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Biophysical approaches to translational control of gene expression pp 51–68Cite as

Molecular Dynamics Simulations of the Ribosome

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Part of the book series: Biophysics for the Life Sciences ((BIOPHYS,volume 1))

Abstract

Structural biology techniques such as crystallography and cryo-EM produce high resolution snap shots of the ribosome at various stages of protein synthesis. Single molecule studies yield time-resolved measurements with low spatial resolution. Currently, there is no experimental technique capable of producing time-resolved trajectories of the ribosome with atomistic resolution. Computer simulations are critical for furthering our understanding of the ribosome because they fill this gap. We review computational studies of the ribosome, including structural modeling, normal mode calculations, coarse grain simulations, and molecular dynamics simulations. Several success stories have occurred, where predictions based on computer simulations were verified experimentally.

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Authors and Affiliations

  1. Theoretical Division, Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, MS K710, Los Alamos, NM, 87545, USA

    Karissa Y. Sanbonmatsu

  2. Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, 75, New York, NY, 10065, USA

    Scott C. Blanchard

  3. Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, San Diego, CA, 92093, USA

    Paul C. Whitford

Authors
  1. Karissa Y. Sanbonmatsu
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  2. Scott C. Blanchard
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  3. Paul C. Whitford
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Correspondence to Karissa Y. Sanbonmatsu or Scott C. Blanchard .

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Editors and Affiliations

  1. College Park, Cell Biology and Molecular Genetics, University of Maryland, Rm. 2135 Microbiology Building, College Park, 20742-4451, Maryland, USA

    Jonathan D. Dinman

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Sanbonmatsu, K.Y., Blanchard, S.C., Whitford, P.C. (2012). Molecular Dynamics Simulations of the Ribosome. In: Dinman, J. (eds) Biophysical approaches to translational control of gene expression. Biophysics for the Life Sciences, vol 1. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3991-2_3

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