Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome

Using explicit-solvent simulations of the 70S ribosome, the barrier-crossing attempt frequency was calculated for aminoacyl-tRNA elbow-accommodation. In seven individual trajectories (200-300 ns, each, for an aggregate time of 2.1 mu s), the relaxation time of tRNA structural fluctuations was determined to be similar to 10 ns, and the barrier-crossing attempt frequency of tRNA accommodation is similar to 1-10 mu s(-1). These calculations provide a quantitative relationship between the free-energy barrier and experimentally measured rates of accommodation, which demonstrate that the free-energy barrier of elbow-accommodation is less than 15 k(B) T, in vitro and in vivo.