Computing Entropies for Binding and Refinement of Protein Structures

Abstract

Entropy plays an important role in protein folding and binding, but is difficult to evaluate; consequently its contribution to free energy is often neglected or locally approximated. We propose a novel method for calculating the change in free energy upon binding using coarse-grained models of proteins by combining multi-body potentials with entropies calculated from elastic network models (ENMs). Multi-body energy potentials have been developed to account for the cooperativity in globular protein structures by an improved accounting of three dimensional interactions and residue packing.