Computational Investigation of Mechanisms of Enzymes Involved in the Anaerob Degradation of Hydrocarbons

在厌氧条件下，碳氢化合物在化学上难以降解，需要强有力的催化剂。在生物化学上，这种反应通常涉及金属蛋白或自由基酶。在这项提案中，我们建议使用计算方法来了解在厌氧条件下降解碳氢化合物的酶的机制。特别是，我们想要研究钨酶乙炔水合酶和苯甲酰辅酶A还原酶BamBC的作用机制，以及甘氨酰自由基酶4-羟基苯乙酸酯的作用机制。这些酶的结构最近在高分辨率下得到了解决，这使得它们可以进行理论研究。为了全面了解这些反应，我们将结合不同的理论技术。通过应用连续介质静电学和蒙特卡罗技术，我们将确定蛋白质的质子化和氧化还原行为。详细的机理研究将通过气相中的量子化学计算以及QM/MM计算来完成，其中蛋白质的活性位置被量子化学处理，周围的蛋白质和溶剂被分子力学经典地处理。一个特别的挑战将是了解钼掺杂蛋白辅因子的复杂质子化和氧化还原行为以及蛋白质环境对其调节。在这个问题上的研究结果可能有助于我们对钼蝶呤酶有更全面的了解，钼蝶呤酶在人体内也参与了许多生化过程。

The chemically difficult degradation of hydrocarbons under anaerobic conditions requires potent catalysts. Biochemically such reaction often involve metalloproteins or radical enzymes. In this proposal, we suggest to use computational methods to understand the mechanism of enzymes that degrade hydrocarbons under anaerobic conditions. In particular, we want to study the mechanism of the tungsten enzymes Acetylene Hydratase and BamBC, a benzoyl-CoA reductase, as well as the mechanism of the glycyl-radical enzyme 4-Hydroxyphenylacetate. The structure of these enzymes has been recently solved at high resolution which makes them accessible to a theoretical investigation. To get a complete picture of the reactions, we will combine different theoretical techniques. By applying continuum electrostatics with Monte Carlo techniques, we will determine the protonation and redox behavior of the proteins. Detailed mechanistic studies will be done by quantum chemical calculations in the gas phase as well as QM/MM calculations in which the active site of the protein is treated quantum chemically and the surrounding protein and solvent classically by molecular mechanics. A particular challenge will be to understand the complex protonation and redox behavior of the molybdopterin cofactor and its modulation by the protein environment. Results on this question may well contribute to our general understanding of molybdopterin enzymes, which are involved in many biochemical processes also in humane.