visible) at pH=7.4 and 370c. Moreover, we

used fluorescence spectroscopic methods for investigating the changes in tertiary structure and

binding properties of enzyme at different temperatures based on the changes in intrinsic

emission.Analyzing the kinetic of the enzyme showed that increasing the concentrations of TiO2

lead to decrease in the enzyme activity. TiO2 acts as un-competitive inhibitor. In addition,

fluorescence data represented the decreasing in intrinsic emission of enzyme in the presence

ofTiO2 nanoparticle, which indicates that the environment of tryptophans changed. This result

demonstrated that the static type of quenching mechanism is involved in the intrinsic quenching

of enzyme on TiO2.

Keywords: Catalase, Kinetic parameter, Intrinsic quenching, TiO2 nanoparticle.


Separation and precipitation of β –lactoglobulin from commercial

whey preparations by NaCl salting out at low pH

Rezvan Kazemi, Reihaneh Kordsedehi, Asghar Taheri-kafrani


Abstract Whey is a by-product of cheese production process that its proteins (wp) have many valuable

functional properties such as foaming and emulsifying ability or gel formation. Cheese

production on an industrial scale causes to produce a large volume of whey. WP, well known for

their nutritional value and versatile functional properties, are widely utilized in the food industry.

WP provides health benefits to humans of all ages by providing specific bioactive components.

The most important of whey protein is β –lg which constitute 48-58 %. (wt) and its

characteristics prevail over the other ones and significantly define the properties of whey.

Technologies currently used for β –Lg isolation combine methods of ion-exchange

chromatography, enzymatic hydrolysis, complex formation, precipitation, electrodialysis and

membrane separation. Although these fractionation techniques can provide effective protein

precipitation at the laboratory scale, most have not been widely implemented for commercial

scale because of their relatively high cost complexity, low productivity, poor selectivity and/or

unacceptable denatured products. The objective of this study was separation of β –Lg fractions

from the other whey proteins, without heat denaturation in both fractions, by a salting out

procedure suitable for scaling up and compatible with food industry requirements. It has been

showed that the greatest protein contents were obtained using salt treament methods.

Keyword: Whey, WP, Precipitation, β –Lg.


Proteins and peptides in camel milk

Mohammad Rabbani Khorasgani and Reihaneh Amini

Department of Biology, Faculty of Sciences, University of Isfahan.

Abstract

Camel milk is an important nutrientin some countries and it has many valuable ingradients with

benificient nutritional, immunological and growth effects. In this article some impotant proteins

and peptids of camel milk are presented as the following: Casein (CN): It is the major protein in

camel milk and the β-CN is the main camel milk casein. Camel milk is similar to human milk in

that it contains a high percentage of β -CN; this high percentage could reflect its higher

digestibility rate and lower incidence of allergy induction in the gut of infants. Glycine and

cystine were found to be significantly lower in dromedary milk caseinCompared to bovine's

milk.Camel milk κ-CN was reported to contain an extra proline residue in its sequence (Pro95).

This additional proline residue is expected to play an important role in the stability of camel milk

κ -CN sequence compared with bovine milk κ –CN sequence .Other properties of camel milk

proteins (casein and whey proteins) compared to bovine milk :- lower electrophoretic mobility,

higher molecular size, broader size distribution of casein particles, more of average micelle

diameter, higher quantity of whey proteins ,higher heat stability and a lower degree of hydrolysis

after reaction with pancreatic enzymes.Whey: antimicrobial agents : Camel milk was reported to

have an antimicrobial effect against gram positive and gram negative bacteria, this inhibitory

activity was attributed to the presence of antimicrobial substances such aslysozyme, hydrogen

peroxide, lactoferrin, lactoperoxidase and immunoglobulins .Other components :Camel milk

whey contains other main components such as serum albumin, and peptidoglycan recognition

protein andinsulin like protein. The intake of camel milk reduced the excessive need for insulin

whichcan help in regulating the blood glucose levels. It is hoped to progress research about

camel milk and beneficial uses of it for human health.

Keywordes: Camel milk, Proteins, Peptides, Casein.


Efficient synthesis and purification of octreotide acetate as a

somatostatin agonist analogue

Fatemeh Baghestani1, Sorour Ramezanpour1, Ali Nikbakht1, Saeed Balalaie1, 2

1Peptide Chemistry Research Center, K. N. Toosi University of Technology, P. O. Box 15875-4416.

Tehran, Iran. 2Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.

Abstract

Pharmaceutical peptides are known as natural drugs with superior characteristics such as high

target affinity, low side effects. Due to these characteristics, they gained a major interest for their

synthesis. Octreotide is an octapeptide that mimics natural somastostatin pharmacologically,

though it is a more potent inhibitor of growth hormone, glucagon. Meanwhile, there are some

radiopeptide based on octreotide.A distinguished point of this compound is the presence of

disulfide bridge in its structure. Recently, it was shown that the number of disulfide bridge in the

structure of peptides has an important role in their activities. In continuation of our research for

the developing of the know-how for the synthesis of pharmaceutical peptides, and especially the

peptides with disulfide bondwe wish to report the synthesis of octreotide acetate as active

pharmaceutical ingredient (API). Octreotide acetate was synthesized through solid phase peptide

synthesis(SPPS) approach, after cleavage, disulfide bridge was introduced followed by final

deprotection, the crude peptide was purified using preparative HPLC.The structure of product

was approved using HR-MS(ESI) data.

