Distinguishing Biomolecular Pathways and Metastable States

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Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.contributorNortheastern Univ-
Autor(es): dc.contributorRice Univ-
Autor(es): dc.creatorOliveira, Antonio B. [UNESP]-
Autor(es): dc.creatorYang, Huan-
Autor(es): dc.creatorWhitford, Paul C.-
Autor(es): dc.creatorLeite, Vitor B. P. [UNESP]-
Data de aceite: dc.date.accessioned2022-02-22T00:09:10Z-
Data de disponibilização: dc.date.available2022-02-22T00:09:10Z-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2019-10-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1021/acs.jctc.9b00704-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/196337-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/196337-
Descrição: dc.descriptionProtein folding occurs in a high dimensional phase space, and the representation of the associated energy landscape is nontrivial. A widely applied approach to studying folding landscapes is to describe the dynamics along a small number of reaction coordinates. However, other strategies involve more elaborate analysis of the complex phase space. There have been many attempts to obtain a more detailed representation of all available conformations for a given system. In this work, we address this problem using a metric based on internal distances between amino acids to describe the differences between any two conformations. Using an effective projection method, we are able to go beyond the typical one-dimensional representation and provide intuitive two dimensional visualizations of the landscape. We refer to this method as the energy landscape visualization method (ELViM). We have applied this methodology using a C-alpha structure-based model to study the folding of two well-known proteins: SH3 domain and protein-A. Our visualization method yields a detailed description of the folding process, making possible the identification of transition state regions, and establishing the paths that lead to the native state. For SH3, we have analyzed structural differences in the distribution of folding routes. The competition between the native and mirror structures in protein A is also discussed. Finally, the method is applied to study conformational changes in the protein elongation factor thermally unstable. Distinct features of ELViM are that it does not require or assume a reaction coordinate, and it does not require analysis of kinetic aspects of the system.-
Descrição: dc.descriptionCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionNSF CAREER award-
Descrição: dc.descriptionCenter for Theoretical Biological Physics - NSF-
Descrição: dc.descriptionUniv Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil-
Descrição: dc.descriptionNortheastern Univ, Dept Phys, Boston, MA 02115 USA-
Descrição: dc.descriptionRice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 USA-
Descrição: dc.descriptionUniv Estadual Paulista, Inst Biociencias Letras & Ciencias Exatas, Dept Fis, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil-
Descrição: dc.descriptionFAPESP: 2018/18668-1-
Descrição: dc.descriptionFAPESP: 2016/19766-1-
Descrição: dc.descriptionFAPESP: 2014/50739-5-
Descrição: dc.descriptionNSF CAREER award: MCB-1350312-
Descrição: dc.descriptionCenter for Theoretical Biological Physics - NSF: PHY-1427654-
Formato: dc.format6482-6490-
Idioma: dc.languageen-
Publicador: dc.publisherAmer Chemical Soc-
Relação: dc.relationJournal Of Chemical Theory And Computation-
???dc.source???: dc.sourceWeb of Science-
Título: dc.titleDistinguishing Biomolecular Pathways and Metastable States-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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