Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics
Carregando...
Arquivos
Data
2018-03-01
Autores
Polotto, Franciele [UNESP]
Drigo Filho, Elso [UNESP]
Chahine, Jorge [UNESP]
Oliveira, Ronaldo Junio de
Título da Revista
ISSN da Revista
Título de Volume
Editor
Elsevier B.V.
Resumo
This work developed analytical methods to explore the kinetics of the time-dependent probability distributions over thermodynamic free energy profiles of protein folding and compared the results with simulation. The Fokker-Planck equation is mapped onto a Schrodinger-type equation due to the well-known solutions of the latter. Through a semi analytical description, the supersymmetric quantum mechanics formalism is invoked and the time-dependent probability distributions are obtained with numerical calculations by using the variational method. A coarse-grained structure-based model of the two-state protein TmCSP was simulated at a C-alpha level of resolution and the thermodynamics and kinetics were fully characterized. Analytical solutions from non-equilibrium conditions were obtained with the simulated double-well free energy potential and kinetic folding times were calculated. It was found that analytical folding time as a function of temperature agrees, quantitatively, with simulations and experiments from the literature of TmCSP having the well-known 'U' shape of the Chevron Plots. The simple analytical model developed in this study has a potential to be used by theoreticians and experimentalists willing to explore, quantitatively, rates and the kinetic behavior of their system by informing the thermally activated barrier. The theory developed describes a stochastic process and, therefore, can be applied to a variety of biological as well as condensed-phase two-state systems. (C) 2017 Elsevier B.V. All rights reserved.
Descrição
Palavras-chave
Quantum mechanics, Schrodinger equation, Folding rates, Structure-based model
Como citar
Physica A-statistical Mechanics And Its Applications. Amsterdam: Elsevier Science Bv, v. 493, p. 286-300, 2018.