Keywords: Somastostatin analogue, Disulfide bridge, Radiopeptide.


Optimization of carbon source for phytase production in submerged

fermentation of a strain of Aspergillus niger and comparison of

enzyme activity between immobilized and free spores

Atefeh Hamzeh 1, Jamshid Fooladi 1, FakhriSadat Hosseini 2

1 Laboratory of Industrial Microbiology, Faculty of Biology, AlzahraUniversity, Tehran, Iran.

2 Faculty of Biology, Alzahra University, Tehran, Iran.

Abstract

The main storage form of phosphorous in plant seeds is Phytic acid (Lopez et al, 2002).6

phosphate groups allow phytate to form complexes with multivalent cations (Dost and Tokul,

2006) and proteins. Therefor phytic acid as an anti-nutrient factor creates various digestion

problems. Phytase is an enzyme that is able to hydrolyzephytic acid and releases inorganic

phosphate and increases bioavailability of minerals. Simple stomached animals have no or very

little amount of this enzyme (Gargova et al.2002). Excreted phytate can be decomposed in soil

and causes environnmental problems.We examined submerged fermentation of Aspergillus niger

for phytase production. Media prepared according to a report (Gonita and Mishra, 2013) but with

4 different carbon sources: glucose 1 %, Malt extract 1%, molasses 1%and sucrose 1 %. The best

carbon source was used for submerged fermentation for comparison between immobilized and

free spores. Then immobilized spores of this study were used for another submerged

fermentation with wheat bran 1 % but without using sodium phytate. Enzyme activity was

determined according to the methodexplained by Engelen et al. (1994). Among 4 differrent

carbon sources,Malt extract 1% had the maximum phytase activity and glucose had minimum

activity because of its inhibitory effect. Vats and Banerjee reported glucose inhibition in 2002.

The immobilized spores indicated higher phytase activity than free spores.Furthermore

immobilized spores in the second media (wheat bran 1 %) showed the maximum phytase

production after 96 hours; therefore wheat bran induced phytase production in immobilized

spores.

Keywords: Phytase ,phytic acid , Submerged fermentation , Aspergillus niger, Immobilization.


An investigation on the structure and function of the cell surface

prostate-specific antigens for development a new generation of

immunotoxins

Mohammad Rastegar Moghadam Baghestani1, Aliakbar Haddad-Mashhadrizeh2, Javad Baharara3

1Department of Biology, Science and Research branch, Islamic Azad University, Khorasan Razavi, Neyshabur, Iran.

2 Celland molecular biotechnology research group, institute of biotechnology, and Department of Biology, Faculty

of Science, Ferdowsi University of Mashhad, Mashhad, Iran.

3 Department of Biology, Mashhad Branch, Islamic Azad University.

Abstract:

Prostate cancer, which is originated from malignancy in prostate tissue, is one of the most

common types of cancer among men. This type of disease, which in the past 20 years is one of

the basic factors of death in the men of the society, led to serious attention for development

prognostic and therapeutic approaches in the health system. Among these strategies,

immunotoxinstherapy with the ability to target specific cancer cells, have momentous position.

However, the development of this type of medication is required to the characterization of the

cancer cell specific antigens. Bearing in mind, cell surface prostate-specific antigens profiling as

well as characterization of them were considered in this study. In this regard, at the first step 15

specific antigen of prostate tissue was collected based on literature review. In-silico expression

assay of the selected antigens were performed via proteinatlas program, on the several of

cancerous and non-cancerous tissue. The nucleotide and protein sequences as well as 3D

structure of the selected antigens were extracted from related databases. Meanwhile,

corresponding ligands of the selected antigens were detected by String, and then evaluated based

on binding assays via Clusproprograms. The results of this research led to reveal some cell

surface prostate-specific antigenswith high expression on the prostate malignancies including

PAGE3, KDM5D, FOLH1as key targets for immunotoxins development of this type of

cancer.On the other hand, among of the 40 kinds of corresponding detected ligandsof these

antigens, HPA062248, HPA049086, HPA010593, HPA000764 with high binding affinity, short

in length and limited in post-translational modification raised as favorable candidate for the

development of this type of medication. However, this capacity would be evaluated after

designing and simulation of the newimmunotoxins in laboratory conditions, which are

considered in our group.

Keywords: Cancer, Prostate, Immunotoxins, Antigen, Ligand.


A comparative study of effects of canola meal bioactive peptides,

antibiotic, probiotic and prebiotic on growth performance, some

blood parameters, intestinal morphology and gut microflora in

broiler chicks

Sadegh Karimzadeh, Mansour Rezaei , Asadolah Teimouri Yansari

Department of Animal Sciences, Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences

& Natural Resources.

