Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.
Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.
复制标题
了解人类酶 15-脂氧合酶-2 催化的花生四烯酸夺氢机制。
DOI：
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发表时间：
2016
影响因子：
5.5
通讯作者：
J. M. Lluch
中科院分区：
文献类型：
--
作者：
R. Suardíaz;P. G. Jambrina;Laura Masgrau;Àngels González;E. Rosta;J. M. Lluch
脂氧合酶 (LOX) 是参与多种脂质介质生物合成的酶家族。就人 15-LOX 而言，15-LOX-1 和 15-LOX-2 亚型表现出略有不同的反应区域特异性和底物特异性，表明底物结合和识别可能不同，这一事实可能与其不同的生物学作用有关。在这里，我们使用长分子动力学模拟、QM(DFT)/MM势能和自由能计算（使用新开发的DHAM方法）来研究花生四烯酸（AA）底物与15-LOX-2的结合模式以及15-LOX-2催化的限速夺氢反应。我们的结果强烈表明，从 15-LOX-2 中的 C13 夺氢仅与 AA 的“尾部优先”方向一致，其羧酸根与 Arg429 相互作用，并且只有 pro-S H13 氢会被夺取（pro-R H13 和 H10 距离受体氧原子太远）。在 B3LYP/6-31G(d) 水平上，15-LOX-2 对 AA 的 pro-S H13 提取的势垒和自由能垒分别为 18.0 和 18.6 kcal/mol。为了分析氢提取过程的动力学，我们确定了与沿状态离散反应坐标的无偏模拟相对应的马尔可夫模型。基于马尔可夫矩阵第二大特征值的计算速率与实验测量结果非常吻合，并且还提供了通过与自由能势垒高度比较来直接确定反应指前因子的方法。我们计算出的指前因子接近 kBT/h 的值。另一方面，我们的结果表明，在整个过程中的某个时刻需要发生整个系统（包括 O2 分子）的自旋反转，以产生最终的氢过氧化物产物，很可能发生在氢转移过程中，这是一种质子耦合电子转移。总体而言，提出了一种与 15-LOX-1 所接受的结合模式不同的结合模式，这为 15-LOX-1 的双重（尽管高度 15-）12/15 区域特异性之前的 15-LOX-2 独家 15-HPETE 生产提供了分子基础。了解这些不同的同工酶如何实现其区域特异性预计将有助于特定抑制剂的设计。
Lipoxygenases (LOXs) are a family of enzymes involved in the biosynthesis of several lipid mediators. In the case of human 15-LOX, the 15-LOX-1 and 15-LOX-2 isoforms show slightly different reaction regiospecificity and substrate specificity, indicating that substrate binding and recognition may be different, a fact that could be related to their different biological role. Here, we have used long molecular dynamics simulations, QM(DFT)/MM potential energy and free energy calculations (using the newly developed DHAM method), to investigate the binding mode of the arachidonic acid (AA) substrate into 15-LOX-2 and the rate-limiting hydrogen-abstraction reaction 15-LOX-2 catalyzes. Our results strongly indicate that hydrogen abstraction from C13 in 15-LOX-2 is only consistent with the "tail-first" orientation of AA, with its carboxylate group interacting with Arg429, and that only the pro-S H13 hydrogen will be abstracted (being the pro-R H13 and H10 too far from the acceptor oxygen atom). At the B3LYP/6-31G(d) level the potential and free energy barriers for the pro-S H13 abstraction of AA by 15-LOX-2 are 18.0 and 18.6 kcal/mol, respectively. To analyze the kinetics of the hydrogen abstraction process, we determined a Markov model corresponding to the unbiased simulations along the state-discretized reaction coordinate. The calculated rates based on the second largest eigenvalue of the Markov matrices agree well with experimental measurements, and also provide the means to directly determine the pre-exponential factor for the reaction by comparing with the free energy barrier height. Our calculated pre-exponential factor is close to the value of kBT/h. On the other hand, our results suggest that the spin inversion of the complete system (including the O2 molecule) that is required to happen at some point along the full process to lead to the final hydroperoxide product, is likely to take place during the hydrogen transfer, which is a proton coupled electron transfer. Overall, a different binding mode from the one accepted for 15-LOX-1 is proposed, which provides a molecular basis for 15-LOX-2 exclusive 15-HPETE production in front of the double (although highly 15-) 12/15 regiospecificity of 15-LOX-1. Understanding how these different isoenzymes achieve their regiospecificity is expected to help in specific inhibitor design.
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DOI：
10.1016/j.bbalip.2014.10.002
发表时间：
2015-04
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
Kuhn H;Banthiya S;van Leyen K
通讯作者：
van Leyen K
影响因子：
13.6
作者：
Dobrian, Anca D.;Lieb, David C.;Cole, Banumathi K.;Taylor-Fishwick, David A.;Chakrabarti, Swarup K.;Nadler, Jerry L.
通讯作者：
Nadler, Jerry L.
影响因子：
15
作者：
Hatcher, E;Soudackov, AV;Hammes-Schiffer, S
通讯作者：
Hammes-Schiffer, S
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
发表时间：
2006
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Tejero,Ismael;Garcia-Viloca,Mireia;Gonzalez-Lafont,Angels;Lluch,JoseM;York,DarrinM
通讯作者：
York,DarrinM
影响因子：
4.4
作者：
Shirts, Michael R.;Chodera, John D.
通讯作者：
Chodera, John D.