Document Detail


Constraints on HIV-1 diversity from protein structure.
MedLine Citation:
PMID:  20881050     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Jeongmin Woo; David L Robertson; Simon C Lovell
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-09-29
Journal Detail:
Title:  Journal of virology     Volume:  84     ISSN:  1098-5514     ISO Abbreviation:  J. Virol.     Publication Date:  2010 Dec 
Date Detail:
Created Date:  2010-11-24     Completed Date:  2011-01-06     Revised Date:  2013-07-03    
Medline Journal Info:
Nlm Unique ID:  0113724     Medline TA:  J Virol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  12995-3003     Citation Subset:  IM    
Affiliation:
Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom.
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MeSH Terms
Descriptor/Qualifier:
Evolution, Molecular*
Genetic Variation*
HIV Infections / genetics*,  virology
HIV-1 / chemistry,  genetics*
Humans
Phylogeny
Selection, Genetic
Sequence Analysis, DNA
env Gene Products, Human Immunodeficiency Virus / chemistry*,  genetics
gag Gene Products, Human Immunodeficiency Virus / chemistry*,  genetics
Chemical
Reg. No./Substance:
0/env Gene Products, Human Immunodeficiency Virus; 0/gag Gene Products, Human Immunodeficiency Virus
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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