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[Theoretical approaches for evaluation of DNA-protein interactions]
S A Vasil'ev1, A V Alekseevskiĭ, S A Spirin
1All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, ul. Timiryazevskaya 42, Moscow, 127550 Russia.
Abstract:
The notion of the DNA-recognizing segment of a protein for three-dimensional structures of DNA-protein complexes was formalized. Algorithms for calculating two parameters, hydrogen bonds and hydrophobic contacts, that characterize the interaction of the DNA-recognizing segment of the protein with the groove DNA major were proposed. DNA-recognizing protein segments in three-dimensional structures (of complexes) were classified according to these two parameters. These data were compared with the classification of the corresponding DNA-recognizing domains according to structure. The contribution of each pair amino acid residue-base to the interaction of protein with the DNA major groove was calculated.