Author | Li, Guangdi | |
Author | Theys, Kristof | |
Author | Verheyen, Jens | |
Author | Peña, Andrea Clemencia Pineda | |
Author | Cunha, Antonio Ricardo Khouri | |
Author | Piampongsant, Supinya | |
Author | Eusébio, Mónica | |
Author | Ramon, Jan | |
Author | Vandamme, Anne Mieke | |
Access date | 2017-08-09T13:09:56Z | |
Available date | 2017-08-09T13:09:56Z | |
Document date | 2015 | |
Citation | LI, G. et al. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biology Direct, v. 10, p. 1, 2015. | pt_BR |
ISSN | 1745-6150 | pt_BR |
URI | https://www.arca.fiocruz.br/handle/icict/20560 | |
Description | Khouri, Antonio Ricardo “Documento produzido em parceria ou por autor vinculado à Fiocruz, mas não consta à informação no documento”. | pt_BR |
Sponsorship | 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]. | pt_BR |
Language | eng | pt_BR |
Publisher | BioMed Central | pt_BR |
Rights | open access | pt_BR |
Subject in Portuguese | HIV-1 | pt_BR |
Subject in Portuguese | Proteínas | pt_BR |
Subject in Portuguese | Protease | pt_BR |
Subject in Portuguese | Métodos | pt_BR |
Subject in Portuguese | Humanos | pt_BR |
Title | A new ensemble coevolution system for detecting HIV-1 protein coevolution | pt_BR |
Type | Article | pt_BR |
DOI | 10.1186/s13062-014-0031-8 | |
Abstract | 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. | pt_BR |
Affilliation | KU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium | pt_BR |
Affilliation | KU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium | pt_BR |
Affilliation | University Duisburg-Essen. University hospital. Institute of Virology. Essen, Germany | pt_BR |
Affilliation | KU 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, Colombia | pt_BR |
Affilliation | KU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium | pt_BR |
Affilliation | KU Leuven - University of Leuven. Rega Institute for Medical Research. Clinical and Epidemiological Virology. Department of Microbiology and Immunology. Leuven, Belgium | pt_BR |
Affilliation | Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia. Lisboa, Portugal | pt_BR |
Affilliation | KU Leuven - University of Leuven. Department of Computer Science. Leuven, Belgium | pt_BR |
Affilliation | KU 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, Portugal | pt_BR |
Subject | HIV-1 | pt_BR |
Subject | Protein coevolution | pt_BR |
Subject | Gag | pt_BR |
Subject | Protease | pt_BR |
Subject | Ensemble coevolution system | pt_BR |
Subject | Sequence-based method | pt_BR |