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Model of ribosome translation and mRNA unwinding

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Abstract

A ribosome is an enzyme that catalyzes translation of the genetic information encoded in messenger RNA (mRNA) into proteins. Besides translation through the single-stranded mRNA, the ribosome is also able to translate through the duplex region of mRNA via unwinding the duplex. Here, based on our proposed ribosome translation model, we study analytically the dynamics of Escherichia coli ribosome translation through the duplex region of mRNA, and compare with the available single molecule experimental data. It is shown that the ribosome uses only one active mechanism (mechanical unwinding), rather than two active mechanisms (open-state stabilization and mechanical unwinding), as proposed before, to unwind the duplex. The reduced rate of translation through the duplex region is due to the occurrence of futile transitions, which are induced by the energy barrier from the duplex unwinding to the forward translocation along the single-stranded mRNA. Moreover, we also present predicted results of the average translation rate versus the external force acting on the ribosome translating through the duplex region and through the single-stranded region of mRNA, which can be easily tested by future experiments.

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Notes

  1. Since the mRNA channel in the 30S subunit is tight now, the mRNA–tRNA complex is fixed to the 30S subunit during relative rotations between the two ribosomal subunits (Fig. 1b, 1b′). Thus, the relative ribosomal rotations can only induce the two tRNAs moving from 50S A and P sites to 50S P and E sites (from Fig. 1b to 1b′) and from 50S P and E sites to 50S A and P sites (from Fig. 1b′ to 1b).

  2. Since the locking of the ribosome prohibits the binding of EF-G.GTP, only aminoacyl-tRNA.EF-Tu.GTP complex can now bind to the ribosome.

  3. In this paper, the spontaneous opening of mRNA base pairs refers to the mRNA unwinding that is induced by the thermal noise and/or the external pulling force to destabilize the mRNA duplex, i.e., it refers to the mRNA unwinding that is not induced by the ribosome translocation along the mRNA.

  4. For simplicity, it is considered here that the time of slow EF-G.GDP release following the unlocking state M (Fig. 2d) is comparable to the time of fast EF-G.GDP release following the locking state 6 (Fig. 2c) plus the time from binding of aminoacyl-tRNA.EF-Tu.GTP through EF-Tu.GDP release.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 10974248).

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Authors and Affiliations

  1. Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China

    Ping Xie

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Xie, P. Model of ribosome translation and mRNA unwinding. Eur Biophys J 42, 347–354 (2013). https://doi.org/10.1007/s00249-012-0879-4

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