Abstract

The aim of the present study was to evaluate the effects of canola meal bioactive peptides (CBP)

produced by enzymatic hydrolysis of canola meal, antibiotic (Virginiamycin®), probiotic

(Bactocell®) and prebiotic (Agrimos®) on growth performance, some blood parameters, gut

microflora and intestinal morphology of broiler chicks. A total of 200 one-day-old Ross 308

male broiler chicks were randomly allocated to 5 dietary treatments with 4 replicates of 10 birds

per each. Birds were fed with a basal diets (Control), 250 mg CBP/kg, 200 mg antibiotic/kg,

0.01% prebiotic and 0.1% probiotic for a 42 d feeding trial. Results indicated that addition of

CBP and probiotic diet increased (P<0.05) body weight gain (BWG) and decresed feed

conversion ratio (FCR) (1-28 d, 29-42 and 1-42 d) (P<0.05). In comparison to the other group,

adding CBP diet improved serum total protein, phosphorus and calcium concentrations (P<0.05).

Also, adding CBP to diet decreased serum cholesterol and triglyceride concentrations (P<0.05).

The villus height, the ratio of villus height to crypt depth of duodenum, jejunum and ileumin in

chicks fed by CBP and probiotic increased and crypt depth significantly decreased (P<0.05).

Adding CBP and probiotic decreased gram negative bacteria’s counts in ileum and caecum

compared to the control group. Results of the present study suggested that CBP probiotic might

use as a functional additive in broiler chicks diet.

Keywords: Canola meal Bioactive Peptides, Probiotic, Prebiotic, Performance, Some blood

Parameters, Intestinal morphology, Broilers.


The investigation of stability of functionalized alkyl-peptide self-

assembly innanofiber form by molecular dynamics simulation

Havva Mehralitabar, Majid Taghdir, Hossein Nadrimanesh

Faculty of Biological Science, TarbiatModares University, Jalal Ale Ahmad Highway, P.O.Box: 14115-111, Tehran,

Iran.

Abstract

The design of amphiphilic alkyl-peptides which can assemble into architectures like nanofiber

and liposomes is applicable in the field of tissue engineering and drug delivery. Nanofiber

formatted fromalkyl-peptidescan reorganize hydrogelswith different physical properties to

mimicthe extracellular matrix of different types of tissues. The aim of this research is to

investigate the stability of the nanofiber structure of alkyl-

peptideFAQRVPPEEEGGGAAAAK(C16) which is functionalized by the sequence of

FAQRVPP with the property of differentiating of neural stem cell to neurons. The all atom

molecular dynamic (MD) simulation applied to simulate a pre-constructed structure of nanofiber

with radially arranging of 9 alkyl-peptides in one layer and 16 numbers of those layers in one

cylindrical structure. The result of 50 ns simulation by Amber package showed that this

functionalized alkyl-peptides cannotconstruct stable structures in fiber form andis broken to two

smaller micelles likeshape. So that it can be proposed, space prevention of bulky structure of

functional group in alkyl-peptide causes the disruption.Therefore, selection of longer alkyl chain

to have a balance between hydrophobic and hydrophilic forces in the fiber or choosing a

combination of functionalized and non-functionalized alkyl-peptide in fiber structure to reduce

the space prevention of functional group in fiber surfacecan increase the stability.These

findingscan help to design the fiber structures with deferent softness or stiffness.

Keywords: Alky-peptide, Self-assembled nanofiber, Tissue engineering, Softness, Stiffness.


Beta keratin solubilization: a new method for blocking sulfydryl

groups

Fateme Rezaei Sadrabadi and Zahra Moosavi-Nejad


Abstract

Feathers are rich sources of beta keratin which are important byproducts of poultry industries

causing environmental disposal problems. Feather is made up of 90% protein which keratin is its

main protein. Due to the highly crosslinkes, it is the fibrous protein, therefore it is resistant to

proteolytic enzymes and has high mechanical stability. Keratinouse materials have been

considered due to essential qualities such as, inherently biocompatibility, biodegradability,

mechanical resistance and frequency. In the present study proteins of feather are dissolved by

urea and β-mercaptoethanol. To prevent aggregation of protein, cysteine residues blocked with

some blocking agent such as iodoacetamide, iodoacetic acid and bromosuccinic acid. In the

present study iodoacetamide and H2O2 were used as blocking agent. After dialysis, the qualities

of antioxidant and the chelating ability of extracted protein were tested by 2, 2-diphenyl-1-

picrylhydrazyl (DPPH) radical scavenging ability and metal chelating assay. 2, 2-diphenyl-1-

picrylhydrazyl radical scavenging abilities of feather keratin that blocked with iodoacetamide

and H2O2 81.71% and 87.78% respectively. Fe2+-chelating ability oftheir was 82.74%

and78.36% respectively. According our results, hydrogen peroxide can be introduced as a

cheaper and more accessible blocking agent for preparing keratin solution.

Keywords: Keratin, Iodoacetamide, H2O2, DPPH, Metal chelating ability.


