Monte Carlo procedure for protein folding in lattice model. Conformational rigidity

TL;DR

This paper introduces a rigorous Monte Carlo method for simulating protein folding on lattice models, incorporating a conformational rigidity parameter to ensure detailed balance, and applies it to small chains with kinetic analysis at low temperatures.

Contribution

It presents a novel Monte Carlo approach that includes a rigidity parameter for accurate protein folding simulation on lattice models, with kinetic analysis capabilities.

Findings

The rigidity parameter ensures detailed balance in the Monte Carlo method.

The method accurately captures folding kinetics at low temperatures.

Arrhenius law coefficients match the main potential barrier.

Abstract

A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance condition. Its properties are discussed and its role during the folding process is elucidated. This method is applied on small chains on two-dimensional lattice. A Bortz-Kalos-Lebowitz type algorithm which allows to study the kinetic of the chains at very low temperature is implemented in the presented method. We show that the coefficients of the Arrhenius law are in good agreement with the value of the main potential barrier of the system.