1H and 15N NMR investigation of the interaction of pyrimidine nucleotides with ribonuclease A

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Abstract
Extensive 1H and 15H NMR investigations of the nucleotide moieties capable of hydrogen bonding to [bovine pancreatic] RNase A were carried out in order to gain more detailed information on the specificity of nucleotide-enzyme interaction. The 1H investigations focused on those protons presumed to be involved in hydrogen bonding between the various nucleotides and the enzyme. In particular these were the imino protons of the uridine nucleotides and the amino protons of the cytidine nucleotides. The technique of 15N-1H double quantum filtering was applied for observation of the resonances of the latter in the nucleotide-enzyme complex. The downfield shift observed for the imino proton resonance of the uridine nucleotides was indicative of hydrogen bond formation to the enzyme. 15N NMR spectra of the free nucleotides and the nucleotide-enzyme complexes were also acquired to examine the possibility of hydrogen bond formation at the N3 site of both pyrimidine bases and the amino group of the cytidine nucleotides. The downfield shift observed for the 15N3 resonance of the uridine nucleotides and the upfield shift observed for the corresponding resonance of the cytidine nucleotides was evidence that the N3 moiety acts as hydrogen donor or hydrogen acceptor in the nucleotide-enzyme complex. The effect of complex formation on the 15N1 resonance of the respective bases was also studied. Both 1H and 15N NMR results indicated subtle differences between the complexes of the 2'' and 3'' nucleotides. The extent of hydrogen bonding as well as the arrangement of the nucleotide base at the active site of the enzyme varies in dependence on the position of the phosphate group. Hydrogen bonding, though not the main binding force between the nucleotides and the enzyme evidently is a major factor of RNase A specificity for pyrimidine nucleotides.