Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria.
Biochemistry. 2014 Jul 29;53(29):4869-79. doi: 10.1021/bi500467h. Epub 2014 Jul 14.
Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen. It has been postulated that during turnover hypochlorite is formed transiently, which might be responsible for the observed irreversible inactivation of these iron proteins. The only charged distal residue in the heme cavity is a conserved and mobile arginine, but its role in catalysis and inactivation is not fully understood. In the present study, the pentameric chlorite dismutase (Cld) from the bacterium Candidatus Nitrospira defluvii was probed for binding of the low spin ligand cyanide, the substrate chlorite, and the intermediate hypochlorite. Simulations were performed with the enzyme in the ferrous, ferric, and compound I state. Additionally, the variant R173A was studied. We report the parametrization for the GROMOS force field of the anions ClO(-), ClO2(-), ClO3(-), and ClO4(-) and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations. The findings suggest that (i) chlorite binding to ferric NdCld occurs spontaneously and (ii) that Arg173 is important for recognition and to impair hypochlorite leakage from the reaction sphere. The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.
绿屈挠菌氯酸盐双加氧酶是一种原核血红素 b 氧化还原酶，可将亚氯酸盐转化为氯离子和氧气。据推测，在周转过程中会短暂形成次氯酸盐，这可能是导致这些铁蛋白不可逆失活的原因。血红素腔中唯一带电荷的远端残基是保守且可移动的精氨酸，但它在催化和失活中的作用尚未完全阐明。在本研究中，研究了来自 Candidatus Nitrospira defluvii 的五聚体氯酸盐双加氧酶（Cld）与低自旋配体氰化物、底物亚氯酸盐和中间产物次氯酸盐的结合情况。模拟在亚铁、三价铁和化合物 I 状态下进行。此外，还研究了变体 R173A。我们报告了阴离子 ClO(-)、ClO2(-)、ClO3(-)和 ClO4(-)的 GROMOS 力场参数化，并描述了亚氯酸盐和次氯酸盐的自发结合、解结合和再结合事件，以及 Arg173 在模拟过程中的构象动力学。研究结果表明：（i）三价铁 NdCld 可自发结合亚氯酸盐，（ii）Arg173 对识别和防止次氯酸盐从反应区域泄漏至关重要。模拟数据与氯酸盐双加氧酶的催化和抑制实验数据进行了讨论。
