Molecular Simulation Of Glycerol Dehydrogenase Of Gluconobacter Oxydans

During the fermentation process of converting glycerol to dihydroxyacetone in Gluconobacter oxydans, we found that increasing the glycerol concertration showed obvious inhibition on the cell growth and dihydroxyacetone production. In order to improve the convertion rate of dihydroxyacetone from glycerol and substrate concertration, we turned to the research on the interaction mechanism between glycerol and glycerol dehydrogenase.At present, the three dimensional structure of glycerol dehydrogenase is unknown, so we need to obtain the 3D-structure and then to find the binding sites of glycerol. Firstly, we adopt the homology modelling method to construct the 3D-structure of glycerol dehydrogenase by Modeller 9v6 software. We got the protein templates from Protein Data Bank. They are 1yiqA, 1kb0A,1kv9A, 1lrwA which show similarities of 38%, 37%, 39%, 38% respectively.Secondly, we did the molecular dynamics simulation of sldha.d7016.pdb using Gromacs 4.0.5. Then we evaluated the simulation result which showed that the quality of the result model was not very high. There are still some places need to be optimized.At last, we did the molecular docking experiment of glycerol and glycerol dehydrogenase using Autodock 4.2, and found out the binding sites: ALA715 and HIS719 through hydrogen-bond analysis.