固氮酶活性位点 FeMo-co 上 N2 和 H2 结合的结构和反应动力学,Dalton Transactions

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固氮酶活性位点 FeMo-co 上 N2 和 H2 结合的结构和反应动力学
Dalton Transactions ( IF 3.5 ) Pub Date : 2021-11-25 , DOI: 10.1039/d1dt03548g
Ian Dance ₁

Affiliation

在固氮酶 (N ₂ → NH _{3 ) 的活性位点 Fe}₇ MoS ₉ C(homocitrate) 簇 FeMo-co上发生的化学反应是神秘的。长期收集的实验信息揭示了 N ₂和 H ₂作用的各个方面，每一个都具有不止一种类型的反应性。本文报告了对完整 FeMo-co 中 H ₂和 N ₂结合的研究，使用蛋白质的 486 个大原子相关部分的密度泛函模拟，产生了 27 个包含 H ₂和/或 N ₂的新结构。exo和endo参与的 Fe 原子 Fe2 和 Fe6 的配位点。_{确定了结合/解离的结合能和过渡态，并描述了 H 2} /N ₂的接近、结合和分离的轨迹，包括这些小分子通过近端蛋白质的扩散。确定了周围氨基酸的影响。FeMo-co在结合H ₂或N ₂时会发生几何变形，这里介绍了计算所涉及的能量成本，即适应能量的过程。已报道结构的适应能范围为 7 至 36 kcal mol ^-1，受 His195 侧链质子化状态的影响。七 N ₂结构和三个 H ₂结构具有负结合自由能，其中包括估计的结合近端蛋白质的 N ₂和 H ₂的熵惩罚。这些受青睐的结构在FeMo-co的exo -Fe2、exo -Fe6 和endo -Fe2 位置具有末端结合的N ₂ ，以及在endo -Fe2 位置结合的H ₂。_{N 2}桥连Fe2 和Fe6 的各种假设结构在endo位置恢复为end-on-N _{2 。}结构也通过评估计算出的结合和解离的势垒。_{H 2}结合的障碍范围为1至20 kcal mol ^{-1 ，H}₂解离的障碍范围为3至18 kcal mol ^-1。_{N 2}结合的障碍，在侧向或端侧模式下，范围为2至18 kcal mol ^-1，而结合的N ₂的解离遇到3至8 kcal mol ^-1的侧向键合障碍和 7 至 18 kcal mol ^-1用于端接键合。这些结果允许制定 H ₂ /N _2的机制交换反应，并确定了三种可行的缔合交换机制和三种解离交换机制。始终保持一致的电子结构和势能表面。确定了与簇变形和金属-配体键形成有关的 Fe2 和 Fe6 自旋种群的变化。

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Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol⁻¹ for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol⁻¹ and barriers to dissociation of H₂ range from 3 to 18 kcal mol⁻¹. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol⁻¹, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol⁻¹ for side-on bonding and 7 to 18 kcal mol⁻¹ for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal–ligand bond formation are identified.

更新日期：2021-12-03

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