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

Xiaotong Zhang, Yafei Jiang, Qiuyun Mao, Hongwei Tan, Xichen Li, Guangju Chen, Zongchao Jia

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Article in Molecules (Basel, Switzerland), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.ACS central science · 2023
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5 · Who and what money

Authors and funding

7 authors.

Xiaotong ZhangKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. ZhangXiT@hotmail.com.

Yafei JiangKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. yafei.jiang@mail.bnu.edu.cn.

Qiuyun MaoKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. 201631150035@mail.bnu.edu.cn.

Hongwei TanKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. hongwei.tan@bnu.edu.cn.

Xichen LiKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. xcli@bnu.edu.cn.

Guangju ChenKey Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. gjchen@bnu.edu.cn.

Zongchao JiaDepartment of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7N 3L6, Canada jia@queensu.ca. jia@queensu.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Models, MolecularProtonsCatalysisMolecular ConformationPeptidesPhosphatesQuantum TheoryRibosomesThermodynamicsWaterPeptidesPhosphatesProtonsWaterDensity Functional Theorypeptide bond formationproton shuttle mechanism

Identifiers

PMID28362358

DOI10.3390/molecules22040571

PMCPMC6154465

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