Induced fit in initial selection and proofreading of aminoacyl-tRNA on theribosome

The fidelity of aminoacyl-tRNA (aa-tRNA) selection by the bacterial ribosom e is determined by initial selection before and proofreading after GTP hydr olysis by elongation factor Tu. Here we report the rate constants of A-site binding of a near-cognate aa-tRNA. The comparison with the data for cognat e aa-tRNA reveals an additional, important contribution to aa-tRNA discrimi nation of conformational coupling by induced fit. It is found that two rear rangement steps that limit the chemical reactions of A-site binding, i.e. G TPase activation (preceding GTP hydrolysis) and A-site accommodation (prece ding peptide bond formation), are substantially faster for cognate than for near-cognate aa-tRNA. This suggests an induced-fit mechanism of aa-tRNA di scrimination on the ribosome that operates in both initial selection and pr oofreading. It is proposed that the cognate codon-anticodon interaction, mo re efficiently than the near-cognate one, induces a particular conformation of the decoding center of 16S rRNA, which in turn promotes GTPase activati on and A-site accommodation of aa-tRNA, thereby accelerating the chemical s teps. As kinetically favored incorporation of the correct substrate has als o been suggested for DNA and RNA polymerases, the present findings indicate that induced fit may contribute to the fidelity of template-programed syst ems in general.