Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.physa.2017.10.021 http://hdl.handle.net/11449/163784 |
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. |
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Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamicsQuantum mechanicsSchrodinger equationFolding ratesStructure-based modelThis 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.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, Rua Cristovao Colombo 2265, BR-15054000 Sao Jose Do Rio Preto, SP, BrazilUniv Fed Triangulo Mineiro, Inst Ciencias Exatas Nat & Educ, Dept Fis, Lab Biofis Teor, Ave Dr Randolfo Borges Jr 1400, BR-38064200 Uberaba, MG, BrazilUniv Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, Rua Cristovao Colombo 2265, BR-15054000 Sao Jose Do Rio Preto, SP, BrazilFAPESP: 2011/17658-3FAPEMIG: APQ-00941-14CNPq: 441730/2014-0Elsevier B.V.Universidade Estadual Paulista (Unesp)Univ Fed Triangulo MineiroPolotto, Franciele [UNESP]Drigo Filho, Elso [UNESP]Chahine, Jorge [UNESP]Oliveira, Ronaldo Junio de2018-11-26T17:44:57Z2018-11-26T17:44:57Z2018-03-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article286-300application/pdfhttp://dx.doi.org/10.1016/j.physa.2017.10.021Physica A-statistical Mechanics And Its Applications. Amsterdam: Elsevier Science Bv, v. 493, p. 286-300, 2018.0378-4371http://hdl.handle.net/11449/16378410.1016/j.physa.2017.10.021WOS:000423892800025WOS000423892800025.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPhysica A-statistical Mechanics And Its Applications0,773info:eu-repo/semantics/openAccess2023-11-05T06:09:25Zoai:repositorio.unesp.br:11449/163784Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-11-05T06:09:25Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
title |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
spellingShingle |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics Polotto, Franciele [UNESP] Quantum mechanics Schrodinger equation Folding rates Structure-based model |
title_short |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
title_full |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
title_fullStr |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
title_full_unstemmed |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
title_sort |
Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics |
author |
Polotto, Franciele [UNESP] |
author_facet |
Polotto, Franciele [UNESP] Drigo Filho, Elso [UNESP] Chahine, Jorge [UNESP] Oliveira, Ronaldo Junio de |
author_role |
author |
author2 |
Drigo Filho, Elso [UNESP] Chahine, Jorge [UNESP] Oliveira, Ronaldo Junio de |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Univ Fed Triangulo Mineiro |
dc.contributor.author.fl_str_mv |
Polotto, Franciele [UNESP] Drigo Filho, Elso [UNESP] Chahine, Jorge [UNESP] Oliveira, Ronaldo Junio de |
dc.subject.por.fl_str_mv |
Quantum mechanics Schrodinger equation Folding rates Structure-based model |
topic |
Quantum mechanics Schrodinger equation Folding rates Structure-based model |
description |
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. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:44:57Z 2018-11-26T17:44:57Z 2018-03-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.physa.2017.10.021 Physica A-statistical Mechanics And Its Applications. Amsterdam: Elsevier Science Bv, v. 493, p. 286-300, 2018. 0378-4371 http://hdl.handle.net/11449/163784 10.1016/j.physa.2017.10.021 WOS:000423892800025 WOS000423892800025.pdf |
url |
http://dx.doi.org/10.1016/j.physa.2017.10.021 http://hdl.handle.net/11449/163784 |
identifier_str_mv |
Physica A-statistical Mechanics And Its Applications. Amsterdam: Elsevier Science Bv, v. 493, p. 286-300, 2018. 0378-4371 10.1016/j.physa.2017.10.021 WOS:000423892800025 WOS000423892800025.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Physica A-statistical Mechanics And Its Applications 0,773 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
286-300 application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier B.V. |
publisher.none.fl_str_mv |
Elsevier B.V. |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803046331901542400 |