QM/MM Calculations Revealing the Resting and Catalytic States in Zinc-Dependent Medium-Chain Dehydrogenases/Reductases
QM/MM Calculations Revealing the Resting and Catalytic States in Zinc-Dependent Medium-Chain Dehydrogenases/Reductases
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DOI：
10.1021/cs501524k
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发表时间：
2015-06-01
期刊：
影响因子：
12.9
通讯作者：
Bocola, Marco
中科院分区：
文献类型：
--
作者：
Dhoke, Gaurao V.;Davari, Mehdi D.;Bocola, Marco
中链脱氢酶/还原酶（MDR）家族的氧化还原酶是由前手性酮生成光学纯醇的优良生物催化剂。用量子力学/分子力学（QM/MM）方法研究了锌催化羰基还原反应中氢化物和质子转移的机理。最近的X-射线结构的锌依赖性羰基还原酶从近平滑假丝酵母（CPCR 2; PDB ID 4C 4 O）显示两个不同的构象的Glu 66和两个位置的催化锌离子。从四种不同的假设状态出发，我们只得到了锌离子和Glu 66的两个极小值，即Zn-rest-Glu（in）和Zn-cat-Glu（out），表明它们是耦合运动。我们用QM/MM操纵的分子动力学（SMD）模拟方法分析了这两种状态在羰基底物还原过程中氢化物转移势垒的依赖性。我们的计算表明，催化状态（Zn-cat - Glu（out））与静息状态（Zn-rest-Glu（in））相比具有类似于20 kcal/mol的低反应势垒。这表明锌离子与Glu的耦合运动不仅影响配体交换，而且影响MDR的催化过程。
Oxido-reductases from medium-chain dehydrogenase/reductase (MDR) family are excellent biocatalysts for the generation of optically pure alcohols from prochiral ketones. The mechanism of hydride and proton transfer steps in zinc-catalyzed carbonyl reduction has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations. The recent X-ray structure of zinc-dependent carbonyl reductase from Candida parapsilosis (CPCR2; PDB ID 4C4O) shows two different conformers of Glu66 and two positions of the catalytic zinc ion. Starting from four different hypothetical states, we obtained only two minima, so-called Zn-rest-Glu(in) and Zn-cat-Glu(out) of zinc ion and Glu66, indicating a coupled movement We analyzed the dependence of barriers for the hydride transfer for these two states in the reduction of carbonyl substrate using QM/MM steered molecular dynamics (SMD) simulations. Our calculations show that the catalytic state (Zn-cat - Glu(out)) has a similar to 20 kcal/mol lower reaction barrier in comparison to the resting state (Zn-rest-Glu(in)). This indicates that the coupled movement of zinc ion and Glu influences not only the ligand exchange but also the catalytic process of MDRs.