[Theoretical approaches for evaluation of DNA-protein interactions].
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.
Vasil'ev
S A
SA
All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, ul. Timiryazevskaya 42, Moscow, 127550 Russia.
Alekseevskiĭ
A V
AV
Spirin
S A
SA
Tashlitskiĭ
V N
VN
Kariagina
A S
AS
D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation
D004268:DNA-Binding Proteins; D010455:Peptides; D004247:DNA
Teoreticheskie podkhody k otsenke spetsificheskogo DNK-belkovogo vzaimodeĭstviia.