Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop

Registro completo de metadados
MetadadosDescriçãoIdioma
Autor(es): dc.contributorScience and Technology of São Paulo (IFSP)-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUniversity at Albany-
Autor(es): dc.contributorEindhoven University of Technology-
Autor(es): dc.contributorLos Alamos National Laboratory-
Autor(es): dc.contributorNational Science Foundation-
Autor(es): dc.creatorViegas, Rafael G.-
Autor(es): dc.creatorSanches, Murilo N.-
Autor(es): dc.creatorChen, Alan A.-
Autor(es): dc.creatorPaulovich, Fernando V.-
Autor(es): dc.creatorGarcia, Angel E.-
Autor(es): dc.creatorLeite, Vitor B. P.-
Data de aceite: dc.date.accessioned2025-08-21T15:16:24Z-
Data de disponibilização: dc.date.available2025-08-21T15:16:24Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2023-09-11-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1021/acs.jcim.3c00426-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/300624-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/300624-
Descrição: dc.descriptionMolecular dynamics (MD) simulations have become increasingly powerful and can now describe the folding/unfolding of small biomolecules in atomic detail. However, a major challenge in MD simulations is to represent the complex energy landscape of biomolecules using a small number of reaction coordinates. In this study, we investigate the folding pathways of an RNA tetraloop, gcGCAAgc, using five classical MD simulations with a combined simulation time of approximately 120 μs. Our approach involves analyzing the tetraloop dynamics, including the folding transition state ensembles, using the energy landscape visualization method (ELViM). The ELViM is an approach that uses internal distances to compare any two conformations, allowing for a detailed description of the folding process without requiring root mean square alignment of structures. This method has previously been applied to describe the energy landscape of disordered β-amyloid peptides and other proteins. The ELViM results in a non-linear projection of the multidimensional space, providing a comprehensive representation of the tetraloop’s energy landscape. Our results reveal four distinct transition-state regions and establish the paths that lead to the folded tetraloop structure. This detailed analysis of the tetraloop’s folding process has important implications for understanding RNA folding, and the ELViM approach can be used to study other biomolecules.-
Descrição: dc.descriptionFederal Institute of Education Science and Technology of São Paulo (IFSP), São Paulo-
Descrição: dc.descriptionDepartment of Physics Institute of Biosciences Humanities and Exact Sciences São Paulo State University (UNESP), São Paulo-
Descrição: dc.descriptionDepartment of Chemistry and the RNA Institute University at Albany-
Descrição: dc.descriptionDepartment of Mathematics and Computer Science Eindhoven University of Technology-
Descrição: dc.descriptionLos Alamos National Laboratory-
Descrição: dc.descriptionPhysics Division National Science Foundation, 2415 Eisenhower Ave-
Descrição: dc.descriptionDepartment of Physics Institute of Biosciences Humanities and Exact Sciences São Paulo State University (UNESP), São Paulo-
Formato: dc.format5641-5649-
Idioma: dc.languageen-
Relação: dc.relationJournal of Chemical Information and Modeling-
???dc.source???: dc.sourceScopus-
Título: dc.titleCharacterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

Não existem arquivos associados a este item.