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REVIEW: Investigation of Ribosomes Using Molecular Dynamics Simulation Methods

G. I. Makarov1,2, T. M. Makarova1,2, N. V. Sumbatyan1,2, and A. A. Bogdanov1,2*

1Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; E-mail: bogdanov@belozersky.msu.ru

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

* To whom correspondence should be addressed.

Received August 5, 2016
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.
KEY WORDS: ribosome, molecular dynamics simulations, allosteric signal transmission

DOI: 10.1134/S0006297916130010