Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka.
Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
J Biomol Struct Dyn. 2022;40(24):14027-14034. doi: 10.1080/07391102.2021.1999329. Epub 2021 Nov 5.
Uracil DNA glycosylase is a key enzyme that identifies and removes damaged bases from DNA in the base excision repair pathway. Experimentalists have identified the possibility of Cd(II) reducing the activity of human uracil DNA glycosylase (hUNG) by binding with the enzyme replacing the catalytic water molecule. The present study focus on the stability variation of the enzyme in the presence and absence of Cd(II) and confirms the reported results with the stability analysis done using molecular dynamic (MD) simulation trajectories. The CavityPlus web server identified seven cavities for the free enzyme as possible binding sites and a cavity containing the active site of the enzyme as the best binding cavity for a ligand. Based on the CavityPlus results and the previously reported work, a free hUNG system and two systems of the enzyme with Cd(II); one with Cd(II) replacing the catalytic water molecule in the active site of the enzyme and the other replacing a non-catalytic water molecule in the active site were generated for the simulation. The simulation trajectories were used for the structural stability analysis of the enzyme in all three systems. The binding free energy of the Cd(II) with the enzyme was calculated using molecular mechanics Poisson Boltzmann surface area method. The results showed that the enzyme achieves comparatively high stability with the removal of catalytic water of the enzyme by Cd(II). Therefore, this supports the previously reported idea that Cd(II) replaces catalytic water molecules and affects enzyme activity.
尿嘧啶 DNA 糖基化酶是一种关键酶，可在碱基切除修复途径中识别和去除 DNA 中的受损碱基。实验人员已经发现 Cd(II) 通过与酶结合并取代催化水分子的方式，有可能降低人尿嘧啶 DNA 糖基化酶 (hUNG) 的活性。本研究重点关注酶在存在和不存在 Cd(II) 时的稳定性变化，并通过使用分子动力学 (MD) 模拟轨迹进行稳定性分析来证实报告的结果。CavityPlus 网络服务器为游离酶鉴定了七个空腔作为可能的结合位点，以及一个包含酶活性位点的空腔作为配体的最佳结合空腔。基于 CavityPlus 的结果和之前的报告工作，为模拟生成了游离 hUNG 系统和两种具有 Cd(II)的酶系统；一种是 Cd(II)取代酶活性位点中的催化水分子，另一种是取代活性位点中的非催化水分子。使用模拟轨迹对所有三个系统中的酶进行结构稳定性分析。使用分子力学 Poisson-Boltzmann 表面面积方法计算了 Cd(II)与酶的结合自由能。结果表明，酶在去除酶的催化水分子时达到了相对较高的稳定性。因此，这支持了之前报道的观点，即 Cd(II)取代催化水分子并影响酶活性。
