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酶催化反应中的良好振动。

Good vibrations in enzyme-catalysed reactions.

机构信息

Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

出版信息

Nat Chem. 2012 Jan 29;4(3):161-8. doi: 10.1038/nchem.1223.

DOI:10.1038/nchem.1223
PMID:22354429
Abstract

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

摘要

近年来,快速运动(飞秒到皮秒)及其在酶催化反应中的潜在作用引起了相当大的兴趣。它们对反应化学的影响是通过研究动力学同位素效应的异常温度依赖性和计算模拟间接推断出来的。但是,这种运动是否可以降低反应坐标上能量势垒的宽度和高度,并有助于量子力学和/或经典核转移化学呢?在这里,我们讨论了当前关于酶促反应的观点,即需要快速的“促进”(或“压缩”)运动来辅助氢转移反应。关键是要直接证明压缩运动的作用,并能够从原子细节上理解这些快速运动的结构起源,但到目前为止,这一点尚未实现。在这里,我们讨论了支持压缩运动作用的间接实验证据,以及从计算模拟中获得的额外见解。

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Dynamics and dissipation in enzyme catalysis.酶催化中的动力学和耗散。
Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16159-63. doi: 10.1073/pnas.1106397108. Epub 2011 Sep 19.
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Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions.二氢叶酸还原酶和其他酶的催化作用源于静电预组织,而不是构象运动。
Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14115-20. doi: 10.1073/pnas.1111252108. Epub 2011 Aug 10.
3
Temperature dependence of the kinetic isotope effects in thymidylate synthase. A theoretical study.
Entropy (Basel). 2025 Mar 29;27(4):365. doi: 10.3390/e27040365.
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Decoupling of the onset of anharmonicity between a protein and its surface water around 200 K.在 200K 左右,蛋白质与其表面水之间非谐性的起始去耦。
Elife. 2024 Aug 19;13:RP95665. doi: 10.7554/eLife.95665.
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Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase.TIM桶状酶小鼠腺苷脱氨酶中与活性相关的溶剂化动力学的时间分辨率
ACS Catal. 2024 Apr 5;14(7):4554-4567. doi: 10.1021/acscatal.3c02687. Epub 2024 Mar 12.
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Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity.底物周转动力学指导酮酸还原异构酶的重新设计以提高比活性。
ACS Catal. 2024 Jun 26;14(14):10491-10509. doi: 10.1021/acscatal.4c01446. eCollection 2024 Jul 19.
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ACS Omega. 2024 Apr 24;9(18):20593-20600. doi: 10.1021/acsomega.4c02383. eCollection 2024 May 7.
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J Org Chem. 2024 Mar 1;89(5):3184-3193. doi: 10.1021/acs.joc.3c02562. Epub 2024 Feb 16.
胸苷酸合成酶中动力学同位素效应的温度依赖性。理论研究。
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