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.
D000596:Amino Acids; D006860:Hydrogen Bonding; D006900:Hydroxylation; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011687:Purines; D011743:Pyrimidines; D012259:Ribonuclease, Pancreatic / Q000378:metabolism*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014961:X-Ray Diffraction / Q000379:methods
D000596:Amino Acids; D011687:Purines; D011743:Pyrimidines; D012259:Ribonuclease, Pancreatic