Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins

Abstract

We investigate various topological and energy parameters from the protein native structure and find combinations of some parameters that are well correlated with the rate of folding/unfolding. For folding, the topological quantity that combines the clustering coefficient and the long-range order (or total contact distance/contact order) has a high correlation with the folding rate, expressed as ln k (F) , obtained from standard experimental conditions. For unfolding, a combination of the impact of edge removal, obtained from the protein structure, and the stability of the native protein structure, as expressed by the free energy change Delta G, gives a good correlation with unfolding rate, ln k (U) .