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Journal Article

Anisotropic Fluctuations in the Ribosome Determine tRNA Kinetics


Noel,  Jeffrey
Max Delbrück Center for Molecular Medicine;
Physical Chemistry, Fritz Haber Institute, Max Planck Society;

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Yang, H., Noel, J., & Whitford, P. C. (2017). Anisotropic Fluctuations in the Ribosome Determine tRNA Kinetics. The Journal of Physical Chemistry B, 121(47), 10593-10601. doi:10.1021/acs.jpcb.7b06828.

Cite as: https://hdl.handle.net/11858/00-001M-0000-002D-EEA8-7
The ribosome is a large ribonucleoprotein complex that is responsible for the production of proteins in all organisms. Accommodation is the process by which an incoming aminoacyl-transfer RNA (aa-tRNA) molecule binds the ribosomal A site, and its kinetics has been implicated in the accuracy of tRNA selection. In addition to rearrangements in the aa-tRNA molecule, the L11 stalk can undergo large-scale anisotropic motions during translation. To explore the potential impact of this protruding region on the rate of aa-tRNA accommodation, we used molecular dynamics simulations with a simplified model to evaluate the free energy as a function of aa-tRNA position. Specifically, these calculations describe the transition between A/T and elbow-accommodated (EA) configurations (~ 20Å displacement). We find that the free-energy barrier associated with elbow accommodation is proportional to the degree of mobility exhibited by the L11 stalk. That is, when L11 is more rigid, the free-energy barrier height is decreased. This effect arises from the ability of L11 to confine, and thereby destabilize, the A/T ensemble. In addition, when Elongation Factor Tu (EF-Tu) is present, the A/T ensemble is further destabilized in an L11-dependent manner. These results provide a framework that suggests how next-generation experiments may precisely control the dynamics of the ribosome.