Molecular simulation of pyrroloquinoline quinine-dependent glycerol dehydrogenase in Gluconobacter oxydans

Abstract

During the fermentation process from glycerol to 1,3-dihydroxyacetone (DHA) by Gluconobacter oxydans, the increase in the concentration of glycerol shows obvious inhibition on the cell growth and DHA production. Researches on the interaction mechanism between glycerol and glycerol dehydrogenase (sldha) are important to improve the conversion rate from glycerol to DHA and to enhance the strains tolerance to glycerol. At present, the 3D structure of sldha is still unknown. So we analysed the 3D structure and then found the binding sites of glycerol with sldha. In the present study, we constructed the 3D structure of sldha by the homology modelling method based on Modeller 9v6 software. Four proteins, 1yiqA, 1kb0A, 1kv9A and 1lrwA, from Protein Data Bank were chosen as templates, since they have the highest similarities with sldha in Protein Data Bank which is 38%, 37%, 39% and 38%, respectively. The molecular dynamics simulation of constructed 3D structure of sldha by Gromacs 4.0.5 was carried out. Finally, the binding sites of Ala715 and H719 were found through the molecular docking simulation between glycerol and sldha by using Autodock 4.2.

Keywords:

• Gluconobacter oxydans
• glycerol dehydrogenase
• homology modelling
• molecular dynamics
• molecular dock

Acknowledgements

The authors wish to acknowledge the financial support by the Natural Science Foundation of Tianjin (No. 09JCYBJC09400), Natural Science Foundation of China (No. 21076148), Research Fund for the Doctoral Program of Higher Education (No. 20100032120012), Program for New Century Excellent Talents in University (NCET-10-0616) and Young Teachers Fund of Tianjin University (TJU-YFF-08B13).