Antioxidant and metal chelating ability of feather keratin

Fateme Rezaei Sadrabadi and Zahra Moosavi-Nejad


Abstract

Feathers are rich sources of beta keratin which are important byproducts of poultry industries

causing environmental disposal problems. Feather is made up of 90% protein which keratin is its

main protein. Due to the highly crosslinkes it is the fibrous protein, therefore it is resistant to

proteolytic enzymes and has high mechanical stability. Keratinouse materials have been

considered due to essential qualities such as, inherently biocompatibility, biodegradability,

mechanical resistance and frequency. In the present study, feather proteins were dissolved by

urea and β-mercaptoethanol at the temperature of 50 o C. After dialysis, the quantities of

antioxidant and the chelating ability of extracted protein were measured by 2, 2-diphenyl-1-

picrylhydrazyl (DPPH) radical scavenging ability and metal chelating assay respectively. 2,2-

diphenyl-1-picrylhydrazyl radical scavenging abilities of feather keratin was 79.21 % and its

Fe2+-chelating ability was 92.06 %. Therefore the feather protein can be used as a cheap

antioxidant and reducing agent without any digestion.

Keywords: Keratin, DPPH, Antioxidant ability, Chelating ability.


Binding of carbon nanotube to carcinoembryonic antigen: A the

oretical approach

Behafarid Ghalandari1,2 and Nazila Eyvazzadeh1,2

1Radiation Research Center, Faculty of Paramedicine, AJA University of Medical Sciences, Tehran, Iran.

2Department of Radiology, Faculty of Paramedicine, AJA University of Medical Sciences, Tehran, Iran.

Abstract

The overexpression of characteristic proteinsin cancer cells provide an opportunity for early

diagnosis of cancer. Among them carcinoembryonic antigen (CEA) is a well-known biomarker

for colorectal cancer diagnosis. On the other hand, the remarkable physicochemical properties of

single walled carbon nanotubes (SWCNTs) make them as one of the most promising materials

for applications in the fast electrochemical technique of biomarker sensing. In addition, SWCNT

is a good candidate for biomarker detection whereas it has complementary structure with

proteins. In this study, the ability of SWCNT with low diameter was investigated as a detector

for CEA. The computational study on CEA/SWCNT system was performed using Gaussian 98

program based on HF method of ab initio at theoretical level of 6-31G basis set at temperature of

25°C. The physical properties of interaction such as predominant binding force, charge

distribution and interaction energy have been investigated. The results show that SWCNT

interaction with CEA has minimum value of interaction energy and electrostatic interaction has

effective role in place of interaction. The results also show significant changes in electrochemical

properties such as charge distribution, dipole moment and polarity of CEA that are detectable

and measurable variables in presence of SWCNT. So, SWCNT with low diameter is a suitable

electrochemical sensor especially for CEA detection and measurement. As a result, this study

develops electrochemical sensorspresence in the early diagnosis of colorectal cancer.

Keywords: CEA, SWCNT, ab initio, Electrochemical properties.


Peroxynitrite-modified human α-Crystallin subunits indicate

improved chaperone-like activity and enhanced protection against

copper-mediated ascorbic acid oxidation

Maryam Ghahramani and Reza Yousefi


Abstract

Ascorbic acid (ASA) plays an important function to protect lens crystallins against oxidative

damages. In the cataractous lenses and during ageing, the increased lenticular level of copper ion

catalyzes, to important level, the conversion of ASA into dehydroascorbate and hydrogen

peroxide (H2O2) which are potentially two important modifying agents of lens proteins. This

study was performed with the aim to assess the structure, chaperone-like activity and protective

ability of peroxynitrite-modified human α-Crystallin subunits in a copper-mediated ASA

oxidation system. Depending on the extent of modification, αA- and αB-Crystallin display an

improved chaperone-like activity and enhanced protective ability against copper-mediated ASA

oxidation. Also, chaperone-like activities of both native proteins and their peroxynitrite-modified

counterparts were increased in the presence of copper ions. In addition, peroxynitrite

modification induced significant changes in structure of the recombinant proteins. Overall, the

enhancement of chaperone-like activity and the increase in ASA protective ability of human α-

Crystallin subunits upon peroxynitrite modification may suggest a new beneficial effect for this

oxidative and nitrative agent in the ocular system.

Keywords: α-Crystallin, Peroxynitrite, Copper ion, Ascorbic acid, Chaperone-like activity.


Investigation the use of plants as host for protein production

Fereshteh Enami Mehmandoost and Hasan Mohabatkar


Abstract

Most bacteria cannot proceed post translational modification properly and this is the reason for focusing

on plant hosts. Also, it reduces the cost of production, this procedure has high efficiency, for example

efficiency of Avidin production in a cluster of maize is higher than a tone of egg, the main aim of

pharming is production with high efficiency. The best plant for commercial use, is tobacco .The reason is

that this plant is well-established for gene transfer and expression, high biomass yield, prolific seed

production and the existence of large scale processing infrastructure. Alternative leafy crops that are

being investigated for pharming include: alfalfa, soybean, lettuce. The possibility of storage in room

temperature makes it more attractive in order not to waste energy. Fruits are major systems for production

of recombinant vaccines and antibody designed for topical application especially potatoes then it can be

replaced by tomato, banana, carrot, lettuce, maize, alfalfa and spinach. Because they are more palatable

than potato. Todays, maize can be used for Avidin, beta glocuronidase and trypsin production the

protein/recombinant protein production can be produced compatible with vermicular plants of each area.

This study compares different ways of transferring gene, growing efficiency in different plants. Also, it

considers ways to minimize potential risks for environment.

Keyword: Protein production, Different plant, Efficiency, Vaccine, Recombinant protein.


