Entropic formulation for the protein folding process: hydrophobic stability correlates with folding rates

TL;DR

This paper models protein folding as two steps influenced by hydrophobic effects and stability, using a 3D lattice model and Monte Carlo simulations to relate folding rates to hydrophobic stability.

Contribution

It introduces a lattice-based kinetic model that links hydrophobic interactions with folding rates, incorporating Tsallis statistics to improve simulation efficiency.

Findings

Hydrophobic interactions suffice for the initial folding stage.

Modified Monte Carlo algorithm accelerates folding simulations.

Folding times are correlated with hydrophobic stability.

Abstract

We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our main tool of investigation is a 3D lattice model provided with a ten-letter alphabet, the stereochemical model. This model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. In order to characterize the folding characteristic time ({\tau}) by two distinct sampling methods, first we present two sets of 10^{3} MC simulations for a fast protein-like sequence. For these sets of folding times, {\tau} and {\tau}_{q} were obtained with the application of the standard Metropolis algorithm (MA), and a modified algorithm (M_{q}A). The results for {\tau}_{q}reveal two things: i) the hydrophobic chain-solvent interactions plus a set of inter-residues steric constraints are enough to emulate the first stage of the process: for each one of the 10^{3} MC performed simulations, the native is always found without exception, ii) the ratio {\tau}_{q}/{\tau}~1/3 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides an innate efficiency to the chain escapes from energetic and steric traps. ...