Ribosomal Dynamics: Intrinsic Instability of a Molecular Machine

  • Haixiao Gao
  • Jamie Le Barron
  • Joachim FrankEmail author
Part of the Springer Series in Biophysics book series (BIOPHYSICS, volume 13)

Ribosomes are molecular machines that translate genetic message into nascent peptides, through a complex dynamics interplay with mRNAs, tRNAs, and various protein factors. A prominent example of ribosomal dynamics is the rotation of small ribosomal subunit with respect to a large subunit, characterized as the “ratchet motion,” which is triggered by the binding of several translation factors. Here, we analyze two kinds of ribosomal ratchet motions, induced by the binding of EF-G and RF3, respectively, as previously observed by cryo-electron microscopy. Using the flexible fitting technique (real-space refinement) and an RNA secondary structure display tool (coloRNA), we obtained quasi-atomic models of the ribosome in these ratchet-motion-related functional states and mapped the observed differences onto the highly conserved RNA secondary structure. Comparisons between two sets of ratchet motions revealed that, while the overall patterns of the RNA displacement are very similar, several local regions stand out in their differential behavior, including the highly conserved GAC (GTPase-associated-center) region. We postulate that these regions are important in modulating general ratchet motion and bestowing it with the dynamic characteristics required for the specific function.


Molecular Machine Intrinsic Instability Ribosome Recycling Factor Genetic Message Ramakrishnan Versus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Wadsworth CenterEmpire State PlazaAlbanyUSA
  2. 2.Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics and Department of Biological SciencesColumbia UniversityUSA

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