Simulating the Coupling of Catalysis and Electron Transfer along Chains of FeS-Clusters in Various Enzymes

铁硫团簇在分子生物能、酶催化、基因调控和修复等多种长程电子传递过程中发挥着重要作用。 在许多这些酶中，铁硫簇排列以使电子能够远距离转移。这类酶的突出实例是异蝶呤和钨蝶呤酶，但也有几种氢化酶。虽然许多这些酶的催化反应已经在相当详细的研究，它们的电子和质子转移反应的连接还没有在相同的详细程度上研究。本计画的目标是扩展现有的电子与质子转移模拟方法，以描述酶中催化反应与催化位点间电荷转移反应的耦合。我们将使用主方程方法来模拟使用微态模型的反应。对于这些计算，需要计算反应速率常数。对于电子和质子转移反应，我们估计这些速率常数使用马库斯理论。这些反应的驱动力是由微观态能量的差异得到的。对于更复杂的化学反应，我们将采用QM/MM计算。为了计算含FeS团簇的蛋白质的微观态能量，我们需要估计这些团簇的可靠模型氧化还原电位。因此，最常见的参与电子转移的FeS团簇的性质将进行研究。模拟方法将被应用于分析两个F420还原和一个NAD还原氢化酶的反应，它们彼此相似，但显示出有趣的差异。我们的模拟可以显示pH和溶液氧化还原电位如何影响酶的还原水平，以及酶的氧化还原状态如何与通过酶的总通量相关联。

Iron-sulfur clusters play central role in many long range electron transfer processes ranging from functions in molecular bioenergetic, in enzyme catalysis, as well as in gene regulation and repair. In many of these enzymes, iron sulfur clusters align to enable electron transfer over large distances. Prominent examples of such enzymes are molybdo- and tungsto-pterin enzymes but also several hydrogenases. While the catalytic reactions of many of these enzymes have been investigated at quite some detail, their connection to the electron and proton transfer reactions has not been studied at the same level of detail. The goal of this project is to extend an existing method for electron and proton transfer simulation to describe the coupling of catalytic reactions and charge transfer reactions between catalytic sites in enzymes. We will use the master equation approach for simulating reactions in using the microstate model. For these calculations, it is required to calculate reaction rate constants. For electron and proton transfer reactions, we estimate these rate constants using Marcus theory. The driving force of these reaction is obtained from the difference of the microstate energies. For more complex chemical reactions, we will employ QM/MM calculations. In order to calculate microstate energies of protein containing FeS clusters, we need to estimate reliable model redox potentials for these clusters. Therefore, the properties of the most common FeS clusters involved in electron transfer will be investigated. The simulation method will be applied to analyze the reaction of two F420-reducing and one NAD reducing hydrogenases, which are similar to each other, but show interesting differences. Our simulating can show how the pH and the solution redox potential influence the reduction level of the enzyme and how the redox state of the enzyme is connected to the overall flux through the enzyme.