PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems

Autores
Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.
Fil: Emperador, Agustí. Institute for Research in Biomedicine; España
Fil: Sfriso, Pedro. Institute for Research in Biomedicine; España
Fil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; España
Fil: Orozco, Modesto. Institute for Research in Biomedicine; España
Materia
Molecular dynamics Simulation
Protein Interaction
Discrete molecular dynamics
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/186239
Acceder
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network_name_str CONICET Digital (CONICET)
spelling PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein SystemsEmperador, AgustíSfriso, PedroVillarreal, Marcos ArielGelpí, Josep LluisOrozco, ModestoMolecular dynamics SimulationProtein InteractionDiscrete molecular dynamicshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.Fil: Emperador, Agustí. Institute for Research in Biomedicine; EspañaFil: Sfriso, Pedro. Institute for Research in Biomedicine; EspañaFil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; EspañaFil: Orozco, Modesto. Institute for Research in Biomedicine; EspañaAmerican Chemical Society2015-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/186239Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-59381549-9618CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.5b00660info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.5b00660info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:23:56Zoai:ri.conicet.gov.ar:11336/186239instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:23:56.828CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
title PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
spellingShingle PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
Emperador, Agustí
Molecular dynamics Simulation
Protein Interaction
Discrete molecular dynamics
title_short PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
title_full PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
title_fullStr PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
title_full_unstemmed PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
title_sort PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems
dc.creator.none.fl_str_mv Emperador, Agustí
Sfriso, Pedro
Villarreal, Marcos Ariel
Gelpí, Josep Lluis
Orozco, Modesto
author Emperador, Agustí
author_facet Emperador, Agustí
Sfriso, Pedro
Villarreal, Marcos Ariel
Gelpí, Josep Lluis
Orozco, Modesto
author_role author
author2 Sfriso, Pedro
Villarreal, Marcos Ariel
Gelpí, Josep Lluis
Orozco, Modesto
author2_role author
author
author
author
dc.subject.none.fl_str_mv Molecular dynamics Simulation
Protein Interaction
Discrete molecular dynamics
topic Molecular dynamics Simulation
Protein Interaction
Discrete molecular dynamics
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.
Fil: Emperador, Agustí. Institute for Research in Biomedicine; España
Fil: Sfriso, Pedro. Institute for Research in Biomedicine; España
Fil: Villarreal, Marcos Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Gelpí, Josep Lluis. Institute for Research in Biomedicine; España
Fil: Orozco, Modesto. Institute for Research in Biomedicine; España
description Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.
publishDate 2015
dc.date.none.fl_str_mv 2015-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/186239
Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-5938
1549-9618
CONICET Digital
CONICET
url http://hdl.handle.net/11336/186239
identifier_str_mv Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto; PACSAB: Coarse-Grained Force Field for the Study of Protein−Protein Interactions and Conformational Sampling in Multiprotein Systems; American Chemical Society; Journal of Chemical Theory and Computation; 11; 12; 11-2015; 5929-5938
1549-9618
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://pubs.acs.org/doi/10.1021/acs.jctc.5b00660
info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.5b00660
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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