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Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure

  • David Campo
  • Zoya Dimitrova
  • Yuri Khudyakov
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

The activities and properties of proteins are the result of interactions among their constitutive amino acids. In the course of natural selection, substitutions which tend to destabilize a particular structure may be compensated by other substitutions which confer stability to that structure. Patterns of coordinated substitutions were studied in two sets of selected peptides. The first is a set of 181 amino acid sequences that were selected in vitro to bind a MHC class I molecule (Kb). The second is a set of 114 sequences of the Hypervariable Region 1 of Hepatitis C virus, which, originating from infected patients, result from natural selection in vivo. The patterns of coordinated substitutions in both datasets showed many significant structural and functional links between pairs of positions and conservation of specific selected physicochemical properties.

Keywords

physicochemical properties amino acid covariation selection 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • David Campo
    • 1
  • Zoya Dimitrova
    • 1
  • Yuri Khudyakov
    • 1
  1. 1.Molecular Epidemiology & Bioinformatics Laboratory, Division of Viral HepatitisCenters for Disease Control and PreventionAtlanta

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