Interaction of protein backbone with nucleic acid bases

A theoretical study of the hydrogen-bonded (HB) complexes between a protein model and nucleic acid bases (NAB) has been carried out. As protein models, N-formylglycinamide (For-Gly-NH2, 2-formylaminoacetamide), 1, in beta- and gamma-conformations and as NABs, the isolated ones, and the AU, GC dimers in the Watson-Crick (WC) disposition have been considered. Only those dispositions with a double HB between the protein model and the nucleic acid bases have been studied. The aromatic CH groups of the nucleic acids have been included as HB donor. The results indicate that the strongest HBs between the individual NAB and the protein models involve the atoms that participate in the formation of the WC dimers. In the trimeric complexes, no significant preference is obtained for the 1-AU trimers studied while in the 1-GC ones the complex where formylglycinamide interacts simultaneously with the carbonyl group of guanine and the amino of cytosine is favored. The electron density of the complexes has been analyzed using the atoms in molecules methodology, finding exponential relationships between the electron density and its Laplacian vs the bond distance. Finally, the effect in the nuclear chemical shielding due to the complexation has been explored. Exponential relationships have been found for the variation of the chemical shift of the H-1 signal for the (NHO)-O-... and (NHN)-N-... interactions with the HB distance.