Proton nuclear magnetic resonance of minor nucleosides in yeast phenylalanine transfer ribonucleic acid. Conformational changes as a consquence of aminoacylation, removal of the Y base, and codon-anticodon interaction

Abstract

The assignments of the resonances of the methyl and methylene groups belonging to the residues dihydrouridine-16 and 17 (C5 and C6), dimethylguanosine-26, N-2-methylguanosine-10, and 7-methylguanosine-46 of yeast tRNAPhe at low temperature are reported. Observing the high-field proton NMR spectral region at different temperatures, the effect of aminoacylation, removal of the Y base, and codon-anticodon interaction on the tertiary structure of yeast tRNAPhe were investigated. The two dihydrouridine residues of tRNAPhe have different environments in aqueous solution: dihydrouridine-16 is more shielded than dihydrouridine-17. The ribothymidine residue from the fragment (47-76) of yeast tRNAPhe and from a tRNA with a partially disrupted structure exhibits multiple conformations arising from different stacking modes between the ribothymidine-54 and the guanosine-53 residue. Upon aminoacylation, the type of guanosine-53 interaction with ribothymidine-54 in the tRNAPhe changes. Removal of the Y base from the anticodon loop of yeast tRNAPhe weakens the thermal stability of the tertiary interactions. The interaction of 2 complementary anticodons in the absence of proteins and of ribosomes results in stabilization of the teritary structure. Codon-anticodon interaction dependent rearrangement of the tertiary structure of yeast tRNAPhe was not observed. The spin-lattice relaxation times of the methyl and methylene groups of the minor nucleosides in yeast tRNAPhe demonstrate that the minor nucleosides undergo rotational reorientation (.tau.c) in the nanosecond range. The observed differences in these .tau.c values indicate a similarity of structure of tRNAPhe in solution and in crystalline form.