Immobilization of human serum albumin on modified graphene

oxide nanosheets

Faransak Jafarian and Abdol Khalegh Bordbar


Abstract

Graphene oxide (GO) was prepared by a modified Hummers method and functionalized by (3-

mercaptopropyl) trimethoxysilane and used for covalent immobilization of human serum

albumin (HSA). The immobilization was carried out by the site-specific covalent binding

between thiol groups of HSA and thiol sulfonate groups on modified GO.The structure of the

prepared nanosheets were characterized by X-ray powder diffraction (XRD). The immobilization

was confirmed by Fourier transform infrared spectroscopy (FT-IR). XRD analysis showed that

the binding process has done no phase change in GO.FT-IR proved the formation of such

GO−O−Si bonds. 2 hour was determined as the optimal time for immobilization and the

maximum amount of immobilized protein was 34.8 mg per gram of support.

Keywords: Immobilization, Graphene oxide, Nanosheets, Human serum albumin.


A combined spectroscopic and molecular docking approaches to

probing binding of daidzein to β-lactoglobulin

Parisa Hatami, Najme .Fani, Abdol Khalegh Bordbar


Abstract

In the present study, the molecular mechanism of daidzein binding to β -lactoglobulin (BLG)

(variants A and B) was investigated by fluorescence quenching, absorption spectroscopy and

molecular docking procedures. Analysis of spectrofluorimetric titration data represented the

formation of 1:1 complex, significant binding affinity, negative value of enthalpy change and

positive value for entropy change and the essential role of hydrogen bonding and van der Waals

interactions in binding of daidzein to BLG. The value of determined Förster΄s distance represents

the static mechanism for quenching of BLG by daidzein. The results of fluorescence competitive

binding expriments characterize the location of daidzein binding site in the outer surface of BLG.

Molecular docking study showed that daidzein binds in the outer surface site of BLG which is

accompanied with some hydrogen bonds. The support of molecular docking results by

biochemical fluorescence experiments confirms the validity of docking calculation.

Keywords: β -lactoglobulin, Daidzein, Fluorescence quenching, Molecular docking,

Thermodynamics parameters.


VEGF-A epitope prediction aim to exploiting in angiogenesis

stimulation in order to tissue restoration using magnetic

nanoparticles Sadegh Khorrami and Hasan Mohabatkar

Faculty Of New Sciences & Technology, University Of Isfahan.

Abstract

Vascular endothelial growth factor was discovered in 1987. Different isoforms of each VEGF

molecule are generated by alternative splicing mechanism. In the meantime VEGF-A is a

dimeric glycoprotein isoform that plays a significant role in the regulation of angiogenesis.

Probably, using magnetic nanoparticle we can target short peptides sequence of this factor

(epitopes) to many goals, such as tissues being destroyed in order to stimulate angiogenesis and

restoration them. For this aim, determination of the protein amino acid sequence and prediction

of epitopes are necessary. Epitopes are of particular interest to both clinical and basic biomedical

researchers as they hold huge potential for vaccine design, disease prevention, diagnosis, and

treatment. Nowadays bioinformatics approaches play a vital role on analyzing amino acid

sequence to select the protective epitopes. In this study VEGF-A amino acidic sequence was

selected from protein data base of NCBI (Accession: NP_001028928.1). Using ExPASy tools,

ProtParam and GOR-4, their physical and chemical parameters and secondary structure

prediction of this Protein were investigated respectively. Then epitope prediction based on

hydrophilicity, flexibility/mobility, accessibility, polarity, exposed surface and turns of each

region were performed by BcePred. According to result, this protein hase 371 amino acids

residue and consist of 18 % extended strand, 28.8 % alpha helix and 56 % random coil. Also B

cell epitope prediction shows in this sequence there are two main epitopes region that are gained

the higher value compared to others: (1) from 98the residue to 103the, EEEKEE, this region is

located in an alpha helix structure. (2) From 160the residue to 165the, PHSPSR, this sequence is

located in random coil region. Hence these peptides have the potential that after practical

experiments are conjugate with magnetic nanoparticles and exploit to stimulate angiogenesis in

tissues being destroyed.

Kaywords: Epitope prediction, VEGF-A, Magnetic nanoparticles, Tissue restoration.

http://web.expasy.org/protparam/


Molecular docking study of HCV proteins with phytochemical

compounds from Prangos uloptera DC

Parisa Dehghani, Masoomeh Alamdaran Mokhtar Nosrati, Mostafa Salehi Rozveh

Department of Biotechnology, Faculty of Advanced Science, University of Isfahan, Iran.

Abstract

Because of high virulence and medicinal resistance of HCV virus during the last decades, many

investigations have been performed to discover and the introduction of anti-HCV drugs. The

results of numerous researchers have been shown that plant derivatives, may control HCV

infection very effectively. The aim of this research is the Bioinformatics study of HCV proteins

(E1, E2) inhibition by phytochemical compounds from Prangos ferulacea plant.In the present

study, the 3D structure of P.uloptera compounds, and HCV proteins was retrieved from the

PubChem and proteins Data Bank (PDB) respectively. After that, molecular docking was

performed by Molegro 5.5 software. The result confirmed that phytochemicals from P. uloptera

especially Alfa-pinion and D-germacrene had appropriate and strong interaction with E1 and E2

protein. Finally, based on the results P. uloptera could be the good candidate for HCVtretment

and more in vitro and invivo investigation about most effective compounds.

