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观点：应用于酶催化的路径采样方法。

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.

机构信息

Department of Chemistry and Biochemistry University of Arizona Tucson, Arizona 85721, United States.

出版信息

J Chem Theory Comput. 2022 Nov 8;18(11):6397-6406. doi: 10.1021/acs.jctc.2c00734. Epub 2022 Oct 28.

DOI:10.1021/acs.jctc.2c00734
PMID:36305863
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9677451/
Abstract

This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.

摘要

本文回顾了过渡态抽样方法在研究酶催化化学反应中的应用。该方法由我们小组于 15 年前首次应用于酶反应，揭示了酶催化中的基本原理，如蛋白质促进振动，还帮助协调了静电预组织与酶功能的动态观点等思想。现在，该方法正被用于帮助揭示人工酶创建所需的蛋白质设计原则。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/f86b4aeb0479/nihms-1850645-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/32d3112ab5f7/nihms-1850645-f0002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/f86b4aeb0479/nihms-1850645-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/32d3112ab5f7/nihms-1850645-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/6125977b082e/nihms-1850645-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/cea8b96802a3/nihms-1850645-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/1de009a3f41d/nihms-1850645-f0005.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027d/9677451/f86b4aeb0479/nihms-1850645-f0007.jpg

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J Phys Chem B. 2022 Jul 28;126(29):5413-5420. doi: 10.1021/acs.jpcb.2c03251. Epub 2022 Jul 13.
2
A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site.双向振动探针揭示了溶液和酶活性部位中不同的电场方向。
Nat Chem. 2022 Aug;14(8):891-897. doi: 10.1038/s41557-022-00937-w. Epub 2022 May 5.
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Manipulating Reaction Energy Coordinate Landscape of Mechanochemical Diaza-Cope Rearrangement.
Nat Commun. 2025 Jan 17;16(1):786. doi: 10.1038/s41467-025-55983-y.
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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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Myosin-Catalyzed ATP Hydrolysis in the Presence of Disease-Causing Mutations: Mavacamten as a Way to Repair Mechanism.肌球蛋白催化致病突变体存在下的 ATP 水解：mavacamten 作为修复机制的一种方法。
J Phys Chem B. 2024 May 16;128(19):4716-4727. doi: 10.1021/acs.jpcb.4c01601. Epub 2024 May 6.
调控机械化学重氮环丙烷[1,5]-σ 迁移反应的能量坐标景观。
Molecules. 2022 Apr 15;27(8):2570. doi: 10.3390/molecules27082570.
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