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Acta Chimica Sinica >

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

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

Article

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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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

Cite this article

Chen Fu , Liu Shushen , Duan Xintian . Molecular Modeling Study on the Three-dimensional Structure of the Luciferase Protein in Vibrio-qinghaiensis sp.-Q67[J]. Acta Chimica Sinica, 2013 , 71(07) : 1035 -1040 . DOI: 10.6023/A13030339

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