Modeling the Interaction of Dodecylphosphocholine Micelles with the Anticoccidial Peptide PW2 Guided by NMR Data

Detalhes bibliográficos
Autor(a) principal: Gomes Neto, Francisco
Data de Publicação: 2013
Outros Autores: Valente, Ana Paula, Almeida, Fabio C. L.
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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spelling 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
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
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instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
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collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/11861/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/11861/2/francisco_gomesneto_etal_IOC_2013.pdf
https://www.arca.fiocruz.br/bitstream/icict/11861/3/francisco_gomesneto_etal_IOC_2013.pdf.txt
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