Universality and diversity of folding mechanics for three-helix bundle proteins

TL;DR

This study uses detailed simulations to analyze the folding mechanisms of two small three-helix bundle proteins, revealing common structural motifs and providing atomic-level insights consistent with experimental data.

Contribution

It offers a comprehensive atomic-level analysis of three-helix bundle protein folding, combining simulations, clustering, and pfold analysis, and predicts Villin folding behavior for future testing.

Findings

Two-helix hairpin is a common folding motif.

Good agreement with experimental Fi-values for protein A.

Predictions made for Villin Fi-values for future validation.

Abstract

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous pfold analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Fi-values is obtained for protein A. Fi-values for Villin are also obtained and left as predictions to be tested by future experiments. Our analysis shows that two-helix hairpin is a common partially stable structural motif that gets formed prior to entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.