[Theoretical conformational analysis of noncovalent complexes of purine nucleotides with ribonuclease]

Semiempirical potential energy calculations have been carried out to locate possible binding sites for purine nucleoside phosphates at the RNase S active center. The nucleobase of adenosine or 8-oxoadenosine was shown to be accommodated at the pyrimidine binding site of the enzyme provided the nucleoside must be "syn". The mutual orientation of 8-oxoadenosine carbonyl group and NH-group of Thr-45 suggests a formation of a corresponding hydrogen bond in the enzyme--nucleotide complex. The formation of the hydrogen bond was postulated earlier to be essential for specific recognition of the substrate by RNase. The results obtained are in good agreement with the postulate. The "leaving group" binding site at the RNase S active center was found to be nonspecific toward conformation (syn-anti) of purine nucleotides studied. In addition, optimal conformation of dinucleosidemonophosphate bound to the enzyme active site was estimated for Pyr-P-Pur substrates.