Biochemistry (Moscow)

, Volume 81, Issue 13, pp 1579–1588 | Cite as

Investigation of ribosomes using molecular dynamics simulation methods

  • G. I. Makarov
  • T. M. Makarova
  • N. V. Sumbatyan
  • A. A. BogdanovEmail author


The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.


ribosome molecular dynamics simulations allosteric signal transmission 



molecular dynamics


nascent peptide exit tunnel


peptidyl transferase center of the ribosome


replica exchange molecular dynamics


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Copyright information

© Pleiades Publishing, Ltd. 2016

Authors and Affiliations

  • G. I. Makarov
    • 1
    • 2
  • T. M. Makarova
    • 1
    • 2
  • N. V. Sumbatyan
    • 1
    • 2
  • A. A. Bogdanov
    • 1
    • 2
    Email author
  1. 1.Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
  2. 2.Lomonosov Moscow State University, Chemistry DepartmentMoscowRussia

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