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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

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ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins.

Tao Ma^1,2,3, Wenhui Li^1,2,3, Zhiping Tang^1,2,3

¹The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China.

International Journal of Molecular Sciences

|May 25, 2024

Summary

We developed ARIP, a new tool to identify protein contact residues by calculating atomic contact volume. ARIP offers a more informative approach than contact area for analyzing molecular interactions and protein structures.

Keywords:

atomic overlap weighted algorithm interatomic contact volume molecular dynamic capture protein structure quantitative analysis residue interaction

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Published on: January 10, 2018

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Protein structure and flexibility are determined by amino acid residue interactions.
These interactions are crucial for protein function and molecular binding.
Accurate identification of residue contacts is essential for understanding these processes.

Purpose of the Study:

Introduce ARIP, a novel computational tool for identifying protein contact residues.
Develop a method to directly calculate atomic contact volume for more informative interaction analysis.
Provide a tool suitable for various applications including molecular dynamics.

Main Methods:

ARIP utilizes a modified dr_sasa algorithm and an atomic overlap weighted algorithm.
Calculates contact area and volume based on van der Waals radii and user-defined solvent radii.
Parameters derived from analysis of ~5000 X-ray crystallography structures.
Capable of analyzing multiple models within a single PDB file.

Main Results:

ARIP directly calculates atomic contact volume, offering more informative insights than contact area.
Contact volume is symmetrically distributed between interacting atoms.
Demonstrated utility in analyzing NMR structures, protein-drug binding, protein-DNA binding, and molecular dynamics simulations.

Conclusions:

ARIP provides a robust method for identifying protein contact residues and analyzing molecular interactions.
The contact volume metric enhances the understanding of intra- and intermolecular interactions.
ARIP is a valuable tool for structural biology, drug discovery, and molecular dynamics research.