Site Preferences Of Nucleic Acid Bases Hydrogen Bonding To Glycine Dipeptide

Studying the hydrogen bonding sites between nucleic acid bases and protein polypeptide has important guiding value in understanding the interaction between nucleic acid and protein.The optimal structures of forty-six hydrogen-bonded complexes,containing one glycine dipeptide molecule and one of the nucleic acid base adenine,thymine,uracil,guanine and cytosine,were obtained at the B3LYP/6-31+G(d,p)level.The binding energies of these complexes were further evaluated at the CP-corrected MP2/aug-cc-pVTZ level.This paper contains there parts as following:1.The site-preferences of the five nucleic acid bases hydrogen bond to glycine dipeptide are explored.The calculation results show that any of the five nucleic acid bases can hydrogen bond to glycine dipeptide through different binding site.The hydrogen-bonded complexes formed through site A3 of adenine,site T1 of thymine,site U1 of uracil,site C1 of cytosine and site G3 of guanine are most stable.Glycine dipeptide can use either site Gly5 or site Gly7 to form hydrogen-bonded complexes with nucleic acid bases,the hydrogen-bonded complexes formed through site Gly5 of glycine are more stable.2.The stability of the hydrogen-bonded complexes is associated with the enthalpy change of the protonation reaction and the deprotonation reaction of the nucleic acid bases.The more negative the enthalpy change of the protonation reaction or the smaller the enthalpy change of the deprotonation reaction,the more stable the hydrogen-bonded complexes.3.Water solvent has great influences on the binding energies of these complexes.