MD and DFT study of glycerol binding in B12-dependent diol dehydratase (CROSBI ID 660874)
Neobjavljeno sudjelovanje sa skupa | neobjavljeni prilog sa skupa
Podaci o odgovornosti
Bilić, Luka ; Tomin, Marko ; Barić, Danijela ; Kovačević, Borislav ; Smith, David Matthew
engleski
MD and DFT study of glycerol binding in B12-dependent diol dehydratase
During biodiesel production a large amount of glycerol is created as a byproduct. Dehydration of glycerol to a more valuable product could be obtained by eco-friendly methods utilizing B12-dependent dehydratases which turn glycerol into 3-hydroxypropanal. However, the unusual property of glycerol is that it is both the supstrate and the irreversible inhibitor of B12-dependent dehydratases. The proposed mechanism of inactivation is based on the crystal structure of B12-dependant diol dehidratase (DDH, PDB code: 3AUJ). This mechanism relies on the position of the hydroxyl group at C(3) atom of glycerol being oriented towards the serine residue (Ser301) in the active site. However, incompleteness of the enzyme in crystal structure (missing adenosyl group), poor resolution (2.1 Å) and small electron density aroud C(3) call for further research. Herein we compare geometrical parameters of the active site of DDH obtained by molecular dynamic simulations (MD) and quantum chemical calculations (DFT) with the crystal structure, and investigate various patterns of glycerol binding in the active site.
B12 ; diol dehydratase ; DDH ; glycerol ; molecular dynamics ; MD ; DFT
nije evidentirano
nije evidentirano
nije evidentirano
nije evidentirano
nije evidentirano
nije evidentirano
Podaci o prilogu
nije evidentirano
nije evidentirano
Podaci o skupu
AMBER Molecular Dynamics workshop 2018 i Spring School in Computational Chemistry 2018 @ CSC
poster
01.01.2018-01.01.2018
Espoo, Finska; Haifa, Izrael