Molecular Dynamics Investigation of a Mechanism of Allosteric Signal Transmission in Ribosomes

Makarov, G.I.; Golovin, A.V.; Sumbatyan, N.V.; Bogdanov, A.A.

Авторы: Makarov G.I., Golovin A.V., Sumbatyan N.V., Bogdanov A.A.
Журнал: Biochemistry (Moscow)
Том: 80
Номер: 8
Год издания: 2015
Издательство: Pleiades Publishing, Ltd
Местоположение издательства: Road Town, United Kingdom
Первая страница: 1047
Последняя страница: 1056
DOI: 10.1134/S0006297915080106
Аннотация: The ribosome is a molecular machine that synthesizes cell proteins in the course of mRNA translation. At the each step of polypeptide chain synthesis the ribosome ligands, tRNA’s and several protein factors, bind and leave the ribosome in strictly coordinated way. Also, it is known that the coordination of these steps is based on interrelated conformational rearrangements of ribosome components. It is generally accepted that coordination of ordered sequence of events in the ribosomal working cyсle is accomplished by signal exchange between ribosome functional centers. Since distances between these centers are rather large, it has been suggested that signal transduction in the ribosome may be performed allosterically. In this work an attempt to explain how the allosteric signal can be transferred from one of the so-called sensory centers of the ribosomal nascent peptide exit tunnel (NPET) to the peptidyl transferase center (PTC) of the E. coli ribosome was made. To address this question we have performed modeling of molecular dynamics of the putative signal-transmission pathway which includes universally conserved 23S rRNA residues A2058, A2059, m2A2503, G2061, A2062 and C2063. It is shown that this rRNA segment constitutes a dynamic ensemble of interrelated conformational states. Moreover, it was observed that these conformation changes can occur as a cascade. It was suggested that restructuring of the А2058-С2063 region of NPET leads to reversible stalling of PTC due to stacking interactions of the functionally important U2585 residue with C2063. The possible role of the observed conformational changes in the regulation of the ribosome work is discussed.
Добавил в систему: Сумбатян Наталия Владимировна

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Molecular Dynamics Investigation of a Mechanism of Allosteric Signal Transmission in Ribosomesстатья

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