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Updated: Jul 10, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Protein mechanical unfolding: a model with binary variables
A Imparato1, A Pelizzola, M Zamparo
1Dipartimento di Fisica, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy. alberto.imparato@polito.it
Abstract:
A simple model, recently introduced as a generalization of the Wako-Saito; 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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