Dynamics of tRNA occupancy and dissociation during translation by the ribosome

Abstract

Repetitive cycles of protein elongation by the ribosome involve dynamic changes in tRNA occupancy and the deacylated-tRNA dissociation plays an important role in the process. Here we present a detailed analysis of the dynamics for the complicated process. We study analytically the dynamic tRNA occupancy and, specifically, the mean time for occupancy of one tRNA molecule, two tRNA molecules and three tRNA molecules during one cycle of protein elongation. The deacylated-tRNA dissociation probability at each state of the elongation cycle is analytically studied. The analyses give quantitative explanations of the available experimental data and provide interesting results: for example, the deacylated tRNA in hybrid P/E state can also be dissociated from the ribosome, as in post-translocation E/E state, but with a dissociation rate in the former being only about 1/20-fold of that in the latter; at low EF-G.GTP concentration, large fractions of the deacylated tRNA molecules are dissociated before the codon recognition in the A site and the ribosome is most of the time occupied by only one tRNA molecule, while at high and in vivo near EF-G.GTP concentration the ribosome is most of the time occupied by two tRNA molecules and the release of a third tRNA occurs mainly after the decoding step; even at high concentrations of EF-G.GTP and aminoacyl-tRNA.EF-Tu.GTP complex, the mean time for occupancy of three tRNA molecules is in the order of milliseconds in one translation cycle, which is much shorter than the in vitro mean translation time of about 1s.