A new ensemble coevolution system for detecting HIV-1 protein coevolution

Detalhes bibliográficos
Autor(a) principal: Li, Guangdi
Data de Publicação: 2015
Outros Autores: Theys, Kristof, Verheyen, Jens, Peña, Andrea Clemencia Pineda, Cunha, Antonio Ricardo Khouri, Piampongsant, Supinya, Eusébio, Mónica, Ramon, Jan, Vandamme, Anne Mieke
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/20560
Resumo: Khouri, Antonio Ricardo “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.
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spelling Li, GuangdiTheys, KristofVerheyen, JensPeña, Andrea Clemencia PinedaCunha, Antonio Ricardo KhouriPiampongsant, SupinyaEusébio, MónicaRamon, JanVandamme, Anne Mieke2017-08-09T13:09:56Z2017-08-09T13:09:56Z2015LI, G. et al. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biology Direct, v. 10, p. 1, 2015.1745-6150https://www.arca.fiocruz.br/handle/icict/2056010.1186/s13062-014-0031-8Khouri, Antonio Ricardo “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.Fonds voor Wetenschappelijk Onderzoek – Flanders (FWO) [PDO/11 to K.T., G.0692.14]; the European Community’s Seventh Framework Programme (FP7/2007-2013) under the project “Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN)” [223131].KU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, BelgiumKU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, BelgiumUniversity Duisburg-Essen. University hospital. Institute of Virology. Essen, GermanyKU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium / Universidad del Rosario. Faculty of Sciences and Mathematics. Clinical and Molecular Infectious Disease Group. Bogotá, ColombiaKU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, BelgiumKU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, BelgiumUniversidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia. Lisboa, PortugalKU Leuven - University of Leuven. Department of Computer Science. Leuven, BelgiumKU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium / Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia. Lisboa, PortugalA key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect position-specific coevolution within and between different proteins. However, an ensemble coevolution system that integrates different methods to improve the detection of HIV-1 protein coevolution has not been developed. Results: We integrated 27 sequence-based prediction methods published between 2004 and 2013 into an ensemble coevolution system. This system allowed combinations of different sequence-based methods for coevolution predictions. Using HIV-1 protein structures and experimental data, we evaluated the performance of individual and combined sequence-based methods in the prediction of HIV-1 intra- and inter-protein coevolution. We showed that sequence-based methods clustered according to their methodology, and a combination of four methods outperformed any of the 27 individual methods. This four-method combination estimated that HIV-1 intra-protein coevolving positions were mainly located in functional domains and physically contacted with each other in the protein tertiary structures. In the analysis of HIV-1 inter-protein coevolving positions between Gag and protease, protease drug resistance positions near the active site mostly coevolved with Gag cleavage positions (V128, S373- T375, A431, F448-P453) and Gag C-terminal positions (S489-Q500) under selective pressure of protease inhibitors. Conclusions: This study presents a new ensemble coevolution system which detects position-specific coevolution using combinations of 27 different sequence-based methods. Our findings highlight key coevolving residues within HIV-1 structural proteins and between Gag and protease, shedding light on HIV-1 intra- and inter-protein coevolution.engBioMed CentralHIV-1ProteínasProteaseMétodosHumanosHIV-1Protein coevolutionGagProteaseEnsemble coevolution systemSequence-based methodA new ensemble coevolution system for detecting HIV-1 protein coevolutioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/20560/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALLi G A new ensemble coevolution....pdfLi G A new ensemble coevolution....pdfapplication/pdf2719454https://www.arca.fiocruz.br/bitstream/icict/20560/2/Li%20G%20A%20new%20ensemble%20coevolution....pdf3e7fc53939b05954a20886729775869cMD52TEXTLi G A new ensemble coevolution....pdf.txtLi G A new ensemble coevolution....pdf.txtExtracted texttext/plain98875https://www.arca.fiocruz.br/bitstream/icict/20560/3/Li%20G%20A%20new%20ensemble%20coevolution....pdf.txta7e370f87a7160417d78ad8a9c508c27MD53icict/205602023-03-15 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dc.title.pt_BR.fl_str_mv A new ensemble coevolution system for detecting HIV-1 protein coevolution
title A new ensemble coevolution system for detecting HIV-1 protein coevolution
spellingShingle A new ensemble coevolution system for detecting HIV-1 protein coevolution
Li, Guangdi
HIV-1
Proteínas
Protease
Métodos
Humanos
HIV-1
Protein coevolution
Gag
Protease
Ensemble coevolution system
Sequence-based method
title_short A new ensemble coevolution system for detecting HIV-1 protein coevolution
title_full A new ensemble coevolution system for detecting HIV-1 protein coevolution
title_fullStr A new ensemble coevolution system for detecting HIV-1 protein coevolution
title_full_unstemmed A new ensemble coevolution system for detecting HIV-1 protein coevolution
title_sort A new ensemble coevolution system for detecting HIV-1 protein coevolution
author Li, Guangdi
author_facet Li, Guangdi
Theys, Kristof
Verheyen, Jens
Peña, Andrea Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
author_role author
author2 Theys, Kristof
Verheyen, Jens
Peña, Andrea Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Li, Guangdi
Theys, Kristof
Verheyen, Jens
Peña, Andrea Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
dc.subject.other.pt_BR.fl_str_mv HIV-1
Proteínas
Protease
Métodos
Humanos
topic HIV-1
Proteínas
Protease
Métodos
Humanos
HIV-1
Protein coevolution
Gag
Protease
Ensemble coevolution system
Sequence-based method
dc.subject.en.pt_BR.fl_str_mv HIV-1
Protein coevolution
Gag
Protease
Ensemble coevolution system
Sequence-based method
description Khouri, Antonio Ricardo “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”.
publishDate 2015
dc.date.issued.fl_str_mv 2015
dc.date.accessioned.fl_str_mv 2017-08-09T13:09:56Z
dc.date.available.fl_str_mv 2017-08-09T13:09:56Z
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 LI, G. et al. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biology Direct, v. 10, p. 1, 2015.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/20560
dc.identifier.issn.pt_BR.fl_str_mv 1745-6150
dc.identifier.doi.none.fl_str_mv 10.1186/s13062-014-0031-8
identifier_str_mv LI, G. et al. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biology Direct, v. 10, p. 1, 2015.
1745-6150
10.1186/s13062-014-0031-8
url https://www.arca.fiocruz.br/handle/icict/20560
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 BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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