Molecular dynamics simulations of various coronavirus main proteinases

Hsuan Liang Liu, Jin Chung Lin, Yih Ho, Wei Chan Hsieh, Chin Wen Chen, Yuan Chen Su

研究成果: 雜誌貢獻文章同行評審

7 引文 斯高帕斯(Scopus)

摘要

In this study, two homology models (denoted as MproST and M proSH) 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.

原文英語
頁(從 - 到)65-77
頁數13
期刊Journal of Biomolecular Structure and Dynamics
22
發行號1
出版狀態已發佈 - 八月 2004

ASJC Scopus subject areas

  • 分子生物學
  • 結構生物學

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