Peptides in Biology
Create peptide antibodies Used in mass spec to identify proteins Can probe protein-protein interactions Function as protein ligands Antimicrobial Peptides
http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/phipsi.gif
Motivation for Peptide Design
Understand how the basic components of proteins function and interact
Abstract out general rules that can be applied to understand protein folding
Design useful and novel protein binders and inhibitors
Utilize the growing pdb structures to refine structures and build novel ones
Apply knowledge to chemicals similar to peptides to create novel structures (foldamers)
Peptide Backbone Reconstruction
Adcock SA. Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield. J Comput Chem. 2004 Jan 15;25(1):16-27.
Reconstruct an all-atom peptide model from a subset (Cαs or Cβs) of the atomic coordinates
Uses of Backbone Reconstruction
Enhancing low-resolution structures Conversion of coarse grain structures into all-
atom models Ab initio folding *Comparative modeling techniques*
Normal mode analysis
Current Methods Use fragment libraries and construct the
backbone with energy, homology or geometric criteria
Perform de novo construction with geometric or energy criteria Statistical positions and frequency tables Molecular dynamics and Monte Carlo Maximize peptide dipole alignments (max H-
bonds)
Algorithm Overview
Library of amino acid peptide sequences (length 3 )
Cα or Cβ coordinates
Overlay peptides on input coords
Dead EndElimination
Predicted Structure
Peptide Backbone Fragments Selected three-residue
backbone fragments from 1336 random nonredundant PDB structures
All the fragments were aligned into a standard frame
Fragments were clustered by RMSD and duplicates were discarded
Fragment Overlap Fragments were overlapped with the input
coordinates by minimizing the sum of squared distances
Kearsley’s method: state the minimization problem as an eigenvalue problem with quaternion algebra not iterative improper rotations aren’t produced no special cases RMSD is easy to calculate
Dead-End Elimination Minimize the energy function:
N
r
N
s
jipairi
N
r
total srErEE1 11
single ),()(
Ene
rgy
ri
rj
ri is residue r with the backbone conformation i
Image: Courtesy of Ivelin
Database-Derived Forcefield
P(occurance) = e-E/RT
EAB = -RT ln(gAB(r))
gAB(r) NAB(r)
http://www.nyu.edu/classes/tuckerman/stat.mech/lectures/lecture_8/node1.html
A BN
i
N
j
BjAiAiAB rrrSrN1 1
)|(|)(
Radial Distribution Function
Results Generally structures are obtained at 0.2-0.6Å
RMSD to crystal structure When compared to a well used server
(MaxSprout) the server was about 20% less accurate
An alternative algorithm worked “better” but author claims training set was biased
Phi-Psi angle correlation was on average 0.95 and 0.88 respectively
Computation can be completed in minutes
Peptides that Target Transmembrane Helices
Methods exist for the design or selection of antibodies for water soluble proteins
Different methods must be developed for membrane proteins due to our lack knowledge
Idea: Develop a peptide alpha helix that can insert into membrane and bind target membrane α-helix
Computational Design of Peptides That Target Transmembrane HelicesHang Yin, Joanna S. Slusky, Bryan W. Berger, Robin S. Walters, Gaston Vilaire, Rustem I. Litvinov, James D. Lear, Gregory A. Caputo, Joel S. Bennett, and William F. DeGrado
(30 March 2007) Science 315 (5820), 1817
Transmembrane Proteins
Embedded in lipid bilayer Difficult to crystallize Underrepresented in PDB Allow communication from
outside to inside of cell
INTEGRIN STRUCTURE, ALLOSTERY, AND BIDIRECTIONAL SIGNALINGM.A. Arnaout, B. Mahalingam, J.-P. Xiong
Annual Review of Cell and Developmental Biology 2005 21, 381-410
Design Overview Choose the target alpha helix sequence Find matching templates in the pdb database to native
binding structure of target helix Thread the target sequence onto one of the template
helices Choose proximal positions to mutate on the other
template helix Mutate those positions to all hydrophobic residue
rotamers and repack
Find Templates The integrin alpha helices that were
chosen as targets contain a small-X3-small motif and a right handed crossing angle
Membrane proteins in the pdb were searched for a helix-helix dimer with this motif and crossing angle
Note: Among the few crystallized membrane helix-helix pairs they seem to fall into a few well defined motifs