Keywords: Molecular docking, HCV, Hepatitis C, E1 and E2proteins, Prangos uloptera.


Investigation the antibacterial effect of peptides derived from cow's

milk protein (caseinate) hydrolysis by lactic acid bacteria

Reihane kordesedehi and Asghar taheri


Abstract

Milk is an excellent source of well balanced nutrients and also exhibits a range of biological

activities. Bioactive peptides have been defined as specific protein fragments that have a positive

impact on body functions or conditions and may ultimately influence health. The beneficial

health effects may be classified as antimicrobial, antioxidative, antithrombotic, antihypertensive

and immunomodulatory. Bioactive peptides can be generated during milk fermentation by the

proteolytic activity of lactic acid bacteria starter cultures. Antibacterial peptides have been

derived from milk proteins , lactoferrin, α- S 1 - casein , α-S2 - casein , k- casein ,a -lactalbumin ,

b- lactoglobulin , and lysozyme .These peptides have been found to be active against a broad

range of pathogenic organisms .With the rise of consumer concerns about the deleterious effects

of chemical preservatives and the increasing preference for natural components, bioactive

peptides have the potential to be used in the formulation of health enhancing nutraceuticals for

food preparations .Addition of these peptides to food products could improve consumer safety as

a result of their antimicrobial properties. In this investigation we show that peptides obtained

after hydrolysis of milk proteins(caseinate) by lactic acid bacteria isolated from Iranain cow's and camel's milk sampels have a high antibacterial activity (zone of inhibition) against E.coli,

salmonella and shigella only after 24-h growth.

Keywords: Antibacterial effect, Peptides, Milk protein, Lactic acid bacteria.


Immobilization of human serum albumin protein on metal-organic

framework material

Atefe Zare and Abdol Khalegh.Bordbar


Abstract

In this study, one of the metal-organic frameworks, MIL-101-NH2(Cr), was synthesized by

solvothermal method and functionalized with 2,4,6-trichloro-1,3,5-triazine (TCT) and used for

covalent immobilization of human serum albumin (HSA). The effect of protein concentration

and the immobilization time for this process were examined and the values of 3 hour and 88.6

mg were obtained for optimal time and maximum amount of immobilized protein on a gram of

support, respectively. The immobilization was confirmed by Bradford method and Fourier

transforms infrared spectroscopy (FT-IR).

Keyword: HSA, Covalent immobilization, Metal-organic framework.


Investigation the antibacterial effect of peptides derived from cow's

milk protein (Betalactaglobulin) hydrolysis by lactic acid bacteria

Rezvan Kazemi and Asghar taheri


Abstract

Milk is an excellent source of well balanced nutrients and also exhibits a range of biological

activities. Bioactive peptides have been defined as specific protein fragments that have a positive

impact on body functions or conditions and may ultimately influence health. The beneficial

health effects may be classified as antimicrobial, antioxidative, antithrombotic, antihypertensive

and immunomodulatory. Bioactive peptides can be generated during milk fermentation by the

proteolytic activity of lactic acid bacteria starter cultures. Antibacterial peptides have been

derived from milk proteins , lactoferrin, α- S 1 - casein , α-S2 - casein , k- casein ,a -lactalbumin ,

b- lactoglobulin , and lysozyme .These peptides have been found to be active against a broad

range of pathogenic organisms .With the rise of consumer concerns about the deleterious effects

of chemical preservatives and the increasing preference for natural components, bioactive

peptides have the potential to be used in the formulation of health enhancing nutraceuticals for

food preparations .Addition of these peptides to food products could improve consumer safety as

a result of their antimicrobial properties. In this investigation we show that peptides obtained

after hydrolysis of milk proteins(β-lactaglobulin) by lactic acid bacteria isolated from Iranain

cow's milk sampels have a high antibacterial activity (zone of inhibition) against E.coli,

salmonella and shigella only after 24-h growth.

Keywors: Antibacterial effect, Peptides, Milk protein, Lactic acid bacteria.


Prediction of post-translational glycosylation of proteins

Masoomeh Alamdaran, Parisa Dehghani, Hassan Mohabatkar


Abstract

Post translational modifications (PTMs) occur in the vast majority of proteins and are essential

for their functions. Most of the PTMs come in the form of proteolytic cleavage events or

covalent modifications at specific amino acid residues. One of the PTMs is protein glycosylation

which can be divided into four main categories mainly depending on the linkage between the

amino acid and the sugar. These are N-linked glycosylation, O-linked glycosylation, C-

mannosylation and glycophosphatidly inositol (GPI) anchors attachments. N-glycosylation is

characterized by the addition of a sugar to the amino group (NH2) of an asparagine. In O-

glycosylation, a sugar is attached to the hydroxyl group (OH2) of a serine or threonine. GPI

anchors refer to glycophosphatidyl-inositol groups attached near the C-terminal of a protein

chain that anchor the protein to the cell membrane. Identification of pair wise patterns

surrounding glycosylation sites and their usage in measure of ratio can be performed to weight

their propensity of association with modified residues. One of the new PTM prediction

programs is GPP (glycosylation prediction program), which predicts glycosylation sites with an

accuracy of 90.8% for serine sites, 92.0% for threonine sites and 92.8% for asparagine sites. This

is significantly better than other glycosylation predictors. GPP is available online at

http://comp.chem.nottingham.ac.uk/glyco/.

