Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
Texto Completo: | https://www.arca.fiocruz.br/handle/icict/11861 |
Resumo: | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Biologia Estrutural e Bioimagem. Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas. Instituto de Bioquímica Médica. Rio de Janeiro, RJ, Brasil. |
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Gomes Neto, FranciscoValente, Ana PaulaAlmeida, Fabio C. L.2015-10-02T12:45:02Z2015-10-02T12:45:02Z2013GOMES NETO, Francisco; VALENTE, Ana Paula; ALMEIDA, Fabio C. L.. Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data. Molecules, v.18, n.8, p.10056-10080, 2013.1420-3049https://www.arca.fiocruz.br/handle/icict/1186110.3390/molecules180810056engMDPIModeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Datainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Biologia Estrutural e Bioimagem. Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas. Instituto de Bioquímica Médica. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Biologia Estrutural e Bioimagem. Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas. Instituto de Bioquímica Médica. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Biologia Estrutural e Bioimagem. Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas. Instituto de Bioquímica Médica. Rio de Janeiro, RJ, Brasil.Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticoccidial peptide PW2, we performed molecular dynamics (MD) simulations guided by NMR experimental data, focusing on strategies to explore the transient nature of micelles, which rearrange on a millisecond to second timescale. We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. The simulation with spontaneous micelle formation provided the adequate environment which replicated the experimental data. The unrestrained MD simulations reproduced the NMR structure for the entire 100 ns MD simulation time. Hidden discrete conformational states could be described. Coulomb interactions are important for initial approximation and hydrogen bonds for anchoring the aromatic region at the interface, being essential for the stabilization of the interaction. Arg9 is strongly attached with phosphate. We observed a helix elongation process stabilized by the intermolecular peptide-micelle association. Full association that mimics the experimental data only happens after complete micelle re-association. Fast micelle dynamics without dissociation of surfactants leads to only superficial binding.Molecular dynamics simulationNMRStructureAntimicrobialMembraneMicellesPeptide structureSimulação de Dinâmica MolecularAntimicrobianaMicelasMembranaPeptídioEstruturaImagem por Ressonância Magnéticainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txttext/plain1914https://www.arca.fiocruz.br/bitstream/icict/11861/1/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD51ORIGINALfrancisco_gomesneto_etal_IOC_2013.pdfapplication/pdf1510231https://www.arca.fiocruz.br/bitstream/icict/11861/2/francisco_gomesneto_etal_IOC_2013.pdf4ce4ab960bf8ed90aa3235f87d64d5baMD52TEXTfrancisco_gomesneto_etal_IOC_2013.pdf.txtfrancisco_gomesneto_etal_IOC_2013.pdf.txtExtracted texttext/plain67046https://www.arca.fiocruz.br/bitstream/icict/11861/3/francisco_gomesneto_etal_IOC_2013.pdf.txt48bd357260935a8009f2a5a9b2c2ab3dMD53icict/118612022-06-24 12:18:53.84oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-06-24T15:18:53Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
dc.title.pt_BR.fl_str_mv |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
title |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
spellingShingle |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data Gomes Neto, Francisco Molecular dynamics simulation NMR Structure Antimicrobial Membrane Micelles Peptide structure Simulação de Dinâmica Molecular Antimicrobiana Micelas Membrana Peptídio Estrutura Imagem por Ressonância Magnética |
title_short |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
title_full |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
title_fullStr |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
title_full_unstemmed |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
title_sort |
Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data |
author |
Gomes Neto, Francisco |
author_facet |
Gomes Neto, Francisco Valente, Ana Paula Almeida, Fabio C. L. |
author_role |
author |
author2 |
Valente, Ana Paula Almeida, Fabio C. L. |
author2_role |
author author |
dc.contributor.author.fl_str_mv |
Gomes Neto, Francisco Valente, Ana Paula Almeida, Fabio C. L. |
dc.subject.en.pt_BR.fl_str_mv |
Molecular dynamics simulation NMR Structure Antimicrobial Membrane Micelles Peptide structure |
topic |
Molecular dynamics simulation NMR Structure Antimicrobial Membrane Micelles Peptide structure Simulação de Dinâmica Molecular Antimicrobiana Micelas Membrana Peptídio Estrutura Imagem por Ressonância Magnética |
dc.subject.decs.pt_BR.fl_str_mv |
Simulação de Dinâmica Molecular Antimicrobiana Micelas Membrana Peptídio Estrutura Imagem por Ressonância Magnética |
description |
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Biologia Estrutural e Bioimagem. Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas. Instituto de Bioquímica Médica. Rio de Janeiro, RJ, Brasil. |
publishDate |
2013 |
dc.date.issued.fl_str_mv |
2013 |
dc.date.accessioned.fl_str_mv |
2015-10-02T12:45:02Z |
dc.date.available.fl_str_mv |
2015-10-02T12:45:02Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
GOMES NETO, Francisco; VALENTE, Ana Paula; ALMEIDA, Fabio C. L.. Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data. Molecules, v.18, n.8, p.10056-10080, 2013. |
dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/11861 |
dc.identifier.issn.pt_BR.fl_str_mv |
1420-3049 |
dc.identifier.doi.pt_BR.fl_str_mv |
10.3390/molecules180810056 |
identifier_str_mv |
GOMES NETO, Francisco; VALENTE, Ana Paula; ALMEIDA, Fabio C. L.. Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data. Molecules, v.18, n.8, p.10056-10080, 2013. 1420-3049 10.3390/molecules180810056 |
url |
https://www.arca.fiocruz.br/handle/icict/11861 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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MDPI |
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MDPI |
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FIOCRUZ |
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FIOCRUZ |
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