Project Details
Projekt
Computational Investigation of Mechanisms of Enzymes Involved in the Anaerob Degradation of Hydrocarbons
Applicant
Professor Dr. Matthias Ullmann
Subject Area
Bioinformatics and Theoretical Biology
Term
from 2009 to 2016
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 71779365
The chemically difficult degradation of hydrocarbons under anaerobic conditions requires potent catalysts. Biochemically such reaction often involve metalloproteins or radical enzymes. In this proposal, we suggest to use computational methods to understand the mechanism of enzymes that degrade hydrocarbons under anaerobic conditions. In particular, we want to study the mechanism of the tungsten enzymes Acetylene Hydratase and BamBC, a benzoyl-CoA reductase, as well as the mechanism of the glycyl-radical enzyme 4-Hydroxyphenylacetate. The structure of these enzymes has been recently solved at high resolution which makes them accessible to a theoretical investigation. To get a complete picture of the reactions, we will combine different theoretical techniques. By applying continuum electrostatics with Monte Carlo techniques, we will determine the protonation and redox behavior of the proteins. Detailed mechanistic studies will be done by quantum chemical calculations in the gas phase as well as QM/MM calculations in which the active site of the protein is treated quantum chemically and the surrounding protein and solvent classically by molecular mechanics. A particular challenge will be to understand the complex protonation and redox behavior of the molybdopterin cofactor and its modulation by the protein environment. Results on this question may well contribute to our general understanding of molybdopterin enzymes, which are involved in many biochemical processes also in humane.
DFG Programme
Priority Programmes
