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化学学报
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化学学报 ›› 2006, Vol. 64 ›› Issue (20): 2079-2085. 上一篇    下一篇

研究论文

谷氨酰胺结合蛋白的分子动力学模拟和自由能计算

胡建平1,2, 孙庭广1, 陈慰祖1, 王存新*,1   

  1. (1北京工业大学生命科学与生物工程学院 北京 100022)
    (2乐山师范学院化学与生命科学系 乐山 614004)
  • 投稿日期:2006-01-10 修回日期:2006-04-05 发布日期:2006-10-28
  • 通讯作者: 王存新

Molecular Dynamics Simulations and Free Energy Calculation on Glutamine-binding Protein

HU Jian-Ping1,2; SUN Ting-Guang1; CHEN Wei-Zu1; WANG Cun-Xin*,1   

  1. (1 College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022)
    (2 Department of Chemistry & Life Sciences, Leshan Normal University, Leshan 614004)
  • Received:2006-01-10 Revised:2006-04-05 Published:2006-10-28
  • Contact: WANG Cun-Xin

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被引次数

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谷氨酰胺结合蛋白(Glutamine-binding protein, GlnBp)是大肠杆菌透性酶系统中一个细胞外液底物专一性结合蛋白, 对于细胞外液中谷氨酰胺(Gln)的运输和传递至关重要. 本文运用分子动力学(Molecular dynamics, MD)模拟采样, 考察了GlnBp关键残基与底物Gln之间的相互作用和GlnBp两条铰链的功能差别; 并采用MM-PBSA方法计算了GlnBp与底物Gln的结合自由能. 结果表明: Ph13, Phe50, Thr118和Ile69与底物Gln的范德华相互作用和Arg75, Thr70, Asp157, Gly68, Lys115, Ala67, His156与底物Gln的静电相互作用是结合Gln的主要推动力; 复合物的铰链区85～89柔性大, 对构象开合提供了结构基础; 而铰链区181～185柔性小, 其作用更多是在功能上把底物Gln限制在口袋中; 自由能预测值与实验值吻合. 本研究很好地解释了GlnBp结构与功能的关系, 为进一步了解GlnBp的开合及转运Gln的机制提供了重要的结构信息.

关键词: GlnBp, 开合运动, 分子动力学, MM-PBSA, 结合自由能

Glutamine-binding protein (GlnBp) is one of the ligand-specific periplasmic binding proteins in the Escherichia coli permease systems, predicted to play an important role in transferring Gln from the pe-riplasmic space to the cytoplasmic space. In this paper, the interaction of the key residues in GlnBp with the ligand Gln and the functional difference between the two hinges in GlnBp were evaluated through molecular dynamics simulation sampling, and the binding free energy of GlnBp with Gln was calculated by the MM-PBSA method. The results show that the main impetus to bind Gln lies in the van der Waals’(VDW) interactions between Gln and Phe13, Phe50, Thr118, Ile69, as well as the electrostatic interactions between Arg75, Thr70, Asp157, Gly68, Lys115, Ala67, His156 and ligand Gln. The hinge region 85～89 whose fluctuation is larger than the hinge region 181～185 has a more flexibility which can provide a structural ba-sis to bind ligand Gln, while the main function of the hinge region 181～185 was proposed to restrict ligand Gln in the pocket of GlnBp. It is found that the result predicted with the MM-PBSA method agrees well with experimental data. The relationship between the structure and function of GlnBp is well illustrated, which provides us with some important structural information on the open-close mechanism of GlnBp and the transportation of Gln.

Key words: GlnBp, open-close motion, molecular dynamics simulation, MM-PBSA, binding free energy