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, Pineda-Peña, Andrea Clemencia, Khouri, Ricardo, Piampongsant, Supinya, Eusébio, Mónica, Ramon, Jan, Vandamme, Anne Mieke
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: https://doi.org/10.1186/s13062-014-0031-8
Resumo: PMID: 25564011 WOS:000349705400001
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spelling A new ensemble coevolution system for detecting HIV-1 protein coevolutionEnsemble coevolution systemGagHIV-1ProteaseProtein coevolutionSequence-based methodAgricultural and Biological Sciences(all)Biochemistry, Genetics and Molecular Biology(all)ImmunologyApplied MathematicsModelling and SimulationEcology, Evolution, Behavior and SystematicsSDG 3 - Good Health and Well-beingPMID: 25564011 WOS:000349705400001Background: A 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. Reviewers: This article was reviewed by Dr. Zoltán Gáspári.Instituto de Higiene e Medicina Tropical (IHMT)TB, HIV and opportunistic diseases and pathogens (THOP)Global Health and Tropical Medicine (GHTM)RUNLi, GuangdiTheys, KristofVerheyen, JensPineda-Peña, Andrea ClemenciaKhouri, RicardoPiampongsant, SupinyaEusébio, MónicaRamon, JanVandamme, Anne Mieke2018-05-14T22:01:56Z2015-01-072015-01-07T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.1186/s13062-014-0031-8eng1745-6150PURE: 1727135http://www.scopus.com/inward/record.url?scp=84924341489&partnerID=8YFLogxKhttps://doi.org/10.1186/s13062-014-0031-8info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:20:29Zoai:run.unl.pt:10362/36935Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:30:42.647531Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.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
Ensemble coevolution system
Gag
HIV-1
Protease
Protein coevolution
Sequence-based method
Agricultural and Biological Sciences(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology
Applied Mathematics
Modelling and Simulation
Ecology, Evolution, Behavior and Systematics
SDG 3 - Good Health and Well-being
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
Pineda-Peña, Andrea Clemencia
Khouri, Ricardo
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
author_role author
author2 Theys, Kristof
Verheyen, Jens
Pineda-Peña, Andrea Clemencia
Khouri, Ricardo
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Instituto de Higiene e Medicina Tropical (IHMT)
TB, HIV and opportunistic diseases and pathogens (THOP)
Global Health and Tropical Medicine (GHTM)
RUN
dc.contributor.author.fl_str_mv Li, Guangdi
Theys, Kristof
Verheyen, Jens
Pineda-Peña, Andrea Clemencia
Khouri, Ricardo
Piampongsant, Supinya
Eusébio, Mónica
Ramon, Jan
Vandamme, Anne Mieke
dc.subject.por.fl_str_mv Ensemble coevolution system
Gag
HIV-1
Protease
Protein coevolution
Sequence-based method
Agricultural and Biological Sciences(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology
Applied Mathematics
Modelling and Simulation
Ecology, Evolution, Behavior and Systematics
SDG 3 - Good Health and Well-being
topic Ensemble coevolution system
Gag
HIV-1
Protease
Protein coevolution
Sequence-based method
Agricultural and Biological Sciences(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology
Applied Mathematics
Modelling and Simulation
Ecology, Evolution, Behavior and Systematics
SDG 3 - Good Health and Well-being
description PMID: 25564011 WOS:000349705400001
publishDate 2015
dc.date.none.fl_str_mv 2015-01-07
2015-01-07T00:00:00Z
2018-05-14T22:01:56Z
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.uri.fl_str_mv https://doi.org/10.1186/s13062-014-0031-8
url https://doi.org/10.1186/s13062-014-0031-8
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1745-6150
PURE: 1727135
http://www.scopus.com/inward/record.url?scp=84924341489&partnerID=8YFLogxK
https://doi.org/10.1186/s13062-014-0031-8
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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