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How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome

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  • Jeffrey K. Noel

    (Center for Theoretical Biological Physics, Rice University
    Max Delbrück Center for Molecular Medicine, Kristallographie
    Fritz Haber Institute of the Max Planck Society)

  • Paul C. Whitford

    (Northeastern University)

Abstract

It has long been recognized that the thermodynamics of mRNA–tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical–chemical properties of the ribosome enable proofreading. To this end, we probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading.

Suggested Citation

  • Jeffrey K. Noel & Paul C. Whitford, 2016. "How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome," Nature Communications, Nature, vol. 7(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13314
    DOI: 10.1038/ncomms13314
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    Cited by:

    1. Clinton A. L. McFeely & Bipasana Shakya & Chelsea A. Makovsky & Aidan K. Haney & T. Ashton Cropp & Matthew C. T. Hartman, 2023. "Extensive breaking of genetic code degeneracy with non-canonical amino acids," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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