Resolving the fine structure in the energy landscapes of repeat proteins

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MetadadosDescriçãoIdioma
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorBarcelona Supercomputing Center (BSC)-
Autor(es): dc.contributorScience and Technology of São Paulo (IFSP)-
Autor(es): dc.contributorRice University-
Autor(es): dc.contributorFacultad de Ciencias Exactas y Naturales-
Autor(es): dc.creatorSanches, Murilo N.-
Autor(es): dc.creatorParra, R. Gonzalo-
Autor(es): dc.creatorViegas, Rafael G.-
Autor(es): dc.creatorOliveira, Antonio B.-
Autor(es): dc.creatorWolynes, Peter G.-
Autor(es): dc.creatorFerreiro, Diego U.-
Autor(es): dc.creatorLeite, Vitor B.P.-
Data de aceite: dc.date.accessioned2025-08-21T20:26:31Z-
Data de disponibilização: dc.date.available2025-08-21T20:26:31Z-
Data de envio: dc.date.issued2023-03-01-
Data de envio: dc.date.issued2023-03-01-
Data de envio: dc.date.issued2022-06-10-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1017/qrd.2022.4-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/240325-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/240325-
Descrição: dc.descriptionAnkyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.-
Descrição: dc.descriptionDepartment of Physics Institute of Biosciences Humanities and Exact Sciences São Paulo State University (UNESP)-
Descrição: dc.descriptionBarcelona Supercomputing Center (BSC)-
Descrição: dc.descriptionFederal Institute of Education Science and Technology of São Paulo (IFSP)-
Descrição: dc.descriptionCenter for Theoretical Biological Physics Rice University-
Descrição: dc.descriptionInstituto de Química Biológica Facultad de Ciencias Exactas y Naturales-
Descrição: dc.descriptionDepartment of Physics Institute of Biosciences Humanities and Exact Sciences São Paulo State University (UNESP)-
Idioma: dc.languageen-
Relação: dc.relationQRB Discovery-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectEnergy landscape visualisation-
Palavras-chave: dc.subjectFolding funnel-
Palavras-chave: dc.subjectMolecular dynamics-
Palavras-chave: dc.subjectProtein folding-
Título: dc.titleResolving the fine structure in the energy landscapes of repeat proteins-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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