Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor
Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor
复制标题
DOI：
10.1021/acs.inorgchem.0c01320
复制
发表时间：
2020-08-17
影响因子：
4.6
通讯作者：
Bjornsson, Ragnar
中科院分区：
文献类型：
--
作者：
Benediktsson, Bardi;Bjornsson, Ragnar
固氮酶负责所有的生物氮还原。然而，如何在原子水平上实现这一点，仍然没有确定。依赖氘的固氮酶已被广泛研究，并且是固氮酶的二氮还原的最活性催化剂。另一方面，依赖钒的形式显示出不同的反应性，能够将CO和CO2还原为烃。直到最近钒固氮酶的VFe蛋白的晶体结构才变得可用，为蛋白质基质内的铁钒辅因子（FeVco）的详细理论研究铺平了道路。晶体结构揭示了两个Fe原子之间的桥接4-原子配体，建议是CO 32-或NO3-配体。使用VFe蛋白质的量子力学/分子力学模型，从1.35埃晶体结构开始，我们系统地探索了FeVco的多种计算模型，考虑CO 32-或NO3-配体，三种不同的氧化还原状态和多个对称性破缺状态。我们发现，只有一个[VFe 7S 8 C（CO 3）]（2-）模型的FeVco再现的FeVco的晶体结构，以及在计算模型中的Fe-Fe和V-Fe距离的比较。此外，具有Fe 2、Fe 3和Fe 5自旋下降（BS 7 -235）的破缺对称解决方案在能量上是优选的。[VFe 7S 8 C（CO 3）]（2-）BS 7 -235模型的电子结构进行了比较，我们的[MoFe 7S 9 C]（-）BS 7 -235模型的FeMoco通过局域轨道分析，并讨论了局部氧化态和不同程度的离域。如先前从Fe X射线吸收光谱研究中发现的，与FeMoco相比，FeVco的Fe部分被还原，并且计算显示Fe 5为局部亚铁。这表明静止状态FeVco类似于FeMoco的未质子化的E-1状态。此外，与FeMoco中的Mo-Fe相互作用相比，FeVco中的V-Fe相互作用不那么强。这些明显的差异，在电子结构的其他类似的辅因子建议的反应性的明显差异的解释。
The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO32- or NO3- ligand. Using a quantum mechanics/ molecular mechanics model of the VFe protein, starting from the 1.35 angstrom crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO32- or NO3- ligand, three different redox states, and multiple broken- symmetry states. We find that only a [VFe7S8C(CO3)](2-) model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe7S8C(CO3)](2-) BS7-235 model is compared to our [MoFe7S9C](-) BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E-1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.