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Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.

ABSTRACT: 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 ?s), 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 ?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.

SUBMITTER: Whitford PC

PROVIDER: S-EPMC2945706 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.

Whitford Paul C PC Onuchic José N JN Sanbonmatsu Karissa Y KY

Journal of the American Chemical Society 20100901 38

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 experiment ...[more]

PMID: 20806913

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