Protein mechanical unfolding: a model with binary variables

Details Protein mechanical unfolding: a model with binary variables Protein mechanical unfolding: a model with binary variables

2007-06-19

arxiv.org/abs/0706.2818v1

J. Chem. Phys. 127, 145105 (2007)

Physics

Condensed Matter

Soft Condensed Matter

Scientific paper

10.1063/1.2776271

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.

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