Out-of-equilibrium versus dynamical and thermodynamical transitions for a model protein

TL;DR

This paper investigates the out-of-equilibrium and equilibrium transitions of a model protein, revealing structural, dynamical, and thermodynamical insights through unfolding pathways and free energy landscape analysis.

Contribution

It introduces a combined approach using out-of-equilibrium dynamics and inherent structure formalism to connect structural transitions with thermal folding/unfolding.

Findings

Identified three structural transitions during unfolding

Reconstructed free energy profiles correlating with thermal transitions

Detected dynamical transitions as precursors to thermal folding

Abstract

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a work fluctuation relation, the system free energy landscape is evaluated. Three different structural transitions are identified along the unfolding pathways. Furthermore, the reconstruction of the the free and potential energy profiles in terms of inherent structure formalism allows us to put in direct correspondence these transitions with the equilibrium thermal transitions relevant for protein folding/unfolding. Through the study of the fluctuations of the protein structure at different temperatures, we identify the dynamical transitions, related to configurational rearrangements of the protein, which are precursors of the thermal transitions.