文章基本信息

标题：Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition
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作者：Zhongyue Yang ; Song Yang ; Peiyuan Yu 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2018
卷号：115
期号：5
页码：E848-E855
DOI：10.1073/pnas.1719368115
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SpnF is the first monofunctional Diels–Alder/[6+4]-ase that catalyzes a reaction leading to both Diels–Alder and [6+4] adducts through a single transition state. The environment-perturbed transition-state sampling method has been developed to calculate free energies, kinetic isotope effects, and quasi-classical reaction trajectories of enzyme-catalyzed reactions and the uncatalyzed reaction in water. Energetics calculated in this way reproduce the experiment and show that the normal Diels–Alder transition state is stabilized by H bonds with water molecules, while the ambimodal transition state is favored in the enzyme SpnF by both intramolecular hydrogen bonding and hydrophobic binding. Molecular dynamics simulations show that trajectories passing through the ambimodal transition state bifurcate to the [6+4] adduct and the Diels–Alder adduct with a ratio of 1:1 in the gas phase, 1:1.6 in water, and 1:11 in the enzyme. This example shows how an enzyme acts on a vibrational time scale to steer post-transition state trajectories toward the Diels–Alder adduct.
关键词：SpnF enzyme ; time-resolved mechanism ; environment-perturbed transition-state sampling ; potential energy surface bifurcation