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doi:10.1534/genetics.105.053249
A more recent version of this article appeared on May 1, 2006.
REGULAR RESEARCH PAPERS |
A novel method to detect intra-molecular coevolution: adding a further dimension to selective constraints analyses
Mario A Fares 1* and Simon A. A. Travers 1
1 National University of Ireland, Maynooth
* To whom correspondence should be addressed. E-mail: mario.fares{at}nuim.ie.
Submitted on November 8, 2005
Revised on December 8, 2005
Accepted on 3 March 2006
Protein evolution depends on intra-molecular coevolutionary networks whose complexity is proportional to the underlying functional and structural interactions amongst sites. Here we present a novel approach that vastly improves the sensitivity of previous methods to detect coevolution through a weighted comparison of divergence between amino acid sites. The analysis of the HIV-1 Gag protein detected convergent adaptive coevolutionary events responsible for the selective variability emerging between subtypes. Coevolution analysis and functional data for heat-shock proteins, Hsp90 and GroEL, highlights that almost all detected coevolving sites are functionally or structurally important. The results support previous suggestions pinpointing the complex inter-domain functional interactions within these proteins and we propose new amino acid sites as important for inter-domain functional communication. Three-dimensional information sheds light on the functional and structural constraints governing the coevolution between sites. Our covariation analyses propose two types of coevolving sites in agreement with previous reports: pairs of sites spatially proximal, where compensatory mutations could maintain the local structure stability; and clusters of distant sites located in functional domains, suggesting a functional dependency between them. All sites detected under adaptive evolution in these proteins belong to coevolution groups, further underlining the importance of testing for coevolution in selective constraints analyses.
Key Words: Atomic distance, HIV-1 gag gene, Heat-shock protein, Intra-molecular coevolution, Selection constraints
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