Peptide Bond Formation Mechanism Catalyzed by Ribosome

Journal of the American Chemical Society
Katarzyna ŚwiderekJuan Bertrán

Abstract

In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708-8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system.

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Citations

Dec 10, 2016·Journal of the American Chemical Society·Agnieszka KrzemińskaKatarzyna Świderek
Mar 25, 2017·RNA Biology·Christoffer LindJohan Åqvist
Apr 1, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xiaotong ZhangZongchao Jia
Jun 22, 2019·Physical Chemistry Chemical Physics : PCCP·Shailja Jain, Kumar Vanka
May 11, 2018·Nucleic Acids Research·Masoud KazemiJohan Åqvist
Nov 24, 2019·Proceedings of the National Academy of Sciences of the United States of America·Daniel RostonQiang Cui
Feb 15, 2019·Frontiers in Chemistry·Sergio MartíKatarzyna Świderek
Aug 3, 2021·Chemical & Pharmaceutical Bulletin·Kazuaki Fukushima, Hiroyoshi Esaki
Mar 27, 2018·Journal of the American Chemical Society·Benjamin FritchEdward P O'Brien
Nov 11, 2021·Microbiology and Molecular Biology Reviews : MMBR·Madhan R TirumalaiGeorge E Fox

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