化学学报 ›› 2011, Vol. 69 ›› Issue (24): 2939-2946.DOI: 10.6023/A1102282 上一篇    下一篇

研究论文

戊烷与颗粒型甲烷单加氧酶的相互作用研究

唐典勇1, 刘嵬2, 胡建平*,1, 孙国峰1, 张元勤1, 常珊3   

  1. (1乐山师范学院化学与生命科学学院分子设计中心 乐山 614004)
    (2成都大学药食同源植物资源开发重点实验室 成都 610106)
    (3华南农业大学信息学院 广州 510642)
  • 收稿日期:2011-02-28 修回日期:2011-01-27 出版日期:2011-12-28 发布日期:2011-08-22
  • 通讯作者: 胡建平 E-mail:hujianping@emails.bjut.edu.cn
  • 基金资助:

    HIV-1整合酶与药物小分子、多肽、DNA识别的分子模拟研究;续随子醇抗癌靶点的确定

Study on the Interactions between Pentane and Particulate Methane Monooxygenase

Tang Dianyong1; Liu Wei2; Hu Jianping*,1; Sun Guofeng1; Zhang Yuanqin1; Chang Shan3   

  1. (1 Molecular Design Center, College of Chemistry and Life Science, Leshan Normal University, Leshan 614004)
    (2 Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu 610106)
    (3 College of Informatics, South China Agricultural University, Guangzhou 510642)
  • Received:2011-02-28 Revised:2011-01-27 Online:2011-12-28 Published:2011-08-22
  • Contact: Jian-Ping HU E-mail:hujianping@emails.bjut.edu.cn

颗粒型甲烷单加氧酶(Particulate methane monooxygenase, PMMO)是一个与细胞膜结合的金属酶, 能将烷烃生物催化为醇. 研究PMMO与烷烃的结合模式及催化机制将有利于设计合成一个新的模拟酶, 进而有效地利用烷烃作为新能源. 用分子对接方法获得了PMMO单体与一系列烷烃的结合模式, 并对PMMO单体和PMMO-戊烷复合物进行了6 ns的分子动力学模拟, 最后对复合物进行了构象成簇及结合能分析. 结果表明, 戊烷结合到靠近Zn2+的疏水口袋中, 该口袋由pmoA亚基的M45~W60和R190~T193以及pmoC亚基的Q161三个片段组成. 动力学结果表明, 与PMMO单体比, PMMO-戊烷复合物保持着相近的运动模式, 但幅度更明显, 另外, 戊烷在疏水口袋中的大幅度运动对于PMMO发挥催化作用是必须的. 结合能计算揭示疏水相互作用是戊烷与PMMO稳定识别的主要驱动力, 所有模拟结果与实验数据吻合较好.

关键词: 颗粒型甲烷单加氧酶, 戊烷, 分子对接, 分子动力学, 相互作用

Particulate methane monooxygenase (PMMO) is an membrane-bound metalloenzyme that catalyses the biological conversion of alkane to alcohol. The study on the binding modes between alkane and the catalytic mechanism of PMMO may aid the design of a new synthetic catalyst, which uses alkane as an alternative new energy source. The binding modes of PMMO with a series of alkanes were obtained via molecular docking method, then two 6 ns molecular dynamics simulations were performed for both PMMO and PMMO-pentane complex systems. Finally, conformation cluster and binding energy analysis were implemented for the complex systems. The results show that pentane binds to the hydrophobic pocket near the zinc ion, which is comprised by three segments (i.e., the residues from M45 to W60, R190 to T193 in pmoA subunit and Q161 in pmoC subunit). Compared with PMMO, PMMO-pentane complex maintains a similar motive mode but a more remarkable motive extent. Additionally, large-scale motion of pentane in the hydrophobic pocket is important for the catalysis of PMMO. The results of binding energy computations still revealed that the stable recognition of PMMO by pentane was mainly driven by the hydrophobic interactions. All the simulation results agree well with experimental data.

Key words: particulate methane monooxygenase, pentane, molecular docking, molecular dynamics, interactions

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