Master equation approach to protein folding and kinetic traps

TL;DR

This paper uses a master equation approach to analyze protein folding dynamics in lattice models, revealing how kinetic traps influence folding times and pathways at different temperatures.

Contribution

It introduces a numerical solution of the master equation for lattice heteropolymers, providing insights into folding kinetics and trap effects not previously detailed.

Findings

Median folding time follows Arrhenius law at low temperatures.

Good folders exhibit kinetic traps within the folding funnel.

Bad folders have traps in non-native energy valleys.

Abstract

The master equation for 12-monomer lattice heteropolymers is solved numerically and 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.