Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels

TL;DR

This paper investigates protein folding kinetics using a diffusive reaction coordinate, combining simulations and analytic theory to show folding resembles a diffusive, funnel-like process.

Contribution

It introduces a quantitative approach linking Monte Carlo simulations with diffusive rate theory for protein folding.

Findings

Diffusive coefficients and free energy profiles match simulation data

Folding process characterized as a diffusive, funnel-like mechanism

Analytic calculations agree with full simulation results

Abstract

The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo simulations of a 27-mer, 3 letter code lattice model, which corresponds roughly to a small helical protein. Analytic folding calculations, using simple diffusive rate theory, agree extremely well with the full simulation results. Folding in this system is best seen as a diffusive, funnel-like process.