H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552

Autores
Masone, Diego Fernando; Ciocco Aloia, Facundo; del Popolo, Mario Gabriel
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent.Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.
Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina
Fil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina
Fil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Queen’s University Belfast. Atomistic Simulation Centre; Reino Unido
Materia
CYTOCHROME C
DOCKING
MEMBRANE
DPPC
PROTEIN-PROTEIN
MOLECULAR DYNAMICS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/10280
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/10280
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552Masone, Diego FernandoCiocco Aloia, Facundodel Popolo, Mario GabrielCYTOCHROME CDOCKINGMEMBRANEDPPCPROTEIN-PROTEINMOLECULAR DYNAMICShttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent.Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; ArgentinaFil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; ArgentinaFil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Queen’s University Belfast. Atomistic Simulation Centre; Reino UnidoElsevier2013-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/10280Masone, Diego Fernando; Ciocco Aloia, Facundo; del Popolo, Mario Gabriel; H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552; Elsevier; Computational Biology And Chemistry; 47; 6-2013; 31-361476-9271enginfo:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1476927113000558info:eu-repo/semantics/altIdentifier/doi/10.1016/j.compbiolchem.2013.05.004info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-29T11:41:13Zoai:ri.conicet.gov.ar:11336/10280instacron: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:34982025-10-29 11:41:13.479CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
title H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
spellingShingle H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
Masone, Diego Fernando
CYTOCHROME C
DOCKING
MEMBRANE
DPPC
PROTEIN-PROTEIN
MOLECULAR DYNAMICS
title_short H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
title_full H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
title_fullStr H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
title_full_unstemmed H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
title_sort H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552
dc.creator.none.fl_str_mv Masone, Diego Fernando
Ciocco Aloia, Facundo
del Popolo, Mario Gabriel
author Masone, Diego Fernando
author_facet Masone, Diego Fernando
Ciocco Aloia, Facundo
del Popolo, Mario Gabriel
author_role author
author2 Ciocco Aloia, Facundo
del Popolo, Mario Gabriel
author2_role author
author
dc.subject.none.fl_str_mv CYTOCHROME C
DOCKING
MEMBRANE
DPPC
PROTEIN-PROTEIN
MOLECULAR DYNAMICS
topic CYTOCHROME C
DOCKING
MEMBRANE
DPPC
PROTEIN-PROTEIN
MOLECULAR DYNAMICS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent.Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.
Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina
Fil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina
Fil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Queen’s University Belfast. Atomistic Simulation Centre; Reino Unido
description In this study we propose a protocol to evaluate membrane-bound cytochrome c oxidase–cytochrome c552 docking candidates. An initial rigid docking algorithm generates docking poses of the cytochrome c oxidase–cytochrome c552, candidates are then aggregated into a 512-DPPC membrane model and solvated in explicit solvent.Molecular dynamic simulations are performed to induce conformational changes to membrane-bound protein complexes. Lastly each protein–protein complex is optimized in terms of its hydrogen bond network, evaluated energetically and ranked. The protocol is directly applicable to other membrane-protein complexes, such as protein–ligand systems.
publishDate 2013
dc.date.none.fl_str_mv 2013-06
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/11336/10280
Masone, Diego Fernando; Ciocco Aloia, Facundo; del Popolo, Mario Gabriel; H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552; Elsevier; Computational Biology And Chemistry; 47; 6-2013; 31-36
1476-9271
url http://hdl.handle.net/11336/10280
identifier_str_mv Masone, Diego Fernando; Ciocco Aloia, Facundo; del Popolo, Mario Gabriel; H-bond refinement for electron transfer membrane-bound protein-protein complexes: cytochrome c oxidase and cytochrome c552; Elsevier; Computational Biology And Chemistry; 47; 6-2013; 31-36
1476-9271
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1476927113000558
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.compbiolchem.2013.05.004
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
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 13.10058

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