Note : Network random walk model of two-state protein folding : Test of the theory

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Title: Note : Network random walk model of two-state protein folding : Test of the theory
Authors: Berezhkovskii, Alexander M.
Murphy, Ronan D.
Buchete, Nicolae-Viorel
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Date: 18-Jan-2013
Abstract: We study two-state protein folding in the framework of a toy model of protein dynamics. This model has an important advantage: it allows for an analytical solution for the sum of folding and unfolding rate constants [A. M. Berezhkovskii, F. Tofoleanu, and N.-V. Buchete, J. Chem. Theory Comput. 7, 2370 (2011)10.1021/ct200281d] and hence for the reactive flux at equilibrium. We use the model to test the Kramers-type formula for the reactive flux, which was derived assuming that the protein dynamics is described by a Markov random walk on a network of complex connectivity [A. Berezhkovskii, G. Hummer, and A. Szabo, J. Chem. Phys. 130, 205102 (2009)10.1063/1.3139063]. It is shown that the Kramers-type formula leads to the same result for the reactive flux as the sum of the rate constants.
Type of material: Journal Article
Publisher: AIP
Copyright (published version): 2013, American Institute of Physics
Keywords: Markov processes;Molecular biophysics;Molecular configurations;Proteins
DOI: 10.1063/1.4776215
Language: en
Status of Item: Peer reviewed
Appears in Collections:Physics Research Collection

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