Origin of Native Driving Force in Protein Folding

TL;DR

This paper derives a parameterized expression that accurately reproduces the Miyazawa-Jernigan potential matrix for protein folding, linking it to physical properties like surface tension and dipole interactions.

Contribution

It introduces a novel analytical expression with adjustable parameters that models the native driving force in protein folding based on physical principles.

Findings

Successfully reproduces the Miyazawa-Jernigan matrix

Parameters relate to water surface tension and dipole interactions

Provides a physical basis for the folding potential

Abstract

We derive an expression with four adjustable parameters that reproduces well the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein structures. The numerical values of the parameters can be approximately computed from the surface tension of water, water-screened dipole interactions between residues and water and among residues, and average exposures of residues in folded proteins.