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一位21世纪修正主义者对酶学转折点的看法。

A 21st century revisionist's view at a turning point in enzymology.

作者信息

Nagel Zachary D, Klinman Judith P

机构信息

Department of Chemistry, University of California, Berkeley, California, USA.

出版信息

Nat Chem Biol. 2009 Aug;5(8):543-50. doi: 10.1038/nchembio.204.

DOI:10.1038/nchembio.204
PMID:19620995
Abstract

Despite the fact that the number of publications associated with the keyword 'enzyme' increases every year, the precise origin of enzyme catalysis has remained unresolved. Because of sustained intensive research efforts from an increasing number of laboratories, detailed information regarding the physics, chemistry and kinetics of enzymes is accumulating rapidly. The growing body of data contains many examples of kinetic behavior that are incompatible with a static view of enzyme catalysis. As a result, numerous laboratories are approaching the consensus that protein motion plays an essential role in enzyme catalysis. A model that incorporates nuclear quantum tunneling together with two classes of protein motion--termed conformational sampling (pre-organization) and reorganization--is recommended as a means of understanding the large body of data for enzyme-catalyzed hydrogen transfers. It should also serve as a vehicle for future efforts in the development of potent enzyme inhibitors and the de novo design of all classifications of enzymes.

摘要

尽管与“酶”这一关键词相关的出版物数量每年都在增加,但酶催化的确切起源仍未得到解决。由于越来越多的实验室持续进行深入研究,有关酶的物理、化学和动力学的详细信息正在迅速积累。不断增加的数据中包含许多与酶催化的静态观点不相容的动力学行为示例。因此,众多实验室逐渐达成共识,即蛋白质运动在酶催化中起着至关重要的作用。一种将核量子隧穿与两类蛋白质运动——称为构象采样(预组织)和重组——相结合的模型,被推荐作为理解大量酶催化氢转移数据的一种方式。它也应成为未来开发强效酶抑制剂以及从头设计各类酶的努力的载体。

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Complete computational design of high-efficiency Kemp elimination enzymes.高效肯普消除酶的完整计算设计
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Fast product release requires active-site water dynamics in carbonic anhydrase.快速的产物释放需要碳酸酐酶活性位点的水动力学。
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Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages.超越对称自组装和有效摩尔浓度:用坚固的有机笼解锁功能性酶模拟物。

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Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance.模拟一系列大豆脂氧合酶突变体中氢转移的温度依赖性动力学同位素效应:非谐性对转移距离的影响。
Chem Phys. 2005 Dec 7;319(1-3):283-296. doi: 10.1016/j.chemphys.2005.05.017.
2
An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling.一个用于酶催化的综合模型源自对氢隧穿的研究。
Chem Phys Lett. 2009 Mar 26;471(4-6):179-193. doi: 10.1016/j.cplett.2009.01.038.
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Nuclear quantum tunneling in the light-activated enzyme protochlorophyllide oxidoreductase.
Beilstein J Org Chem. 2025 Feb 24;21:421-443. doi: 10.3762/bjoc.21.30. eCollection 2025.
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Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits.三种不同的异质性蛋白酶体β亚基中的静电预组织
ACS Catal. 2024 Oct 2;14(20):15237-15249. doi: 10.1021/acscatal.4c04964. eCollection 2024 Oct 18.
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Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα)-Barrel Enzyme of Histidine Biosynthesis HisF.移动环的构象调节控制组氨酸生物合成HisF的(βα)桶状酶中的催化作用。
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Interplay of structural preorganization and conformational sampling in UDP-glucuronic acid 4-epimerase catalysis.结构预组织和构象采样在 UDP-葡萄糖醛酸 4-差向异构酶催化中的相互作用。
Nat Commun. 2024 May 8;15(1):3897. doi: 10.1038/s41467-024-48281-6.
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Hydrophobicity-Based Force Field In Enzymes.基于疏水性的酶力场
ACS Omega. 2024 Feb 7;9(7):8188-8203. doi: 10.1021/acsomega.3c08728. eCollection 2024 Feb 20.
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J Chem Phys. 2023 Oct 28;159(16). doi: 10.1063/5.0167991.
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Brief Bioinform. 2023 Jul 20;24(4). doi: 10.1093/bib/bbad189.
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J Am Chem Soc. 2023 Jan 18;145(2):1334-1341. doi: 10.1021/jacs.2c11728. Epub 2022 Dec 29.
光激活酶原叶绿素酸酯氧化还原酶中的核量子隧穿
J Biol Chem. 2009 Feb 6;284(6):3762-7. doi: 10.1074/jbc.M808548200. Epub 2008 Dec 10.
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Driving force analysis of proton tunnelling across a reactivity series for an enzyme-substrate complex.酶-底物复合物中质子隧穿跨反应活性序列的驱动力分析
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Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16543-8. doi: 10.1073/pnas.0808413105. Epub 2008 Oct 22.
6
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