A Simple Model of Protein Folding Kinetics Based on Native Topology

Abstract

The folding rates of two-state proteins range over six orders of magnitude: from microseconds to seconds. These folding rates correlate with contact order, a simple measure of the topology of the native structure. The question we would like to answer is the following: What physical principles underlie the correlation between folding rates and contact order? To answer this question, we’re developing a simple master equation model based on native contacts and loop-closure entropies. Our hypothesis is that folding proceeds mostly through the closure of small loops, and that large loop closures are slower and less important.