Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00, Lund, Sweden.
Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, D-37077, Göttingen, Germany.
Sci Rep. 2018 Mar 16;8(1):4684. doi: 10.1038/s41598-018-22751-6.
Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39-49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
亚硫酸氧化酶是一种单核钼酶，可在包括人类在内的许多生物体中将亚硫酸盐氧化为硫酸盐。基于实验和计算研究，已经提出了三种不同的反应机制。在这里，我们使用组合量子力学（QM）和分子力学（QM/MM）方法研究了所有三种方法，包括使用大基组、非常大的 QM 区域（803 个原子）和 QM/MM 自由能微扰进行计算。我们的结果表明，该酶的设计遵循一种机制，其中亚硫酸盐底物的硫原子与 Mo 离子的赤道氧配体直接反应，形成 Mo 结合的硫酸盐产物，该产物在第二步中解离。第一步是限速步骤，其势垒为 39-49 kJ/mol。低势垒是通过围绕底物的复杂氢键网络获得的，该网络在反应过程中得以保留。该网络有利于底物去质子化，并不利于其他两种反应机制。我们已经研究了钼喋呤配体的氧化和还原形式的反应，量子精化计算表明该蛋白质中的配体处于正常的还原四氢形式。
