The protein folding transition-state ensemble from a Gō-like model

Abstract

Characterizing the structure of transition states (TS) is a first step towards understanding two-state protein folding mechanisms. However, a direct experimental characterization of these states is challenging and indirect information derived from protein engineering methodologies (ϕ-value analysis) is often difficult to interpret. We present here a theoretical study on the nature of the transition state ensemble for three representative proteins covering the major structural classes using a mean-field C_α-based Gō-model. We identify that transition state ensembles are dominated by local contacts, indicating that most non-local contacts form only upon crossing the macroscopic folding free energy barrier. We demonstrate that the mean ϕ-value corresponds to the fraction of stabilization energy gained at the barrier-top in two-state-like systems, and that it depends monotonically on the stability conditions. Furthermore, we show that there is a fundamental connection between small destabilization and large ϕ-values that in turn depends on the location of the mutated residue in the structure. These results that are in agreement with the recent empirical findings highlight the importance of local energetics in determining folding mechanisms.