On understanding proton transfer to the biocatalytic [Fe-Fe]H sub-cluster in [Fe-Fe] H2ases: QM/MM MD simulations
On understanding proton transfer to the biocatalytic [Fe-Fe]H sub-cluster in [Fe-Fe] H2ases: QM/MM MD simulations
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DOI：
10.1016/j.bbabio.2011.01.011
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发表时间：
2011-05-01
影响因子：
4.3
通讯作者：
Pachter, R.
中科院分区：
文献类型：
--
作者：
Hong, G.;Cornish, A. J.;Pachter, R.
通过结合第一性原理和经验分子动力学模拟，研究了脱硫弧菌（DdH）和巴斯德梭菌（CpI）[Fe - Fe]氢化酶中向[Fe - Fe](H)亚簇的质子转移。考虑了从DdH和CpI的X射线晶体结构推断出的途径，即分别为（Glu159 -> Ser198 -> Glu156 -> water460 -> Cys178 -> DTMA([Fe - Fe](H)）和（Glu282 -> Ser319 -> Glu279 -> water612 -> Cys299）。在我们的结果中，很容易观察到DdH中[Fe - Fe](H)亚簇从Cys178到DTMA的质子转移，特别是当[Fe - Fe](H)处于还原态（[Fe - I - Fe - I]）或质子化远端铁Fe - d的混合价态（[Fe - I - Fe - II - H - ](H)）时。提出了一种协同机制，在DdH中质子从Glu159经Ser198转移到Glu156以及从Glu156经water460转移到Cys178很容易发生，在CpI中从Glu282经Ser319转移到Glu279以及从Glu279经water612转移到Cys299也很容易发生。质子转移特性的理论预测与[Fe - Fe]氢化酶假定的生物催化机制一致，在该机制中质子结合在Fe - d上，提供了迄今为止尚未探索的验证。通过与突变CpI酶相对于野生型蛋白质的实验产氢活性数据的一致性，对计算结果进行了定性验证。最后，模拟提供的见解，部分结合实验验证，对于建立未来探索此类酶活性位点质子转移的方法非常重要，可能对仿生类似物也很重要。由爱思唯尔公司出版。
Proton transfer to the [Fe-Fe](H) sub-cluster in the Desulfovibrio desulfuricans (DdH) and Clostridium pasteurianum (CpI) [Fe-Fe] hydrogenases was investigated by a combination of first principles and empirical molecular dynamics simulations. Pathways that can be inferred from the X-ray crystal structures of DdH and CpI, i.e., (Glu159 -> Ser198 -> Glu156 -> water460 -> Cys178 -> DTMA([Fe-Fe](H) ) and (Glu282 -> Ser319 -> Glu279 -> water612 -> Cys299), respectively, were considered. Proton transfer from Cys178 to DTMA in the [Fe-Fe](H) sub-cluster in DdH was readily observed in our results, specifically when [Fe-Fe](H) was in the reduced state ([Fe-I-Fe-I]) or in the mixed valence state for the protonated distal iron Fe-d ([Fe-I-Fe-II-H-](H)). A concerted mechanism is proposed, where proton transfer in DdH from Glu159 to Glu156 via Ser198 and Glu156 to Cys178 via water460 readily occurred, as well as from Glu282 to Glu279 via Ser319 and Glu279 to Cys299 via water612 in Cpl. The theoretical prediction of the proton transfer characteristics is consistent with the assumed biocatalytic mechanism of the [Fe-Fe] hydrogenases in which the proton binds at Fe-d, providing confirmation that has not been explored so far. The computational results were qualitatively validated by the agreement with experimental hydrogen production activity data for mutated CpI enzymes, relative to the wild-type protein. Finally, the insight provided by the simulations, combined, in part, with experimental validation, are important for establishing an approach in future exploration of proton transfer to the active site in this class of enzymes, and possibly also for biomimetic analogs. Published by Elsevier B.V.