Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems

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Autor(es): dc.contributorUniversity of Florida-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.creatorCruzeiro, Vinícius Wilian D.-
Autor(es): dc.creatorFeliciano, Gustavo Troiano [UNESP]-
Autor(es): dc.creatorRoitberg, Adrian E.-
Data de aceite: dc.date.accessioned2022-02-22T00:29:29Z-
Data de disponibilização: dc.date.available2022-02-22T00:29:29Z-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-02-26-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1021/jacs.9b11433-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/200127-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/200127-
Descrição: dc.descriptionCoupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions becomes very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force-field-based and GPU-accelerated approach, which allows the simulations to be executed with high computational performance.-
Descrição: dc.descriptionDepartment of Chemistry University of Florida-
Descrição: dc.descriptionDepartamento de Físico-Química Instituto de Química Universidade Estadual Paulista (Unesp)-
Descrição: dc.descriptionDepartamento de Físico-Química Instituto de Química Universidade Estadual Paulista (Unesp)-
Formato: dc.format3823-3835-
Idioma: dc.languageen-
Relação: dc.relationJournal of the American Chemical Society-
???dc.source???: dc.sourceScopus-
Título: dc.titleExploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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