دورية أكاديمية
أعرض في EDS

HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models.

التفاصيل البيبلوغرافية
العنوان: HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models.
المؤلفون: Del Amparo R; Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain., Arenas M; Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain.; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.; Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain.
المصدر: Genes [Genes (Basel)] 2021 Dec 27; Vol. 13 (1). Date of Electronic Publication: 2021 Dec 27.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101551097 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4425 (Electronic) Linking ISSN: 20734425 NLM ISO Abbreviation: Genes (Basel) Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel : MDPI
مواضيع طبية MeSH: Evolution, Molecular* , Models, Genetic* , Models, Statistical*, HIV Infections/*virology , HIV Protease/*genetics , HIV-1/*genetics , Integrases/*genetics, Algorithms ; Amino Acid Substitution ; Computer Simulation ; HIV Protease/metabolism ; HIV-1/enzymology ; Humans ; Integrases/metabolism ; Phylogeny
مستخلص: Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.
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فهرسة مساهمة: Keywords: HIV; phylogenetic reconstruction; protein evolution; substitution model of protein evolution; viral integrase; viral protease
المشرفين على المادة: EC 2.7.7.- (Integrases)
EC 3.4.23.- (HIV Protease)
تواريخ الأحداث: Date Created: 20220121 Date Completed: 20220221 Latest Revision: 20240405
رمز التحديث: 20240405
مُعرف محوري في PubMed: PMC8774313
DOI: 10.3390/genes13010061
PMID: 35052404
قاعدة البيانات: MEDLINE
الوصف
تدمد:2073-4425
DOI:10.3390/genes13010061