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Molecular Simulation of Glycerol Dehydrogenase of Gluconobacter Oxydans

Author: XiaZhenDong
Tutor: LuWenYu
School: Tianjin University
Course: Biochemical Engineering
Keywords: Gluconobacter oxydans Glycerol dehydrogenase Homology modeling Molecular Dynamics Docking
CLC: TQ920.1
Type: Master's thesis
Year: 2010
Downloads: 40
Quote: 0
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Abstract


In a fermentation process using the the Gluconobacter oxydans conversion Gan Yousheng into dihydroxyacetone , we found that the improvement of the glycerol concentration for cell growth and dihydroxyacetone generated significantly inhibit the efficiency of the conversion of glycerol in order to improve the Gluconobacter oxydans , enhanced strains substrate tolerance, we turned to study the mechanism of action of the glycerol dehydrogenase and substrate glycerol . As the the Gluconobacter oxydans the glycerol dehydrogenase 3D structure is unknown , so we need to obtain the three-dimensional structure of the glycerol dehydrogenase to find the sites of action of the glycerol dehydrogenase and glycerol . First, homology modeling using Modeller 9v6 homology modeling software to build the three-dimensional structure of glycerol dehydrogenase . The protein template 1yiqA , 1kb0A , 1kv9A and 1lrwA, homology of 38% , 37% , 39% and 38% , respectively . Second, the resulting model this article using molecular dynamics software Gromacs 4.0.5 homology modeling sldha.d70 16.pdb 10ns molecular dynamics simulation , and resulting model em2.pdb the geometry and energy evaluation the evaluation showed that the general quality of the model , there is room for optimization . Finally, The molecular docking software Autodock 4.2 glycerol dehydrogenase and glycerol molecule molecular docking experiments and analysis to identify the role of glycerol dehydrogenase and glycerol sites : ALA715 HIS719 through hydrogen bonds .

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