Structural and Spectroscopic Properties of the Peroxodiferric Intermediate of Ricinus communis Soluble Δ9 Desaturase
Structural and Spectroscopic Properties of the Peroxodiferric Intermediate of Ricinus communis Soluble Δ9 Desaturase
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DOI：
10.1021/ic2018067
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发表时间：
2012-03-05
影响因子：
4.6
通讯作者：
Solomon, Edward I.
中科院分区：
文献类型：
--
作者：
Srnec, Martin;Rokob, Tibor Andras;Solomon, Edward I.
采用大尺度量子和分子力学方法（QM/MM）和量子力学方法（QM）对可溶性Delta（9）去饱和酶（Delta D-9）进行了计算，研究了光谱上定义的过氧二铁（P）中间体的各种结构模型.这使我们能够为Delta D-9的反应机制的初始阶段制定一致的机制图，Delta D-9是一种重要的二价铁非血红素铁酶，其切割烷烃链中的C-H键，导致双键的高度特异性插入。方法（密度泛函理论（DFT），时间依赖性DFT（TD-DFT），QM（DFT）/MM，和TD-DFT与静电嵌入）进行了基准测试，证明了已知的光谱效应和结构扰动所造成的基板结合到二铁Delta D-9可以定性再现。我们发现，结构模型的光谱（吸收，圆二色性（CD），振动和Miissbauer）的特性最好的相关性与实验数据的P中间体对应的mu-1，2-O-2（2-）结合模式。Glu 196与其中一个铁中心（Fe-B）的配位被证明是灵活的，单齿结合提供与光谱数据更好的一致性，并且双齿结构在能量上略微有利（1-10 kJ mol（-1））。还结合P中间体的可能活化来评估包含额外质子或水分子的其他可能结构。具体而言，我们建议，质子化的过氧化物部分，可能之前由水结合在铁-A的协调领域，可能是负责的P中间体在三角洲D-9转换成一种形式，能够氢提取。最后，结果进行了比较与最近的研究结果相关的核糖核苷酸还原酶和甲苯/甲烷单加氧酶。
Large-scale quantum and molecular mechanical methods (QM/MM) and QM calculations were carried out on the soluble Delta(9) desaturase (Delta D-9) to investigate various structural models of the spectroscopically defined peroxodiferric (P) intermediate. This allowed us to formulate a consistent mechanistic picture for the initial stages of the reaction mechanism of Delta D-9, an important diferrous nonheme iron enzyme that cleaves the C-H bonds in alkane chains resulting in the highly specific insertion of double bonds. The methods (density functional theory (DFT), time-dependent DFT (TD-DFT), QM(DFT)/MM, and TD-DFT with electrostatic embedding) were benchmarked by demonstrating that the known spectroscopic effects and structural perturbation caused by substrate binding to diferrous Delta D-9 can be qualitatively reproduced. We show that structural models whose spectroscopic (absorption, circular clichroism (CD), vibrational and Miissbauer) characteristics correlate best with experimental data for the P intermediate correspond to the mu-1,2-O-2(2-) binding mode. Coordination of Glu196 to one of the iron centers (Fe-B) is demonstrated to be flexible, with the monodentate binding providing better agreement with spectroscopic data, and the bidentate structure being slightly favored energetically (1-10 kJ mol(-1)). Further possible structures, containing an additional proton or water molecule are also evaluated in connection with the possible activation of the P intermediate. Specifically, we suggest that protonation of the peroxide moiety, possibly preceded by water binding in the Fe-A coordination sphere, could be responsible for the conversion of the P intermediate in Delta D-9 into a form capable of hydrogen abstraction. Finally, results are compared with recent findings on the related ribonudeotide reductase and toluene/methane monooxygenase enzymes.