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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

1
Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
2
Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7N 3L6, Canada jia@queensu.ca
*
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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Abstract

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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