Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator.
Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator.
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DOI：
10.3389/fmicb.2022.1073315
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发表时间：
2022
影响因子：
5.2
通讯作者：
Mroginski, Maria Andrea
中科院分区：
文献类型：
--
作者：
Dragelj, Jovan;Karafoulidi-Retsou, Chara;Katz, Sagie;Lenz, Oliver;Zebger, Ingo;Caserta, Giorgio;Sacquin-Mora, Sophie;Mroginski, Maria Andrea
关键词：
包括至少一个二分架构，大亚基的[NiFe]-氢化酶窝藏催化镍-铁网站，而小亚基房屋的电子转移Fe-S簇的阵列。最近，一些[NiFe]-氢化酶大亚基已被分离，显示出完整的氧化还原活性催化辅因子。在这项计算研究中，我们研究了这些金属蛋白之一，即大亚基HoxG的膜结合氢化酶从贪铜菌（CnMBH），针对其构象和机械稳定性，使用分子建模和长的全原子高斯加速分子动力学（GaMD）。我们的模拟预测，孤立的HoxG在水溶液中是稳定的，并保留了很大一部分的机械性能，但失去了刚性的活性位点周围的区域，在对比MBH异二聚体。受显示HoxG蛋白质二聚化的生化数据和揭示具有较高二聚体含量的蛋白质制剂中[NiFe]辅因子的稳定性增加的IR测量的启发，还进行了同源二聚体形式的相应模拟。虽然单体亚基包含几个灵活的区域，我们的数据预测恢复刚性同源二聚体模型。此外，我们计算了增强采样与GaMD，它显示了大量的正电荷在蛋白质表面，特别是在溶剂暴露的前二聚体接口的模型的静电特性。这些数据提供了关于[NiFe]核心被保护免于解聚的方式的新见解，并为酶锚定到表面提供了提示，这是进一步研究这些最小酶的必要信息。
Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel–iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.
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影响因子：
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