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

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dc.creatorLi, Guangdispa
dc.creatorTheys, Kristofspa
dc.creatorVerheyen, Jensspa
dc.creatorPineda-Peña, Andrea-Clemenciaspa
dc.creatorKhouri, Ricardospa
dc.creatorPiampongsant, Supinyaspa
dc.creatorEusébio, Mónicaspa
dc.creatorRamon, Janspa
dc.creatorVandamme, Anne-Miekespa
dc.date.accessioned2020-05-26T00:02:47Z
dc.date.available2020-05-26T00:02:47Z
dc.date.created2015spa
dc.description.abstractBackground: 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. © Li et al.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1186/s13062-014-0031-8
dc.identifier.issn17456150
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/23525
dc.language.isoengspa
dc.publisherBioMed Central Ltd.spa
dc.relation.citationIssueNo. 1
dc.relation.citationTitleBiology Direct
dc.relation.citationVolumeVol. 10
dc.relation.ispartofBiology Direct, ISSN:17456150, Vol.10, No.1 (2015)spa
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84924341489&doi=10.1186%2fs13062-014-0031-8&partnerID=40&md5=a2516db1dde236133699aff9944085fbspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subject.keywordHuman immunodeficiency virus 1spa
dc.subject.keywordgageng
dc.subject.keywordHuman immunodeficiency virus proteinasespa
dc.subject.keywordProtein bindingspa
dc.subject.keywordViral proteinspa
dc.subject.keywordArea under the curvespa
dc.subject.keywordBiologyspa
dc.subject.keywordChemistryspa
dc.subject.keywordGeneticsspa
dc.subject.keywordHumanspa
dc.subject.keywordHuman immunodeficiency virus 1spa
dc.subject.keywordMolecular evolutionspa
dc.subject.keywordMolecular modelspa
dc.subject.keywordProceduresspa
dc.subject.keywordProtein databasespa
dc.subject.keywordProtein tertiary structurespa
dc.subject.keywordReproducibilityspa
dc.subject.keywordStatistical modelspa
dc.subject.keywordArea Under Curvespa
dc.subject.keywordComputational Biologyspa
dc.subject.keywordDatabaseseng
dc.subject.keywordEvolutioneng
dc.subject.keywordGag Gene Productseng
dc.subject.keywordGene Productseng
dc.subject.keywordHIV Proteasespa
dc.subject.keywordHIV-1spa
dc.subject.keywordHumansspa
dc.subject.keywordModelseng
dc.subject.keywordModelseng
dc.subject.keywordProtein Bindingspa
dc.subject.keywordProtein Structureeng
dc.subject.keywordReproducibility of Resultsspa
dc.subject.keywordViral Proteinsspa
dc.subject.keywordEnsemble coevolution systemspa
dc.subject.keywordGagspa
dc.subject.keywordHIV-1spa
dc.subject.keywordProteasespa
dc.subject.keywordProtein coevolutionspa
dc.subject.keywordSequence-based methodspa
dc.titleA new ensemble coevolution system for detecting HIV-1 protein coevolutionspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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