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Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome

Nature Structural Biology volume 7, pages 1027–1031 (2000)Cite this article

Abstract

Upon transpeptidylation, the 3′ end of aminoacyl-tRNA (aa-tRNA) in the ribosomal A site enters the A/P hybrid state. We report that transpeptidylation of Phe-tRNA to fMetPhe-tRNA on Escherichia coli ribosomes substantially lowers the kinetic stability of the ribosome–tRNA complex and decreases the affinity by 18.9 kJ mol−1. At the same time, the free energy of activation of elongation factor G dependent translocation decreases by 12.5 kJ mol−1, indicating that part of the free energy of transpeptidylation is used to drive translocation kinetically. Thus, the formation of the A/P hybrid state constitutes an important element of the translocation mechanism.

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Figure 1: Kinetic stability of A site tRNA complexes.
Figure 2: Effect of spermine on fMetPhe-tRNAPhe binding to the A site.
Figure 3: Effect of Mg2+ on fMetPhe-tRNAPhe binding to the A site.
Figure 4: Stability of Phe-tRNAPhe binding to the A site.
Figure 5: Rapid kinetics of translocation.

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Acknowledgements

We thank C. Gualerzi for strains overproducing initiation factors, V. Makhno for purified tRNAs, and P. Striebeck and S. Möbitz for expert technical assistance. The work was supported by the Deutsche Forschungsgemeinschaft, the Volkswagen-Stiftung, the European Union, the Alfried Krupp von Bohlen und Halbach-Stiftung, and the Fonds der Chemischen Industrie.

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Authors and Affiliations

  1. Institute of Molecular Biology, University of Witten/Herdecke , Witten, D-58448, Germany

    Yuri P. Semenkov & Wolfgang Wintermeyer

  2. Sankt Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, 188350, Russia

    Yuri P. Semenkov

  3. Institute of Physical Biochemistry, University of Witten/Herdecke , Witten, D-58448, Germany

    Marina V. Rodnina

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  1. Yuri P. Semenkov
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Correspondence to Wolfgang Wintermeyer.

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Semenkov, Y., Rodnina, M. & Wintermeyer, W. Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome. Nat Struct Mol Biol 7, 1027–1031 (2000). https://doi.org/10.1038/80938

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