The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics

TL;DR

This study investigates how local thermal fluctuations influence protein folding kinetics, using nonextensive statistical mechanics and Monte Carlo simulations to analyze the dependence of folding time on temperature and a nonextensive parameter.

Contribution

It introduces a model incorporating local thermal fluctuations into protein folding kinetics via nonextensive statistical mechanics, focusing on the search mechanism stage.

Findings

Local thermal fluctuations significantly affect folding times.

The nonextensive parameter $q$ modulates the folding kinetics.

Monte Carlo simulations reveal temperature dependence of folding times.

Abstract

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process with two consecutive and independent stages, namely the search mechanism and the overall productive stabilization; ($ii$) the folding kinetics results from a mechanism as fast as can be; and ($iii$) at nanoscale dimensions, local thermal fluctuations may have important role on the folding kinetics. Here the first stage of folding process (search mechanism) is focused exclusively. The effects and consequences of local thermal fluctuations on the configurational kinetics, treated here in the context of non extensive statistical mechanics, is analyzed in detail through the dependence of the characteristic time of folding ($\tau$) on the temperature $T$ and on the nonextensive parameter $q$.The model used consists of effective residues forming a chain of 27 beads, which occupy different sites of a $3-$D infinite lattice, representing a single protein chain in solution. The configurational evolution, treated by Monte Carlo simulation, is driven mainly by the change in free energy of transfer between consecutive configurations. ...