Fig. 20. Correlated co-adaptive substitutions exemplified by the pair of amino acid residues forming the so-called salt bridge by opposite charged side groups. Only those substitutions that retain the salt bridge are permitted.
PROTEINS: COMPUTER ANALYSIS OF STRUCTURE, FUNCRION, AND EVOLUTION
D.A.Afonnikov, I.I.Titov, A.S.Frolov, N.A.Kolchanov
We have developed the computer system CRASP for analyzing structure-function organization and evolution of proteins. The method is based on detection of co-adaptive (in terms of physico-chemical parameters) pairwise substitutions of amino acid residues in proteins (Fig. 20). Interactions between amino acid residues are determined by their physico-chemical parameters; therefore, we believe that this approach can be a useful tool to reveal important interactions in protein globules. We used this system to study various families of globular proteins, including DNA-binding domains of regulatory proteins (Fig. 21). Groups of pairwise-correlated substitutions are frequently found in DNA-binding domains and are likely to provide for the retention of certain protein properties during the evolution.
Fig. 20. Correlated co-adaptive substitutions exemplified by the pair of amino acid
residues forming the so-called salt bridge by opposite charged side groups. Only those
substitutions that retain the salt bridge are permitted.
Fig. 21. (a) The bZIP domain primary structure; (b) Tertiary structure of the DNA-protein complex (bZIP); (c) Matrix of the pairwise correlation coefficients between the isoelectiric point values of amino acids for the bZIP types of DNA-binding domains of CREB-AP1 family transcription factors. Blue, the pairs of position with significant negative correlations; red, with positive correlations. The correlating pairs of positions located at N- and C-termini of the main region are given in ovals. QN and QC denotes net isoelectric point values for amino acids at positions 227-229 and 248-252 correspondingly.
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