Threading and Allowable Mutations
Change the amino acid identities of one of the alpha helices to that of the target sequence (αIIB)
Align the small-X3-small motif Allow mutations (for design of
“anti” helix) at positions close to helix-helix interface (pink)
Repacking “Anti” peptide designed with Monte
Carlo simulated annealing At each step one residue identity is
changed, and then the rotamers are optimized with DEE
The new energy is then calculated with a linearly damped Lennard-Jones potential and membrane depth-dependent knowledge based potential
Accept structure based on a Boltzman coin flip
Testing the Design
Target membrane was integrin αIIb alpha helix Integrins are inactive when the α-subunit helix is
bound to the β-subunit helix and active when not bound
αIIb causes the aggregation of platelets through binding with fibrinogen
Platelet inhibitor through signal transduction
ADP scavenger (ADP stimulates plate aggregation)
Inhibits binding to fibrinogen
Extensions Currently this method is restricted to dimers
and helices that are non-polar Could include motifs with polar side chains Design for multispan bundles rather than dimers
Use negative design to avoid amyloid formation or binding to undesired targets
Improve scoring function to account for more interaction types
http://sb.web.psi.ch/images/amtb_in_membrane.png
Membrane Targeting Helices
Probe TM helix binding and function by targeting different membrane helices
Characterize folding of membrane proteins by blocking alpha helices as they form
Requires novel testing methods in order to determine whether helix is actually binding and affecting function
Moving Past Peptides: Foldamers
Proteins and RNA are unique in that they adopt specific compact, stable conformations
Biology has been fairly constrained so there should be much potential for other compactly folded polymers
Foldamer: “any polymer with a strong tendency to adopt a specific compact conformation”
Gellman, SH. Foldamers: A manifesto. Acc. Chem. Res.1998, 31, 173-180
http://www.geneticengineering.org/chemis/Chemis-NucleicAcid/Graphics/tRNA.jpg
Creating Foldamers
Find new backbone units with suitable folding propensities
Give the created foldamer interesting chemical functions
Be able to produce foldamers efficiently
Foldamer Uses
Test our understanding of protein function Since all our analysis has been on only α-amino
acids, have we “overfit” our understanding Develop new building blocks and molecular
frameworks for the design of pharmaceuticals, diagnostic agents, nanostructures, and catalysts
Foldamers as versatile frameworks for the design and evolution of functionCatherine M Goodman, Sungwook Choi, Scott Shandler & William F DeGrado
Nature Chemical Biology 3, 252-262 (2007)
Predictability of Secondary Structure
Adding salt bridges spaced one turn apart introduce stability
Charged groups at helix ends stabilize according to their polarity
α-amino acid knowledge can be transferred about stabilization by disulfides, covalent bridges, and binding of metal ions
Aromatic Oligomers
Size of monomer and substitution of aromatic ring provide reliable determination of helical radius
Jiang, H., Leger, J.M. & Huc, I. Aromatic -peptides. J. Am. Chem. Soc. 125, 3448–3449 (2003).
Designing Foldamer Function
Foldamers can interrupt Tat/TAR binding Penetrate bacterial cells in a passive process Have antimicrobial properties dependent on
the length and hydrophobicity Mimics to interrupt protein-protein
interactions with Ki up to 0.8 uM and 7.1nm By using an α/β sequence a ten-fold
higher affinity was found than the native peptide ligand
Foldamer Tertiary Structure A zinc finger-like motif
was recently built consisting of β-peptides with a β hairpin and 14-helix
An octomer consisting of β-peptides was created with only non-covalent interactions
Benefits of Foldamers
Foldamers are more resistant to enzymatic attack then peptides
Fewer monomeric units are needed to adopt a well-defined secondary structure
Can be used as a strategic method to downsize peptides to small molecules
Natural Peptide 14-helix β-peptide Arylamide foldamer Phenylalkylnyl
Summary
Peptide design can be used in a variety of ways Backbone reconstruction Antibodies for membrane proteins Foldamers
All of these methods help us understand how proteins fold and the underlying rules, which will allow better models and hopefully better functional designs
Top Related