Rate Determining Factors in Protein Model Structures

TL;DR

This paper investigates how protein folding rates relate to native state geometry using a statistical physics model, revealing a strong linear correlation with contact order that varies with geometry class.

Contribution

It introduces a simple model to analyze the rate-geometry relationship in proteins, highlighting the dependence of the rate on contact order and geometry class.

Findings

Logarithm of folding rate correlates linearly with absolute contact order.

Slope of the rate-contact order relationship depends on geometry class.

Results align with experimental observations.

Abstract

Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical physics model, and focus on two classes of model geometries, representing ideal parallel and antiparallel structures. We find that the logarithm of the rate shows an almost perfect linear correlation with the "absolute contact order", but the slope depends on the particular class considered. We discuss these findings in the light of experimental results.