Keywords: Post-translational modification, Glycosylation, Glycosylation prediction program.

http://comp.chem.nottingham.ac.uk/glyco/


Effectiveness of a number of natural product in improving viability

of probiotic bacteria in Iranian diary product

Afouz Khalili Samani and Asghar Taheri-Kafrani


Abstract

Recognized to confer health benefits to consumers, probiotics such as Lactobacillus acidophilus

are commonly incorporated into fermented dairy products; among which yogurt is a popular

delivery vehicle. To materialize most of the putative health benefits associated with probiotics,

an adequate amount of viable cells must be delivered at the time of consumption. However, the

loss in their viabilities during refrigerated storage has been demonstrated previously. This study

focused on the effects of a number of natural product like citrus extract, Saffron extract, and

tomato extract in improving viability of probiotic bacteria in Iranian diary product such as yogurt

and cheese. For this purpose, inoculated samples were incubated aerobically at 42°C until milk

coagulation. Samples were examined for biomass and pH changes. Cell viability and post-

acidifying activity of strains were measured. The viability of yoghurt and probiotic bacteria was

assessed during manufacture and 35 days storage of yoghurt supplemented with four levels of

extracts, using four commercial starter cultures.

Keywords: Dairy product, Improving viability, Probiotic bacteria, Lactic acid bacteria.


Effect of Polyoxometalates (POMs) on glioblastoma cancer cells

Laleh Ranjbaran1, Raheleh Masoudi1, Marjan Moghayedi2, Elaheh K.Goharshadi3

1Biology Department, College of Sciences, Shiraz University, Shiraz, Iran.

2 Department of Chemistry, Ferdowsi University of Mashhad, International Campus, Mashhad, Iran.

3 Department of Chemistry, Ferdowsi University of Mashhad, Mashhad 91779, Iran.

Abstract

Polyoxometalates (POMs) are stable metal-oxide inorganic compounds, which have shown a

great potential of antitumor and antiviral activities.The aim of this study was to investigate the

effects of POMs on glioblastoma cancer cell lines’ viability. For this aim, we treated the cells

with different concentrations of several POMs such as H3PW12O40, H3PMo12O40 and

H4SiW12O40and determined the viability of the cellsusing MTTassay. Our results showed that

POMs compoundshave different effects on the glioblastomacells. It was found that higher

concentrations of H3PMo12O40 are able to reduce the cancer cell survival while the two other

compounds did not show any effect on these cells.We conclude that POMs might be effective

compounds for treatment of glioblastoma.

Keyword: Polyoxometalates (POMs), Glioblastoma, Cell viability, Cancer.


Prediction of phosphorylation sites of proteins from their amino

acid sequence

Parisa Rabiei and Hasan Mohabatkar


Abstract

Post translational modification (PTMs) are of the most important modifications that can

significantly regulate the functionality of proteins. Glycosylation, methylation, hydroxylation,

phosphorylation and ubiquitylation are the most common PTMs than can control the metabolism

and activity of a cell. Experimentally, identification of PTMs is done by mass spectrometery

(MS) which is a very expensive and time consuming approach. Therefore, a computational

method based on a reliable dataset is demanded for in silico prediction the PTM of proteins from

their amino acid sequences. In the term of prediction several parameters are introduced to

evaluate the performance of these tools such as Sensitivity (Sn), Specificity (Sp), Matthew’s

correlation coefficient (MCC) and Accuracy(Acc) which are measured based on the number of

false positive (FP), false negative (FN), true positive (TP) and true negative (TN) predictions.

Additionally, to increase the evaluation efficiency of the predictions, some factors are important,

like having a valid training and testing datasets, using the appropriate and powerful algorithms or

operation engines, and performing a cross-validation test to examine the reliability of the server.

In this study, it is attempted to investigate and compare the state-of-the- art servers which present

user-friendly prediction tools for phosphorylation, such as PhosphoBase ELM, PhosphoSite,

NetPhosK and PhosphOrtholog. In addition their accuracy, specificity and sensitivity are

declared and discussed.

Keyword: Post translational modification, Phosphorylation, Prediction servers.


Functionalized superparamagnetic graphene oxide nanoparticles as

a matrix for glucose oxidase immobilization


Department of Biotechnology, Faculty of Advanced Sciences and technologies, University of Isfahan, Isfahan, Iran.

Abstract

Glucose oxidase (β-D-glucose: oxygen 1-oxidoreductase; GOD) catalyzes the oxidation of β-D-

glucose to gluconic acid using oxygen as an electron acceptor. Nowdays, glucose oxidase is

receiving a lot of attention due to its extensive applications in pharmaceutical, food, beverage,

chemical, clinical chemistry, biotechnology and other industries. Superparamagnetic graphene

oxide nanoparticles were synthesised and then functionalized with cyanuric chloride to create a

biocompatible matrix for glucose oxidase immobilization. The structure attributes of the

immobilized glucose oxidase and support were characterized by transmission electron

microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectra

(FTIR), thermo-gravimetric analysis (TGA) and vibrating sample magnetometer (VSM) analysis.

