Reconstructing the free energy landscape of a mechanically unfolded model protein

TL;DR

This paper reconstructs the free energy landscape of a model protein during mechanical unfolding using out-of-equilibrium methods, demonstrating consistency between approaches and linking structural transitions to thermodynamics.

Contribution

It introduces and compares two methods—extended Jarzynski equality and inherent structures—for reconstructing free energy landscapes from mechanical unfolding data.

Findings

Good agreement between EJE and IS methods around the folding transition

Structural transitions relate to thermodynamical folding aspects

Methods reliably reproduce equilibrium free energies

Abstract

The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the ``folding transition'' we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.