Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)
Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)
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DOI：
10.1021/ic701251j
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发表时间：
2008-05-19
影响因子：
4.6
通讯作者：
Cramer, Stephen P.
中科院分区：
文献类型：
--
作者：
Guo, Yisong;Wang, Hongxin;Cramer, Stephen P.
本文利用Fe-57核共振波谱（NRVS）研究了产甲烷古菌马布尔根产甲烷热杆菌（methanotherbacter marburgensis）铁-硫无团簇氢化酶Hmd中的铁位点。通过与顺式（CO）(2)连接的Fe模型化合物Fe(S2C2H4)(CO)(2)(PMe3)(2)的比较，以及合理的活性位点结构的正态模拟，对光谱进行了解释。对于该模型复合体，从优化的Urey-Bradley力场和互补密度泛函理论（DFT）计算中进行的正态分析得出了一致的结果。对于Hmd，先前的红外光谱研究在1944和2011 cm（-1）处发现了强CO拉伸模式，这被解释为顺式- fe (CO)(2)连接的证据。NRVS数据进一步揭示了Fe位点的动力学，揭示了Fe-CO在494、562、590和648 cm-1处的拉伸和弯曲模式，与提出的顺式Fe(CO)2连接一致。NRVS还揭示了一个类似于311 cm（-1）的Fe-S拉伸运动带和另一个类似于380 cm（-1）的可重复特征。基于Urey-Bradley力场的正态模态分析可以很好地模拟Hmd的Fe-57态偏振动密度（PVDOS），该模型适用于五坐标顺式（CO）(2)连接的Fe位，外加半胱氨酸、水和吡啶酮辅因子配体。没有水配体的“截断”模型也可以用来匹配NRVS数据。Hmd NRVS数据的最终解释，包括DFT分析，等待活性部位的三维结构。
We have used Fe-57 nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)(2)-ligated Fe model compound, Fe(S2C2H4)(CO)(2)(PMe3)(2), as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)(2) ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm-1, consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at similar to 311 cm(-1) and another reproducible feature at similar to 380 cm(-1). The Fe-57 partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)(2)-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.