Ising-Like Model for Protein Mechanical Unfolding

Abstract

The mechanical unfolding of proteins is studied by extending the Wako-Saitô-Muñoz-Eaton model. This model is generalized by including 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. We determine equilibrium force-extension curves for the titin and study the mechanical unfolding of this molecule, finding good agreement with experiments. By using an extended form of the Jarzynski equality, we compute the free energy landscape of the PIN1 as a function of the molecule length.

Unified Model of Dynamic Forced Barrier Crossing in Single Molecules

“…This result explicitly demonstrates that for single-barrier states loaded slowly by an external field, the force spectrum can be universally modeled by the phenomenological Bell hypothesis. Equation (3) may find use in monte carlo modeling of complex systems, such as protein unfolding [26], where individual transitions can be pseudo-randomly selected by inverse transform sampling [27]. The theory presented here is general to a broad range of condensedmatter and materials science studies of dynamicallyforced, thermally activated transitions in single-molecule systems.…”

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

“…The short-hand notation is exploited, eg. [39] or [40]). The second term, .2), the solvent is competing with the polymer for H-bond formation, depending on the ratio J/I.…”

Phase diagram of the Wako-Saitô-Muñoz-Eaton β hairpin model obtained from the partition-function zeros

“…A class of toy models called Go-like models bias the Hamiltonian toward its native structure [5][6][7][8][9][10][11][12][13][14][15][16]. The Go-like models are based on the assumption that the native structure of a protein contains much information on the folding process.…”