Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

TL;DR

This paper develops a non-Markovian transition state theory for protein folding that incorporates frequency-dependent friction and identifies effective reaction coordinates based on system dynamics.

Contribution

It introduces a variational transition state theory accounting for non-Markovian effects and dynamic reaction coordinates in protein folding kinetics.

Findings

The theory reduces to classical Kramers approach when non-Markovian effects are ignored.

It provides a framework to identify optimal reaction coordinates for folding.

The approach does not assume barrier size or memory time of friction.

Abstract

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.