DFT Study of a Model System for the Dealkylation Step Catalyzed by AlkB
DFT Study of a Model System for the Dealkylation Step Catalyzed by AlkB
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DOI：
10.1007/s12539-010-0092-z
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发表时间：
2010-03-01
影响因子：
4.8
通讯作者：
Cisneros, G. Andres
中科院分区：
文献类型：
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作者：
Cisneros, G. Andres
E.大肠杆菌AlkB是一种DNA修复酶，其通过非血红素铁和作为辅因子的α-酮戊二酸催化DNA的去甲基化。提出的反应机理可以分为四个阶段。第一阶段涉及辅因子和分子氧与活性位点中的Fe结合。这之后是形成一个高自旋状态的铁基中间体，沿着与CO2和琥珀酸。随后，Fe中心上的O原子重新取向。最后一个阶段包括碱基的氧化去甲基化以产生天然DNA碱基和甲醛。该阶段还包括反应中的限速步骤。在这里，AlkB的反应机理的最后阶段已被研究的活性位点的DFT方法的模型。最小结构已被计算的所有中间体沿着的路径在三重态和五重态自旋。我们的结果指出五重态更稳定，与以前报道的计算一致。已经获得了五重态中沿着沿着这最后一个阶段的所有步骤的势能垒。在第一步中，与铁基中间体的Fe中心结合的氧从甲基部分提取氢原子。该第一步对应于反应中的限速步骤。该步骤的计算势垒为26.7 kcal/mol。随后的步骤是高度放能的。这个充满活力的图片是在定性协议与以前报道的结果。对于在活性位点中具有琥珀酸酯的模型，计算的铁基中间体和最终产物之间的能量差为-75.7 kcal/mol，对于其中琥珀酸酯被水替代的模型为-49.3 kcal/mol。我们计算的机制与以前报道的机制略有不同。这些结果表明可能存在不止一种机制。这是目前正在调查的从头算QM/MM方法。
E. coli AlkB is a DNA repair enzyme that catalyzes the de-methylation of DNA by means of a non-heme iron and alpha-keto glutarate as a co-factor. The proposed reaction mechanism can be separated in four stages. The first stage involves the binding of the co-factor and molecular oxygen to the Fe in the active site. This is followed by the formation of a ferryl intermediate in a high-spin state, along with CO2 and succinate. Subsequently, the O atom on the Fe center is reoriented. The last stage comprises the oxidative de-methylation of the base to produce the native DNA base and formaldehyde. This stage also includes the rate limiting step in the reaction. Here, the last stage of the proposed reaction mechanism of AlkB has been studied for a model of the active site with DFT methods. Minimum structures have been calculated for all intermediates along the path in triplet and quintet spin states. Our results point to the quintet states as more stable, in agreement with previously reported calculations. Potential energy barriers have been obtained for all the steps along this last stage in the quintet state. In the first step the oxygen bound to the Fe center of the ferryl intermediate abstracts a hydrogen atom from the methyl moiety. This first step corresponds to the rate limiting step in the reaction. The calculated barrier for this step is 26.7 kcal/mol. The subsequent steps are highly exoergic. This energetic picture is in qualitative agreement with previously reported results. The calculated energy difference between the ferryl intermediate and the final product is -75.7 kcal/mol for a model with succinate in the active site and -49.3 kcal/mol for a model where the succinate is replaced by water. Our calculated mechanism is slightly different than the previously reported one. These results suggest the possibility of more than one mechanism. This is currently under investigation by ab initio QM/MM methods.