Liu H-L, Lin J-C, Ho Y, Hsieh W-C, Chen C-W, Su Y-C
Department of Chemical Engineering and Graduate Institute of Biotechnology, National Taipei University of Technology, 1 Section 3 Chung-Hsiao East Road, Taipei, Taiwan 10608.
J Biomol Struct Dyn. 2004 Aug;22(1):65-77. doi: 10.1080/07391102.2004.10506982.
In this study, two homology models (denoted as MproST and MproSH) of main proteinase (Mpro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed based on the crystal structures of Mpro from transmissible gastroenteritis coronavirus (TGEV) (MproT) and human coronavirus HcoV-229E (MproH), respectively. Both MproST and MproSH exhibit similar folds as their respective template proteins. These homology models reveal three distinct functional domains as well as an intervening loop connecting domains II and III as found in both template proteins. A catalytic cleft containing the substrate binding sites S1 and S2 between domains I and II are also observed. S2 undergoes more significant structural fluctuation than S1 during the 400 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft, while S1 is situated in the very bottom of this cleft. The thermal unfolding of these proteins begins at domain III, where the structure is least conserved among these proteins. Mpro may still maintain its proteolytic activity while it is partially unfolded. The electrostatic interaction between Arg40 and Asp186 plays an important role in maintaining the structural integrity of both S1 and S2.
在本研究中，基于传染性胃肠炎冠状病毒（TGEV）的主蛋白酶（Mpro）（MproT）和人冠状病毒HcoV - 229E的Mpro（MproH）的晶体结构，分别构建了与严重急性呼吸综合征相关的新型冠状病毒主蛋白酶（Mpro）的两个同源模型（分别记为MproST和MproSH）。MproST和MproSH都呈现出与其各自模板蛋白相似的折叠结构。这些同源模型揭示了三个不同的功能域，以及在两个模板蛋白中都存在的连接结构域II和III的中间环。在结构域I和II之间还观察到一个包含底物结合位点S1和S2的催化裂隙。在400皮秒的分子动力学模拟过程中，S2比S1经历更显著的结构波动，因为它位于催化裂隙的开口处，而S1位于该裂隙的最底部。这些蛋白质的热解折叠从结构域III开始，在这些蛋白质中该结构域的保守性最低。Mpro在部分解折叠时可能仍保持其蛋白水解活性。Arg40和Asp186之间的静电相互作用在维持S1和S2的结构完整性方面发挥着重要作用。
