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2013 , Vol. 71 >Issue 07: 1035 - 1040

DOI: https://doi.org/10.6023/A13030339

研究论文

青海弧菌荧光素酶蛋白三维结构的分子模拟研究

  • 陈浮 ,
  • 刘树深 ,
  • 段欣甜
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  • 同济大学环境科学与工程学院长江水环境教育部重点实验室 上海 200092

收稿日期: 2013-03-27

  网络出版日期: 2013-05-02

基金资助

项目受国家自然科学基金(Nos. 21177097, 20977065)和高等学校博士学科点专项科研基金(No. 20120072110052)资助.

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Molecular Modeling Study on the Three-dimensional Structure of the Luciferase Protein in Vibrio-qinghaiensis sp.-Q67

  • Chen Fu ,
  • Liu Shushen ,
  • Duan Xintian
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  • Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092

Received date: 2013-03-27

  Online published: 2013-05-02

Supported by

Project supported by the National Natural Science Foundation of China (Nos. 21177097, 20977065) and Specialized Research Fund for the Doctoral Program of Higher Education (20120072110052).

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摘要

基于荧光素酶催化发光的生物发光技术在化学、生命与环境科学等领域得到广泛应用. 部分萤火虫和发光细菌的荧光素酶晶体三维结构已经解析出来. 青海弧菌(Vibrio qinghaiensis sp.-Q67, 简称Q67)是从青海湖青海裸鲤中提取的一种新型淡水发光细菌, 已用于化学品的生物检测及毒性评价. 然而, 其催化发光过程中最重要的荧光素酶三维结构尚未解析, 阻碍了化学品对Q67产生毒性的机理研究进程. 本工作通过异源二聚体同源建模与分子动力学模拟方法构建了Q67荧光素酶的三维结构. 研究结果表明, Q67荧光素酶蛋白有α和β两个多肽亚基, 范德华力是维持α/β稳定结构的主要作用力, 而α/β亚基携带的净电荷产生的静电相互作用不利于体系稳定. 缔合的专一性则由α/β亚基接触面上的极性基团之间的氢键实现. 底物黄素单核苷酸与Q67荧光素酶的结合位点在α亚基活性口袋中, β亚基有利于保持α亚基活性口袋的稳定性.

关键词： 异源二聚体; 荧光素酶; 同源建模; 淡水发光菌; 分子动力学

本文引用格式

陈浮 , 刘树深 , 段欣甜 . 青海弧菌荧光素酶蛋白三维结构的分子模拟研究[J]. 化学学报, 2013 , 71(07) : 1035 -1040 . DOI: 10.6023/A13030339

Abstract

Bioluminescence technique derived from the luciferase-based catalization reactions has been widely used in chemistry, biological assay and environmental science. The three-dimensional crystal structures of luciferase proteins in some firefly and luminescent bacteria were elucidated. Vibrio qinghaiensis sp.-Q67 (Q67), one of freshwater luminescent bacteria which was extracted from Gymnocypris przewalskii in Qinghai lake, has been used in biological assay and toxicity evaluation of many chemicals. However, the crystal structure of the luciferase (the most important catalyzer to bioluminescent) in Q67 is still not established, which hinders the process of the study on the molecular mechanism of toxicities of chemicals to Q67. In this study, the three dimensional structure of bacterial luciferase in Q67 was constructed by using the heterodimeric homology modeling combined with the molecular dynamics simulation which were performed with explicit TIP3P water. The simulation system was equilibrated at 4 ns, and was prolonged for another 4 ns for extracting the equilibrium trajectories at the 8th ns. The stability of the system was monitored through the convergences of energy, temperature, and global root mean square deviation (RMSD). The ptraj modules in the AMBER software were used to analyze hydrogen bond occupancy between α and β subunit. And then, the molecular mechanics generalized born surface area method was applied to identify critical amino acids of the α and β subunits that interact with each other during the native heterotetrameric structure formation. It was shown that the luciferase in Q67 is a heterdimer including two polypeptide subunits (α and β) and the stabilization of this heterodimer was mainly determined by the van der waals force. The specificity of association is realized by hydrogen bonds formed between subunits. However, the electrostatic interaction from the net charge on α and β subunit is unfavorable to the stability of the dimer. The active sites of flavin mononucleotide binding to the luciferase in Q67 are located in the active pocket of α subunit. The β subunit is helpful to keep the structural stability of the active sites on the α subunit.

Key words： heterodimer; luciferase; homology modeling; freshwater luminescent bacteria; molecular dynamics

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