Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase.
Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase.
复制标题
脂氧合酶中氢原子转移的大动力学同位素效应和温度依赖性的模拟。
DOI：
10.1021/ja037233l
复制
发表时间：
2004
期刊：
影响因子：
--
通讯作者：
Warshel,Arieh
中科院分区：
文献类型：
--
作者：
Olsson,MatsHM;Siegbahn,PerEM;Warshel,Arieh
阐明核量子力学（NQM）效应在酶催化中的作用是当前重要的研究课题。尽管在这一领域取得了巨大的实验进展，但重要的是要有能够评估和分析核量子力学对催化作用的贡献的理论方法。在这项研究中，我们使用的催化反应的脂氧合酶，这是一个非常大的动力学同位素效应的特点，作为一个具有挑战性的测试情况下，我们的模拟方法。这是通过应用量子经典路径（QCP）方法与经验价键势能面。我们的计算策略评估相关的NQM修正和再现大观察到的动力学同位素效应和H原子转移反应的温度依赖性，而不太成功的D原子转移反应。然而，我们的研究的重点不是探索同位素效应的温度依赖性，而是开发和验证用于计算核量子力学对活化自由能的贡献的方法。在这里，我们发现，计算和观察到的活化自由能之间的偏差是小的H和D在所有研究的温度。本研究还探讨了酶和溶液反应中重组能的性质。发现外层重组能非常小。这反映了所考虑的反应涉及非常小的电荷转移的事实。这一发现的含义进行了讨论的框架内的定性振动模型。本研究的要点是，然而，严格的QCP方法提供了一个可靠的计算工具，即使当给定的反应包括大隧道贡献的NQM催化的贡献进行评估。有趣的是，我们的研究结果表明，NQM在脂氧合酶反应的影响是相似的酶和参考溶液反应，因此不有助于催化。我们在其他酶的研究中也得出了类似的结论。
Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.