A role of elementary interactions between nucleic-acid base and amino-acid side chains in specificity of ribonuclease

Several X-ray structures of model crystals that contain hydroxyl group and nucleic-acid bases suggest that hydroxyl group interacts preferentially with pyrimidines than with purines through hydrogen bonds. This explains a role of Thr 45 and Ser 123 at the B1 site of RNAase A. The stacking energies of nucleic-acid bases with the protonated imidazolyl group are estimated to be in the order of C greater than A greater than G greater than U from 1H-NMR spectra and CNDO/2 calculations. Such interactions, in addition to hydrogen bondings, would stabilize the binding of substrates at the B2 site.