高等学校化学学报 ›› 2010, Vol. 31 ›› Issue (5): 1039-1044.

• 研究论文 • 上一篇    下一篇

Y-S-R基序与卟啉辅基之间的氢键网络在sGC-HNOX结构域中的作用

张跃斌, 程瑛琨, 吕明, 张华利, 李正强   

  1. 吉林大学分子酶学工程教育部重点实验室, 长春 130021
  • 收稿日期:2009-08-27 出版日期:2010-05-10 发布日期:2010-05-10
  • 通讯作者: 李正强, 男, 博士, 教授, 博士生导师, 主要从事酶的结构与功能研究. E-mail: lzq@jlu.edu.cn
  • 基金资助:

    国家自然科学基金(批准号: 30570404, 30670458)和吉林大学研究生“985工程”创新计划项目资助.

Function of the Hydrogen-bonding Network Between the Y-S-R Motif and the Heme Propionate Groups in sGC-HNOX Domain

ZHANG Yue-Bin, CHENG Ying-Kun, LÜ Ming, ZHANG Hua-Li, LI Zheng-Qiang*   

  1. Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130021, China
  • Received:2009-08-27 Online:2010-05-10 Published:2010-05-10
  • Contact: LI Zheng-Qiang. E-mail: lzq@jlu.edu.cn
  • Supported by:

    国家自然科学基金(批准号: 30570404, 30670458)和吉林大学研究生“985工程”创新计划项目资助.

摘要:

利用分子动力学方法研究了sGC-HNOX结构域中Y-S-R基序与卟啉丙酸基团形成的氢键网络在sGC-HNOX结构域中的作用. RMSD分析结果表明, 该氢键网络的存在可以有效地稳定sGC-HNOX结构域的构象, 并且这种稳定作用不影响sGC-HNOX结构域的二级结构、体积以及溶剂可及表面积. 分子动力学轨迹的主成分分析及卟啉平面构象分析结果表明, Y-S-R基序与卟啉丙酸基团形成的氢键网络在sGC-HNOX结构域中的主要作用是使4-E基序稳定地结合于7-H基序, 从而使sGC-HNOX结构域成为一个空间联系紧密的整体.

关键词: sGC-HNOX结构域; Y-S-R基序; 分子动力学; 主成分分析; 最小二乘法

Abstract:

Molecular dynamics methods were implemented to investigate the functions of hydrogen-bonding network between the conserved Y-S-R motif and the heme propionate groups in sGC-HNOX domain. The RMSD analysis reveals that the hydrogen-bonding network can stabilize the conformation of sGC-HNOX domain conspicuously during our simulation. The secondary structure, radius of gyration and solvent-accessible surface area of sGC-HNOX domain are not disturbed by the restraint hydrogen-bonding network. The principal component analysis on trajectory data and the heme configuration analysis indicate that the essential function of hydrogen-bonding network is to stabilize the binding of 4-E motif to 7-H motif, which is related to the structu-ral integrity of sGC-HNOX domain.

Key words: sGC-HNOX domain; Y-S-R motif; Molecular dynamics; Principal component analysis; Least-square method