| Full text | |
| Author(s): |
Polotto, Franciele
[1]
;
Drigo Filho, Elso
[1]
;
Chahine, Jorge
[1]
;
de Oliveira, Ronaldo Junio
[2]
Total Authors: 4
|
| Affiliation: | [1] Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, Rua Cristovao Colombo 2265, BR-15054000 Sao Jose Do Rio Preto, SP - Brazil
[2] Univ Fed Triangulo Mineiro, Inst Ciencias Exatas Nat & Educ, Dept Fis, Lab Biofis Teor, Ave Dr Randolfo Borges Jr 1400, BR-38064200 Uberaba, MG - Brazil
Total Affiliations: 2
|
| Document type: | Journal article |
| Source: | PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS; v. 493, p. 286-300, MAR 1 2018. |
| Web of Science Citations: | 4 |
| Abstract | |
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. (AU) | |
| FAPESP's process: | 11/17658-3 - Computational studies on protein folding and applications in the study of enzymes involved in bioethanol production |
| Grantee: | Vitor Barbanti Pereira Leite |
| Support Opportunities: | Regular Research Grants |