Universality classes in folding times of proteins

TL;DR

This study uses simplified molecular dynamics models to identify three universality classes in protein folding times, revealing how folding kinetics depend on protein structure type and contact potential variations.

Contribution

It demonstrates the existence of three distinct kinetic universality classes in protein folding times based on structure type and contact potential, expanding understanding of folding kinetics.

Findings

Three kinetic universality classes identified for protein folding times.

Scaling exponents differ for alpha, alpha-beta, and beta proteins.

Contact potential and structure type influence folding time scaling.

Abstract

Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes which are correlated with the types of structure: the alpha-, alpha--beta-, and beta- proteins have the scaling exponents of about 1.7, 2.5, and 3.2 respectively. The three classes merge into one when the contact range is truncated at a 'reasonable' value. We elucidate the role of the potential associated with the chirality of a protein.