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Molecules 2017, 22(4), 571; doi:10.3390/molecules22040571

Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study

Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7N 3L6, Canada
Authors to whom correspondence should be addressed.
Received: 2 February 2017 / Revised: 17 March 2017 / Accepted: 28 March 2017 / Published: 31 March 2017
(This article belongs to the Special Issue Foldamers: Synthesis and Applications)
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In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in a charge-separated intermediate that is stabilized by the N terminus of L27 and the A-site A76 5′-phosphate. The ribose A2451 bridges the proton shuttle pathway, thus plays critical role in the reaction. The calculated 27.64 kcal•mol−1 free energy barrier of the distal proton shuttle mechanism is lower than that of eight-membered ring transition state. The distal proton shuttle mechanism studied in this work can provide new insights into the important biological peptide synthesis process. View Full-Text
Keywords: peptide bond formation; Density Functional Theory; proton shuttle mechanism peptide bond formation; Density Functional Theory; proton shuttle mechanism

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Zhang, X.; Jiang, Y.; Mao, Q.; Tan, H.; Li, X.; Chen, G.; Jia, Z. Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study. Molecules 2017, 22, 571.

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