S.Prasanth Kumar, S.Prasanth Kumar, BioinformaticianBioinformatician

Molecular Interaction

Protein-DNA InteractionProtein-DNA Interaction

S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA

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DNA-Protein Binding

Specific binding of proteins to a wide variety of nucleicacids underlies all aspects of gene expression, includinggenome replication, repair, transcription and RNA metabolism.

Classical Examples:Bacterial restriction system, Transcriptional regulationDNA mismatch repair

Instance:PNA-DNA interaction

PNA

DNA

Mechanisms of DNA-Protein Binding

Release of water molecules and ions

DNA & Protein structure conformations

Water at Interface : Helps in Electrostatic repulsions between like charges of protein and DNA

Facilitates H bonding between protein and DNA

Hence, water is important for binding

Recognition Principles of DNA

Watson-Crick Rule

Major Groove Edges Prominent

HBA & HBD

N atom

O atom

W Site in Wide Groove

S Site in Small Groove

Recognition Principles of DNA

DNA-Protein Contact Propensities

Protein-DNA Crystal Structures

Select Non redundant structures

Study Interaction

Interaction with Bases Interaction with Sugar Interaction with Phosphate

Backbone Interaction

DNA-Protein Contact Propensities

Luscombe et al 2001

How Protein Recognizes its Site on DNA

Protein uses SAA

Protein uses +ve and/or polar residues

Protein recognizes phosphate and base atoms

Protein measures contact distance e.g. <3.4 Angstrom

Protein converges to contact by folding mechanism

How Protein Recognizes its Site on DNA

Other Structural Parameters

H- bonded atoms found in tight clusters (next slide)

van der Waals contacts of aa and bases are distant & dispersed

Adenine

Spatial Interaction Patterns

N atom

O atomR

Kano & Sarai 2001

Role of Solvated Cations in Charge Neutralization

Solvated Cations

Cations interact with Guanine of Major Groove to neutralize Charges

Role of Methylation in Charge Neutralization

Used Methylphosphonate analogs in DNA duplexes

Methyl group neutralizes phosphate

Only phosphates in Minor groove

DNA Bending Strategy

Excess charge on one side of DNA makes to bend towards neutralized regions

Cations accumulated for phosphate neutralization at a region is the reason for DNA bending

Shape Complementarity

Electrostatic potential prominent

Protein’s Independent Binding Domains

LacI repressor

Known Domains

Zn finger

Leu zipper

Electrostatic Patches

+ve

-ve

DNA binding protein Non-DNA binding protein

-ve

+ve

Practical based on Protein-Protein-DNA Interaction DNA Interaction is followingis following

Special thanks to Wilma K. Olson for her illustrations presented in this lecture