Transition states in protein folding kinetics: Modeling Phi-values of small beta-sheet proteins

TL;DR

This study models and interprets mutational Phi-values in small beta-sheet proteins, revealing how specific structural elements influence folding transition states and kinetics, with implications for understanding protein folding mechanisms.

Contribution

The paper introduces a structural model of the transition state in small beta-sheet proteins that explains mutational Phi-values and folding kinetics more accurately than previous models.

Findings

Good agreement with experimental Phi-values

Transition state involves formation of either one of two hairpins

Model captures negative Phi-values, aiding interpretation

Abstract

Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Phi-values for two small beta-sheet proteins, the PIN and the FBP WW domain. The native structure of these WW domains comprises two beta-hairpins that form a three-stranded beta-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in Molecular Dynamics folding-unfolding simulations of a small designed three-stranded beta-sheet protein. We obtain good agreement with the experimental data (i) by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins, and (ii) by fitting a single parameter, the relative degree to which hairpin 1 and 2 are formed in the transition state. The model helps to understand how mutations affect the folding kinetics of WW domains, and captures also negative Phi-values that have been difficult to interpret.