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 μs), the relaxation time of tRNA structural fluctuations was determined to be ∼10 ns, and the barrier-crossing attempt frequency of tRNA accommodation is ∼1-10 μs(-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.
Whitford
Paul C
PC
Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, MS K710, Los Alamos, New Mexico 87545, USA. whitford@lanl.gov
Onuchic
José N
JN
Sanbonmatsu
Karissa Y
KY
D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*
D012346:RNA, Transfer, Amino Acyl
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