화학공학소재연구정보센터
Journal of Physical Chemistry B, Vol.104, No.9, 2148-2153, 2000
Revealing the role of water in the acid-base interaction between the phosphate groups of DNA and the amino acid side chains of proteins: A density functional theory study of molecular models
Salt bridges between DNA and the Lys, Arg, and His side chains of proteins are studied at the B3-LYP/6-31G(d) level of theory using molecular models. Calculations show that for His the stabilization of the [deprotonated DNA phosphate group](-)- -[protonated protein basic group](+) bridge requires its solvation by at least three water molecules. By analogy with acid-base interactions in inorganic chemistry, this is accounted for by the structure of the protonated His basic group (the imidazole ring), which does not allow the interaction of this group with the deprotonated phosphate group of DNA by more than one strong H-bond. For Lys and Arg the 2-fold H-bonding interaction between the acid and base residues is strong enough to stabilize the related ion-pair complexes without solvation, For all three salt linkages the nonspecific acid-base interaction is energetically permitted with a few water molecules lying between the oppositely charged acid and base moieties, For the used molecular models the difference in energy between the specific and nonspecific interactions is within 5 kcal/mol, The "specific" and "nonspecific" states of the salt bridges substantially differ from each other in both the bridge length and the relative arrangement of acid and base residues. This may play a significant role in the biological functioning of DNA-protein assemblages providing the structural adaptability of the salt linkages to the requirements of multicontact interactions between DNA and proteins.