Master equation approach to protein folding

TL;DR

This paper uses a master equation approach to analyze protein folding dynamics, revealing how folding times and kinetic traps vary with temperature and folding quality.

Contribution

It provides an exact analysis of folding dynamics for heteropolymers on a lattice, highlighting the role of kinetic traps and relaxation times.

Findings

Folding time follows Arrhenius law at low temperatures.

Good folders exhibit kinetic traps in the folding funnel.

Bad folders have traps in non-native energy valleys.

Abstract

The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders, significant kinetic traps appear in the folding funnel whereas for bad folders, the traps also occur in non-native energy valleys.