ArticleJournal of virology2010
Constraints on HIV-1 diversity from protein structure.
Article in Journal of virology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Functional and Structural Determinants of Long- and Short-Term Evolution of Herpesvirus Proteins.Molecular biology and evolution · 2025Article
- New SHIVs and Improved Design Strategy for Modeling HIV-1 Transmission, Immunopathogenesis, Prevention and Cure.Journal of virology · 2021Article
- Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.Science (New York, N.Y.) · 2021Article
- Genetic divergence of HIV-1 B subtype in Italy over the years 2003-2016 and impact on CTL escape prevalence.Scientific reports · 2018Article
- Adaptive HIV-1 evolutionary trajectories are constrained by protein stability.Virus evolution · 2017Article
- Collective Infectious Units in Viruses.Trends in microbiology · 2017Review
- Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.PLoS biology · 2017Article
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- Genetic Consequences of Antiviral Therapy on HIV-1.Computational and mathematical methods in medicine · 2015Review
- Uneven genetic robustness of HIV-1 integrase.Journal of virology · 2015Article
- Genetic diversity of the highly variable V1 region interferes with Human Immunodeficiency Virus type 1 envelope functionality.Retrovirology · 2013Article
- Amino acid sequence diversity of the major human papillomavirus capsid protein: implications for current and next generation vaccines.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2013Article
- Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1.PLoS biology · 2013Article
- Neutralizing antibodies and control of HIV: moves and countermoves.Current HIV/AIDS reports · 2012Review
- Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints.Retrovirology · 2011Article
- HIV-1 envelope accessible surface and polarity: clade, blood, and brain.Bioinformation · 2011Article
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Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high rate of HIV-1 evolution contributes to immune escape, enables the virus to escape drug therapy, and may underlie the difficulty of producing an effective vaccine. Identifying constraints on HIV evolution is therefore of prime importance. To investigate this problem, we examined the relationships between sequence diversity, selection, and protein structure. We found that while there was an increase in sequence diversity over time, this variation had a tendency to be limited to specific structural regions. When individual sites were analyzed, there was, in contrast, substantial and widespread evolutionary constraint over gag and env. This constraint was present even in the highly variable envelope proteins. The evolutionary significance of an individual site is indicated by the change in selection pressure along the time course: increasing entropy indicates that the site is evolving predominantly in a more "clock"-like manner, low entropy values with no increase indicate a high degree of constraint, and high entropy values indicate a lack of constraint. Few sites display high degrees of turnover. Mapping these sites onto the three-dimensional protein structure, we found a significant difference between evolutionary rates for regions buried in the core of the protein and those on the surface. This constraint did not change over the time period analyzed and was not subtype dependent, as similar results were found for subtypes B and C. This link between sequence and structure not only demonstrates the limits of recent HIV-1 evolution but also highlights the origins of evolutionary constraint on viral change.
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