Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.
Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.
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大豆脂氧合酶-1 催化的氢提取中压缩增强了酶动力学和隧道效应。
DOI：
10.1021/jp066263i
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发表时间：
2006
期刊：
影响因子：
--
通讯作者：
York,DarrinM
中科院分区：
文献类型：
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作者：
Tejero,Ismael;Garcia-Viloca,Mireia;Gonzalez-Lafont,Angels;Lluch,JoseM;York,DarrinM
对大豆脂氧合酶-1（SLO-1）催化的限速夺氢反应进行了全微观模拟。这种酶表现出最大的，弱的温度依赖性，实验H/D动力学同位素效应（KIE）的生物系统的报告。这里使用的理论模型包括完整的酶与水分子的溶剂化壳，Fe（III）-OH-辅因子，和亚油酸底物。我们采用混合QM（PM 3/d-SRP）/MM方法描述整个体系的势能面，采用多维隧道效应的整体平均变分过渡态理论（EA-VTST/MT）计算反应速率常数和初级KIE。计算结果表明，野生型活性中心酶的压缩导致隧道效应对夺氢速率的贡献巨大（99%）。重要的是，活性位点变得更加灵活的Ile 553 Ala突变体反应物复合物模拟（其中一个显着的温度依赖性KIE已被实验确定），从而证明了所提出的关键作用的门控促进模式在SLO-1催化的反应。最后，结果表明，野生型酶的计算KIE有一个重要的依赖于势垒宽度。
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, experimental H/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includes the complete enzyme with a solvation shell of water molecules, the Fe(III)-OH-cofactor, and the linoleic acid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surface of the whole system, and the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational results show 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 Ile553Ala mutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentally determined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed by SLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an important dependence on the barrier width.