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首页> 外文期刊>Chemical Physics: A Journal Devoted to Experimental and Theoretical Research Involving Problems of Both a Chemical and Physical Nature >A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism
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A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

机译：涉及核糖体中两种水分子的肽键形成的理论模型研究支持两步和八元环机构

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摘要

The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O90 and H150 in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.
机译：核糖体是催化蛋白质合成的大分子机。 STROBEL组报告的动力学同位素效应分析支持两步机制。然而，源自亲核胺的质子的目的地是不确定的。使用相同的反应模型和理论水平进行包括水分子的不同机制的计算模拟。从亲核氮中形成具有质子转移的四面体中间体，是当两个水分子参与肽键形成时的速率限制步骤。形成与O90和H150在部位中形成氢键的第一水分子可以降低反应屏障。结合溶剂同位素效应分析的结果，我们得出结论，其中水分子在速率限制步骤中介导氨基和碳氧气之间的质子梭的三个质子转移机制是有利的机制。我们的结果将屏蔽光线，更好地了解核糖体的反应机制。

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