An apparent conformational change in tRNA Phe that is associated with the peptidyl transferase reaction

Abstract

Fluorescence techniques were used to detect changes in the conformation of tRNA Phe that may occur during the peptidyl transferase reaction in which the tRNA appeara to move between binding sites on ribosomes. Such a conformational change may be a fundamental part of the translocation mechanism by which tRNA and mRNA are moved through ribosomes. E. coli tRNA Phe was specifically labeled on acp 3U 47 and s 4U 8 or at the D positions 16 and 20. The labeled tRNAs were bound to ribosomes as deacylated tRNA Phe or AcPhe-tRNA. Changes in fluorescence quantum yield and anisotropy were measured upon binding to the ribosomes and during the peptidyl transferase reaction. In one set of experiments non-radiative energy transfer was measured between a coumarin probe at position 16 or 20 and distance between the probes increases during deacylation of AcPhe-tRNA as a result of peptide bond formation. a fluorescein attached to acp 3U 47 on the same tRNA Phe molecule. The results indicate that the apparent All of the results are consistent with but in themselves do not conclusively establish that tRNA undergoes a conformational change as well as movement during the peptidyl transferase reaction.