Inter-residue interaction is a determinant of protein folding kinetics

Abstract

In recent years, there have been many breakthroughs in the prediction of protein folding kinetics using empirical and theoretical methods. These predictions focus primarily on the structural parameters in concert with contacting residues. The non-covalent contacts are a simplified model of the interactions found in proteins. Here we investigate the physico-chemical origin and derive the approximate formula ln k(f)=a+b×Σ1/d(6), where d is the distance between different residues of the protein structure. It achieves -0.83 correlation with experimental over 57 two- and multi-state folding proteins, indicating that protein folding kinetics is determined by the interactions between all pairs of residues. The interaction is a short-range coupling that is effective only when two residues are in close proximity, consistent with the dominant role of the contacts in determining folding rates.