These nanoparticles were improved the optimum conditions of immobilized enzyme rather than

free enzyme such as storage stability, thermostability, catalytic activity, pH dependence and the

half-life of an enzyme. Also, the apparent Km and ν max for free and immobilized glucose

oxidases were estimated. All these results reflects the success of the immobilization process.

Keywords: Glucose oxidase, Superparamagnetic graphene oxide, Cyanuric chloride,

Immobilization, Catalytic activity.


Immobilization of glucose oxidase on superparamagnetic/chitosan

nanoparticles


Department of Biotechnology, Faculty of Advanced Sciences and technologies, University of Isfahan, Isfahan, Iran.

Abstract

Glucose oxidase enzyme (GOD) is an oxido-reductase that catalyses the oxidation of glucose to

hydrogen peroxide and D-glucono-δ-lactone. This enzyme was covalently immobilized onto

superparamagnetic chitosan nanoparticles using cyanuric chloride (CC), forming (SPCh-CC).

The size of the chitosan functionalized magnetic nanoparticles was measured using X-ray

diffraction (XRD) pattern and transmission electron microscopy (TEM). The enzyme activity

assays of the obtained bioconjugate showed an enhanced thermostability and pH-dependence

treatment in contrast with that of free glucose oxidase. The immobilized GOD maintained more

than half of its initial activity after 10 cycles. The free and immobilized glucose oxidase kinetic

parameters (Km and νmax) were determined by Michaelis-Menten equation and the results showed

an improvement in kinetic parameters. The results of this study showed that SPCh-CC

nanocarriers can be an ideal option for immobilization of glucose oxidase.

Keywords: Glucose oxidase, Superparamagnetic chitosan nanoparticle, Cyanuric chloride,

Enzyme activity.


Comparing the physiochemical properties and alpha helix

percentages of different organisms’ Lactate dehydrogenases by

bioinformatics tool

Afrouz Khalili Samani, Parisa Rabiei and Hasan Mohabatkar


Abstract

Lactate dehydrogenase (LD) has a significant role in metabolism, and is found nearly in all kind

of cells. LD converts the lactate to pyruvic acid reversibly by catalyzing the NAD+ to NADH in

the absence of O2. In this study, 20 sequences among different geniuses, including Lactobacillus

casei, Lactobacillus delbrueckii, Enterococcus faecium, Rhizopus oryzae, Amylomyces rouxii

and Homo sapiens were selected to compare properties. For this analysis Protparam was applied

which is a useful tool that represents the physiochemical features of proteins and is available at

(http://web.expasy.org/protparam/protparam-doc.htm). Furthermore, the secondary structure of

proteins was predicted using GOR4 (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=

npsa_gor4.html). A number of parameters including molecular weight (MW), isoelectric pH (pI)

and the percentage of alpha helix and cystein were measured and the respective diagrams were

drawn. Based on the results and diagrams, although, there is no evidence of significant

differences in the MW, alpha helix percentage and pI between lower to higher geniuses, the most

similarity was seen intrageniusly.

Keyword: Lactate dehydrogenase, Protparam, Physiochemical features, GOR4

http://web.expasy.org/protparam/protparam-doc.htm

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page


Studying the effect of changing the micro/nano roughness and

wettability of polypropylene (PP) films on the protein adsorption

Elham Shirani and Amir Razmjou


Abstract

Fouling is a result of the combination of sieving and the adsorption of particulates and

compounds onto a surface. Recently, the development of new materials or the

surface modification of sample to make them less prone to fouling has become a point of interest

for both researchers and industry. These new antifouling samples can be generated through either

anti-adhesion or anti-microbial approaches. In the anti-adhesion approaches, the surface

architecture of samples is changed to prevent or reduce the adsorption of foulants via changing

the roughness and the wettability or incorporating fouling release agents. The anti-microbial

approaches are based on killing the organisms, and suppressing the biofilm formation by

disrupting bacterial colonizations. Shifting the wettability of the surface toward

superhydrophobicity could reduce the interaction between feed water solution and surface

thereby reducing the risk of fouling. Considering the fact that protein adsorption is known as the

first stage of biofilm formation, reducing the protein adsorption is the key factor of excluding

biofilm formation. In this work, an attempt has been made to create

a superhydrophobic polypropylene (PP) surface with water contacts angle of above 150°. The PP

films were characterized by SEM, EDAX, AFM, contact angle goniometry, surface free energy,

Bradford and biofilm formation assay. Results showed a significantly low protein adsorption and

biofilm formation on the modified superhydrophobic surfaces. It should be pointed out here that

this modification promise a widespread application of PP sheets on industry and medicine fields.

Keywords: Protein adsorption, Biofilm formation, Superhydrophobicity, Bradford assay.

In the name of Godisobc.com/files/2conf-isfahan.pdfHTTP://UI.CNF.IR/PPS 4 states that the global...

Documents

Transcript of In the name of Godisobc.com/files/2conf-isfahan.pdfHTTP://UI.CNF.IR/PPS 4 states that the global...