An Ising-Like model for protein mechanical unfolding

Abstract

The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a model is generalized by including the effect of an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. In the case of titin we determine equilibrium force-extension curves and study nonequilibrium phenomena in the frameworks of dynamic loading and force clamp protocols, verifying theoretical laws and finding the position of the kinetic barrier which hinders the unfolding of the molecule. The PIN1 molecule is used to check the possibility of computing the free energy landscape as a function of the molecule length by means of an extended form of the Jarzynski equality.

4 pages + appendix

References in corpus (7)

• A nonequilibrium equality for free energy differences
• Exact Solution of the Munoz-Eaton Model for Protein Folding
• Probing molecular free energy landscapes by periodic loading
• Kinetics of the Wako-Saito-Munoz-Eaton Model of Protein Folding
• Mechanical properties of the domains of titin in a Go-like model
• Exactness of the cluster variation method and factorization of the equilibrium probability for the Wako-Saito-Munoz-Eaton model of protein folding
• Evaluation of free energy landscapes from manipulation experiments

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