Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
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DOI：
10.1002/jcc.10154
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发表时间：
2003-01-30
影响因子：
3
通讯作者：
Gao, JL
中科院分区：
文献类型：
--
作者：
Garcia-Viloca, M;Alhambra, C;Gao, JL
应用分子动力学伞形采样模拟和多维隧道效应的整体平均变分过渡态理论（EA-VTST/MT）计算了两种Mg ~（2+）离子存在下木糖异构酶催化木糖异构化为木酮糖的反应速率。计算包括确定活化分布的自由能和透射系数的系综平均。的势能函数是由一个组合的QM/MM/SVB方法，涉及PM 3的量子力学（QM）的子系统，CHARMM 22和TIP 3 P的分子力学（MM）的环境，和一个简单的价键（SVB）的本地功能的两个键距离的氢化物转移反应。模拟证实了Whitlow等人基于动力学和X射线数据假设的机制的基本特征（Whitlow. M.;霍华德，A. J.道：芬泽尔，B。C.的; Poulos，T. L.的; Winborne，E. Gilliland，G. L. Proteins 1991，9，153）和林格，Petsko，及其同事（Labie，A.;艾伦，K.- N.的;佩茨科湾一、林格。D. Biochemistry 1994，33，5469）。这种机制涉及一个速率决定1.2-氢化物位移与前和后质子转移。包含量子力学振动能对于计算活化自由能是重要的，并且量子力学隧穿效应对于计算动力学同位素效应（KIE）是必不可少的。计算结果表明，85%的反应是通过隧穿过程进行的，15%的反应是通过过势垒过程进行的。分子动力学模拟表明，质子和氢化物转移反应是由活性位中移动的Mg 2+离子的呼吸运动所辅助的，为氢化物转移过程中Mg 2+离子的协同运动提供了证据. (C)2002 Wiley Periodicals，Inc.
We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to-xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow. M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E. Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe. D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1.2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events, The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step. (C) 2002 Wiley Periodicals, Inc.