Transition states in protein folding

TL;DR

This paper discusses how to characterize the transient, unstable transition states in two-state protein folding, using mutational data and novel modeling approaches to better understand folding mechanisms.

Contribution

It introduces a new interpretation of mutational data focusing on cooperative substructures, improving the understanding of transition states in protein folding.

Findings

Traditional methods focus on residue-level structure in transition states.

Novel approach emphasizes cooperative substructures like alpha-helices.

Splitting free energy changes clarifies transition state characterization.

Abstract

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as alpha-helices and beta-hairpins. By splitting up mutation-induced free energy changes into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation.