Kinetics of the Wako-Saito-Munoz-Eaton Model of Protein Folding

TL;DR

This paper analyzes a simplified, exactly solvable model of protein folding, studying its kinetics and comparing theoretical predictions with simulations and real protein data.

Contribution

It introduces a kinetic analysis framework for the Wako-Saito-Munoz-Eaton model, proving properties of free energy decrease and equilibrium recovery.

Findings

Free energy decreases monotonically over time.

The model's folding rate bounds the exact rate.

Kinetics agree with Monte Carlo simulations and real protein data.

Abstract

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach, for which we prove that (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the infinite time limit, and (iii) the folding rate is an upper bound of the exact one. The kinetics is compared to the exact one for a small peptide and to Monte Carlo simulations for a longer protein, then rates are studied for a real protein and a model structure.