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Investigation of ribosomes using molecular dynamics simulation methods

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Abstract

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.

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Abbreviations

MD:

molecular dynamics

NPET:

nascent peptide exit tunnel

PTC:

peptidyl transferase center of the ribosome

REMD:

replica exchange molecular dynamics

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Authors and Affiliations

  1. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia

    G. I. Makarov, T. M. Makarova, N. V. Sumbatyan & A. A. Bogdanov

  2. Lomonosov Moscow State University, Chemistry Department, 119991, Moscow, Russia

    G. I. Makarov, T. M. Makarova, N. V. Sumbatyan & A. A. Bogdanov

Authors
  1. G. I. Makarov
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  2. T. M. Makarova
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  3. N. V. Sumbatyan
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  4. A. A. Bogdanov
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Corresponding author

Correspondence to A. A. Bogdanov.

Additional information

Original Russian Text © G. I. Makarov, T. M. Makarova, N. V. Sumbatyan, A. A. Bogdanov, 2016, published in Uspekhi Biologicheskoi Khimii, 2016, Vol. 56, pp. 3–24.

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Makarov, G.I., Makarova, T.M., Sumbatyan, N.V. et al. Investigation of ribosomes using molecular dynamics simulation methods. Biochemistry Moscow 81, 1579–1588 (2016). https://doi.org/10.1134/S0006297916130010

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