Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
School Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
J Phys Chem B. 2020 Nov 19;124(46):10353-10364. doi: 10.1021/acs.jpcb.0c08976. Epub 2020 Nov 4.
Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by description of enzymatic catalytic steps carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) potential along with the computation of the potential of mean force (PMF) to estimate the free energy barriers for the studied transformations: dehydrochlorination of γ-, (-)-α-, and (+)-α-HCH by LinA-type I and -type II variants. The applied combination of computational techniques allowed us not only to characterize two LinA types but also to point to the most important differences between them and link their features to catalytic efficiency each of them possesses toward the respective ligand. More importantly it has been demonstrated that type I protein is more mobile, its active site has a larger volume, and the dehydrochlorination products are stabilized more strongly than in the case of type II enzyme, due to differences in the residues present in the active sites. Additionally, interaction energy calculations revealed very interesting patterns not predicted before but having the potential to be utilized in any attempts of improving LinA catalytic efficiency. On the basis of all these observations, LinA-type I protein seems to be more preorganized for the dehydrochlorination reaction it catalyzes than the type II variant.
在此，我们展示了对 LinA 及其两种变体进行深入模拟研究的结果。在我们的分析中，我们结合了使用分子动力学模拟对有和没有结合底物（六氯环己烷（HCH）异构体）的蛋白质构象动力学进行探索，随后通过提取最常访问的构象及其特征，并使用对称适应微扰理论（SAPT）计算详细描述活性位点中发生的相互作用，对 LinA 亚基的构象空间进行了详细研究。使用混合量子力学/分子力学（QM/MM）势能对酶催化步骤进行了描述，并计算了平均力势（PMF），以估计研究转化的自由能势垒：LinA 型 I 和 II 变体对γ-、（-）-α-和（+）-α-HCH 的脱氯化氢作用。应用的计算技术组合不仅使我们能够表征两种 LinA 类型，还能够指出它们之间的最重要差异，并将它们的特征与其对各自配体的催化效率联系起来。更重要的是，已经证明 I 型蛋白质更具流动性，其活性位点具有更大的体积，并且脱氯化氢产物的稳定性比 II 型酶更强，这是由于活性位点中存在的残基不同所致。此外，相互作用能计算揭示了以前没有预测到的非常有趣的模式，但具有提高 LinA 催化效率的任何尝试的潜力。基于所有这些观察结果，LinA 型 I 蛋白似乎比 II 型变体更适合其催化的脱氯化氢反应。
