Physicochemical correlation between amino acid sites in short sequences under selective pressure

Authors:
David Campo;Zoya Dimitrova;Yuri Khudyakov
Affiliations:
Molecular Epidemiology & Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention., Atlanta, GA;Molecular Epidemiology & Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention., Atlanta, GA;Molecular Epidemiology & Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention., Atlanta, GA
Venue:
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Year:
2008

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Abstract

The activities and properties of proteins are the result of interactionsamong their constitutive amino acids. In the course of natural selection, substitutionswhich tend to destabilize a particular structure may be compensated byother substitutions which confer stability to that structure. Patterns of coordinatedsubstitutions were studied in two sets of selected peptides. The first is aset of 181 amino acid sequences that were selected in vitro to bind a MHC classI molecule (Kb). The second is a set of 114 sequences of the Hypervariable Region1 of Hepatitis C virus, which, originating from infected patients, resultfrom natural selection in vivo. The patterns of coordinated substitutions in bothdatasets showed many significant structural and functional links between pairsof positions and conservation of specific selected physicochemical properties.