Enzyme Dynamics and Tunneling Enhanced by Compression in the Hydrogen Abstraction Catalyzed by Soybean Lipoxygenase-1

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• 作者：Ismael Tejero ; Mireia Garcia-Viloca ; À ; ngels Gonzá ; lez-Lafont ; Jos&eacute ; M. Lluch ; Darrin M. York
• 刊名：Journal of Physical Chemistry B
• 出版年：2006
• 出版时间：December 7, 2006
• 年：2006
• 卷：110
• 期：48
• 页码：24708 - 24719
• 全文大小：503K
• 年卷期：v.110,no.48(December 7, 2006)
• ISSN：1520-5207

文摘

A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1(SLO-1) has been carried out. This enzyme exhibits the largest, and weakly temperature dependent, experimentalH/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includesthe complete enzyme with a solvation shell of water molecules, the Fe(III)-OH^- cofactor, and the linoleicacid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surfaceof the whole system, and the ensemble-averaged variational transition-state theory with multidimensionaltunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational resultsshow that the compression of the wild-type active site enzyme results in the huge contribution of tunneling(99%) to the rate of the hydrogen abstraction. Importantly, the active site becomes more flexible in the Ile553Alamutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentallydetermined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed bySLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an importantdependence on the barrier width.