A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition

sThe ribosome is a dynamic particle that undergoes many structural changes during translation. We show through chemical probing with dimethyl sulfate (DMS) that conformational changes occur at several nucleotides in the pepti dyl transferase center upon alterations in pH, temperature, and monovalent ion concentration, consistent with observations made by Elson and coworkers over 30 years ago. Moreover, we have found that the pH-dependent DMS react ivity of A2451 in the center of the 23S rRNA peptidyl transferase region, a scribed to a perturbed pKa of this base, occurs only in inactive 50S and 70 S ribosomes. The degree of DMS reactivity of this base in the inactive ribo somes depends on both the identity and amount of monovalent ion present. Fu rthermore, G2447, a residue proposed to be critical for the hypothesized pK a perturbation, is not essential for the conditional DMS reactivity at A245 1. Given that the pH-dependent change in DMS reactivity at A2451 occurs onl y in inactive ribosomes, and that this DMS reactivity can increase with inc reasing salt (independently of pH), we conclude that this observation canno t be used as supporting evidence for a recently proposed model of acid/base catalyzed ribosomal transpeptidation.