物理化学学报 >> 2014, Vol. 30 >> Issue (7): 1347-1353.doi: 10.3866/PKU.WHXB201404301

生物物理化学 上一篇    下一篇

细菌化学趋向性受体聚集体的相互作用

余大启1,2, 涂豫海2,3, 来鲁华1,2   

  1. 1. 北京大学化学与分子工程学院, 分子动态与稳态国家重点实验室, 北京分子科学国家实验室, 北京 100871;
    2. 北京大学定量生物学中心, 北京 100871;
    3. IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, USA
  • 收稿日期:2014-04-15 修回日期:2014-04-29 发布日期:2014-06-30
  • 通讯作者: 来鲁华 E-mail:lhlai@pku.edu.cn
  • 基金资助:

    国家自然科学基金(21173013)资助项目

Molecular Interactions of Bacterial Chemoreceptor Assemblies

YU Da-Qi1,2, TU Yu-Hai2,3, LAI Lu-Hua1,2   

  1. 1. Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China;
    2. Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China;
    3. IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
  • Received:2014-04-15 Revised:2014-04-29 Published:2014-06-30
  • Contact: LAI Lu-Hua E-mail:lhlai@pku.edu.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (21173013).

摘要:

细菌化学趋向性受体的最小结构单元为二聚体,在细胞膜上这些二聚体会聚集成大团簇. X射线晶体结构和低分辨电镜结构测定表明,这些团簇有两类不同的形式,一种是在晶体结构中观察到的倒金字塔式二聚体的三聚体重复形成的聚集,另一种为由二聚体尾部相互盘绕形成的拉链状聚集. 有关拉链状聚集的详细分子模型目前尚不清楚. 本文使用蛋白质-蛋白质对接的方法研究了大肠杆菌丝氨酸化学趋向性受体Tsr 二聚体之间的相互作用. 分子对接计算表明,倒金字塔式聚集和拉链状聚集的基本复合物都是可以出现的,相应复合物的分子动力学模拟表明这些结构都具有一定的稳定性. 对于所获得的拉链状聚集体的基本复合物结构模型进行了详细的二聚体作用界面分析,发现二聚体间主要通过静电和疏水作用形成复合物,其中Arg388、Phe373 和Ile377是形成拉链状聚集的关键作用残基. 所建立的Tsr 拉链状聚集的结构模型有助于揭示细菌化学趋向性受体在细胞膜上聚集的分子机制,为进一步的聚集理论及模拟研究提供了基础.

关键词: 化学趋向性受体, 聚集体, 分子相互作用, 蛋白质-蛋白质对接, 分子动力学模拟

Abstract:

Bacterial chemoreceptors form homodimers that assemble into large clusters on cell membranes to respond to external signals. These clusters have been found to have two different types of patterns: one is composed of inverted pyramid like trimers-of-dimers observed in the X-ray crystal structures, and the other is formed by the zipper like overlap of tips of dimers, as revealed by low-resolution electron microscopy. The detailed molecular model of the zipper like assemblies has remained unknown until now. Using protein-protein docking method, we studied the interactions between serine chemoreceptor Tsr dimers in Escherichia coli. The basic complexes for the two types of clustering patterns were both found in the docking complexes. Molecular dynamics simulations confirmed that these complexes were stable to a certain extent. Protein-protein interface analysis indicated that electrostatic and hydrophobic interactions are the dominant driving forces for zipper like complex formation. Arg388, Phe373, and Ile377 are the key interfacial residues that stabilize the zipper like complexes. The molecular models for the zipper like complexes provide insight into the mechanisms of bacterial chemoreceptor assemblies on membranes and serve as a basis for further theoretical and simulation studies.

Key words: Chemoreceptor, Assembly, Molecular interaction, Protein-protein docking, Molecular dynamics simulation

MSC2000: 

  • O641.3