高等学校化学学报

高等学校化学学报 ›› 2009, Vol. 30 ›› Issue (9): 1835.

• 研究论文 • 上一篇    下一篇

拟南芥TIR1与生长素IAA相互作用的分子对接及分子动力学研究

王腾, 孙宏伟, 陈兰, 沈荣欣, 赖城明   

  1. 南开大学化学学院, 天津 300071
  • 收稿日期:2008-09-25 出版日期:2009-09-10 发布日期:2009-09-10
  • 通讯作者: 孙宏伟, 男, 博士, 教授, 主要从事分子模拟及结构化学研究. E-mail: sunhw@nankai.edu.cn
  • 基金资助:

    国家高技术研究发展专项经费(批准号: 2006AA10A213)和南开大学“南开之星”高性能计算项目资助.

Docking and Molecular Dynamics Simulation Studies of Interaction Between Arabidopsis TIR1 and Auxin IAA

WANG Teng, SUN Hong-Wei*, CHEN Lan, SHEN Rong-Xin, LAI Cheng-Ming   

  1. Department of Chemistry, Nankai University, Tianjin 300071, China
  • Received:2008-09-25 Online:2009-09-10 Published:2009-09-10
  • Contact: SUN Hong-Wei. E-mail: sunhw@nankai.edu.cn
  • Supported by:

    国家高技术研究发展专项经费(批准号: 2006AA10A213)和南开大学“南开之星”高性能计算项目资助.

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被引次数

6

摘要：

基于最新得到的拟南芥运输抑制剂响应蛋白质1(TIR1)与吲哚乙酸(IAA)复合物的晶体结构, 使用分子对接方法和分子动力学方法对TIR1与生长素IAA相互作用的方式进行了研究. 分子对接结果表明, 通过逐级考察辅酶InsP6和中心水分子的影响, 发现辅酶InsP6和中心水分子对生长素IAA正确结合到活性位点有重要作用. 分子动力学结果表明, 复合物体系在整个模拟过程中较为稳定, 2个水分子相继作为中心水分子与生长素IAA形成了稳定的氢键作用, IAA与活性位点处残基的相互作用与晶体结构相比略有差异.

关键词: 拟南芥TIR1; 吲哚乙酸(IAA); 辅酶InsP6; 分子对接; 分子动力学模拟

Abstract:

On the basis of the complex crystal structure of transport inhibitor response 1(TIR1) and indole-3-acetic acid(IAA) obtained recently, systematic docking and molecular dynamics studies of interaction between auxin IAA and TIR1 have been performed using autodock 3.0 and NAMD 2.5 packages. The docking results indicate that the co-factor InsP6 and central water molecule play important roles in binding to the TIR1 pocket for auxin IAA correctly. The complex of TIR1 and auxin IAA was stable during the MD simulation, and stable hydrogen bond interaction had been formed between two water molecules which acted as central water molecule one after the other with auxin IAA. The interaction between auxin IAA and active residues around binding site was a little different from that in crystal structure.

Key words: Arabidopsis TIR1; Indole-3-acetic acid(IAA); InsP6; Docking; Molecular dynamics simulation

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