Molecular Dynamics Simulations of the Ribosome

  • Karissa Y. Sanbonmatsu
  • Scott C. Blanchard
  • Paul C. Whitford
Part of the Biophysics for the Life Sciences book series (BIOPHYS, volume 1)


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.


Molecular Dynamic Simulation Peptidyl Transferase Peptidyl Transferase Center Entropic Barrier Single Molecule Study 
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 Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Theoretical DivisionLos Alamos National Laboratory, Theoretical Biology and Biophysics GroupLos AlamosUSA
  2. 2.Department of Physiology and BiophysicsWeill Cornell Medical CollegeNew YorkUSA
  3. 3.Center for Theoretical Biological Physics and Department of PhysicsUniversity of California at San DiegoSan DiegoUSA

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