Protein mechanical unfolding: a model with binary variables

TL;DR

This paper introduces a simplified lattice model with binary variables to study protein unfolding under force, providing exact solutions for equilibrium and kinetic properties, and validating results with simulations and experiments.

Contribution

It presents a new binary-variable lattice model for protein unfolding, offering exact solutions and insights into energy landscapes and kinetic responses under force.

Findings

Model accurately predicts unfolding kinetics

Simulation results agree with experimental data

Jarzynski equality helps reconstruct free energy landscapes

Abstract

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model proteins, together with their energy landscape, are studied on the basis of the exact solution of the model. Afterwards, the kinetic response of the molecules to a force is considered, discussing both force clamp and dynamic loading protocols and showing that theoretical expectations are verified. The kinetic parameters characterizing the protein unfolding are evaluated by using computer simulations and agree nicely with experimental results, when these are available. Finally, the extended Jarzynski equality is exploited to investigate the possibility of reconstructing the free energy landscape of proteins with pulling experiments.