物理化学学报 >> 2012, Vol. 28 >> Issue (10): 2411-2417.doi: 10.3866/PKU.WHXB201209072

生物物理化学 上一篇    下一篇

Mpro-C蛋白三维结构域交换的机理: 来自分子模拟的线索

黄永棋1,2,3, 康雪1,4, 夏斌1,4,5, 刘志荣1,2,3   

  1. 1 北京大学化学与分子工程学院, 北京 100871;
    2 北京大学分子动态与稳态结构国家重点实验室, 北京分子科学国家实验室, 北京 100871;
    3 北京大学定量生物学中心, 北京 100871;
    4 北京核磁共振中心, 北京 100871;
    5 北京大学生命科学学院, 北京 100871
  • 收稿日期:2012-08-13 修回日期:2012-09-07 发布日期:2012-09-26
  • 通讯作者: 刘志荣 E-mail:LiuZhiRong@pku.edu.cn
  • 基金资助:

    国家重点基础研究发展计划项目(973) (2009CB918500, 2003CB514104)和国家自然科学基金(20973016, 10721403, 31170682)资助

Mechanism of 3D Domain Swapping for Mpro-C: Clues from Molecular Simulations

HUANG Yong-Qi1,2,3, KANG Xue1,4, XIA Bing1,4,5, LIU Zhi-Rong1,2,3   

  1. 1 College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China;
    2 State Key Laboratory for Structural Chemistry of Unstable and Stable Species and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, P. R. China;
    3 Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China;
    4 Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, P. R. China;
    5 School of Life Sciences, Peking University, Beijing 100871, P. R. China
  • Received:2012-08-13 Revised:2012-09-07 Published:2012-09-26
  • Supported by:

    The project was supported by the National Key Basic Research Program of China (2009CB918500, 2003CB514104) and National Natural Science Foundation of China (20973016, 11021463, 31170682).

摘要:

SARS冠状病毒主蛋白酶(Mpro)在病毒的蛋白酶切过程中发挥着重要作用. Mpro的晶体结构显示它存在两种形式的二聚体: 一种是发生三维结构域交换的形式, 另一种是非交换的形式. Mpro的C端结构域(Mpro-C)单独表达时也能形成与全长Mpro类似的三维结构域交换二聚体. 三维结构域交换通常发生在蛋白质的表面, 但Mpro-C 的结构域交换却发生在疏水核心. 在本文中, 我们利用分子动力学模拟及三维结构域交换预测算法研究了Mpro-C 中被高度埋藏的核心螺旋片段发生交换的机理. 我们发现基于结构与基于序列的已有算法都不能正确预言出Mpro-C和Mpro中发生结构域交换的铰链区位置. 分子模拟结果表明Mpro-C中的交换片段在天然态下埋藏得很好, 但在变性单体中则会被释放并暴露在外面. 因此, 在完全或部分解折叠状态下交换片段的打开有助于促进单体间的相互作用及结构域交换二聚体的形成.

关键词: SARS冠状病毒, 主蛋白酶, 分子模拟, 结构域交换, 蛋白质-蛋白质相互作用, 蛋白质解折叠

Abstract:

SARS coronavirus main protease (Mpro) is a key enzyme involved in the extensive proteolytic processing of the virus? polyproteins. The crystal structure of Mpro reveals that the enzyme exists in two different homo-dimeric forms: a three-dimensional (3D) domain-swapped form; and a non-3D domain-swapped form. The isolated C-terminal domain (Mpro-C) also forms a 3D domain-swapped structure similar to the full-length protein. Unlike conventional 3D domain-swapped structures, in which the swapped regions are located on the surface, Mpro-C swaps a helix at the core of a folded domain. In this work, we used molecular dynamics simulations and 3D domain-swapping predictions to investigate how a highly buried core helix in the helix bundle structure of Mpro-C can be swapped. We found that both structure- and sequence-based methods failed to predict the location of the hinge loop in Mpro-C and Mpro. Extensive molecular dynamics simulations were performed to investigate the structural properties of the unfolded monomer and the 3D domain-swapped dimer of Mpro-C. We found that, although the swapped region was buried in the native state, it was exposed in the unfolded monomer. Our results suggest that the opening of the swapped region in the fully or partially unfolded state may promote interactions between monomers and the formation of domain-swapped dimers.

Key words: SARS coronavirus, Main protease, Molecular simulation, Domain swapping, Protein-protein interaction, Protein unfolding

MSC2000: 

  • O641