Computational Insights into Five- versus Six-Coordinate Iron Center in Ferrous Soybean Lipoxygenase

Soybean lipoxygenase (SLO) serves
as a prototype for fundamental
understanding of hydrogen tunneling in enzymes. Its reactivity depends
on the active site structure around a mononuclear, nonheme iron center.
The available crystal structures indicate five-coordinate iron, while
magnetic circular dichroism experiments suggest significant populations
of both five-coordinate (5C) and six-coordinate (6C) iron in ferrous
SLO. Quantum mechanical calculations of gas phase models produce only
6C geometries. Herein mixed quantum mechanical/molecular mechanical
(QM/MM) calculations are employed to identify and characterize the
5C and 6C geometries. These calculations highlight the importance
of the protein environment, particularly two Gln residues in a hydrogen-bonding
network with Asn694, the ligand that can dissociate. This hydrogen-bonding
network is similar in both geometries, but twisting of a dihedral
angle in Asn694 moves its oxygen away from the iron in the 5C geometry.
These insights are important for future simulations of SLO.

大豆脂氧合酶（Soybean lipoxygenase, SLO）是研究酶内氢隧穿（hydrogen tunneling）机制的原型体系。其反应活性依赖于单核非血红素铁中心（mononuclear nonheme iron center）周围的活性位点（active site）结构。现有晶体结构显示铁为五配位状态，而磁圆二色性（magnetic circular dichroism）实验表明，亚铁态SLO中同时存在大量五配位（5C）和六配位（6C）铁物种。气相模型的量子力学计算（quantum mechanical calculations）仅能得到六配位几何结构。本文采用混合量子力学/分子力学（QM/MM）计算方法，对五配位和六配位的几何结构进行鉴定与表征。计算结果凸显了蛋白质环境的重要性，尤其是与可解离配体天冬酰胺694（Asn694）形成氢键网络（hydrogen-bonding network）的两个谷氨酰胺（Gln）残基。两种几何结构对应的氢键网络基本相似，但天冬酰胺694的二面角（dihedral angle）扭转会使其氧原子远离五配位结构中的铁原子。这些研究发现对未来开展SLO的相关模拟研究具有重要指导意义。