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"From sequence to function: how do sequence and structure determine specificity and selectivity of proteins."
The focus of our research is protein design: molecular modeling of enzyme-solvent systmes to predict enzyme variants with improved specificity, selectivity, and stability, and investigating sequence-function relationships of large protein families.
Design of useful enzymes:
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We develop quantitative models to understand the molecular basis of substrate specificity, regio- and stereoselectivity of enzymes,
and to design enzymes with improved biocatalytic properties. Some enzymes we are investigating are used as biocatalysts in organic synthesis,
like lipases, esterases, epoxide hydrolases, bacterial P450 monooxygenases, and dehydrogenases. Here, our goal is to improve their activity,
specificity, and selectivity towards industrially relevant substrates. Recently we started also a project on modelling of the molecular basis of
protein purification by studying the interaction of proteins with chromatography materials. Other enzymes like beta-lactamases are of medical interest,
as they confer resistance to pathogenic organisms. Here, we analyze the relationship between genetic diversity and the substrate profile of the
respective variant, especially the long-range effects of mutations.
Software and hardware: docking of substrates (FlexX), molecular dynamics simulations (AMBER) on our BioCORTEX PC cluster
Ongoing projects:
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| Mihaele Antonovici |
Molecular modeling of the binding of peptides and proteins to ceramic surfaces
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Alexander Seifert |
Design of bacterial P450 variants with improved selectivity
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| Sven Benson |
Modelling of the molecular basis of substrate specificity (Excellence Cluster Simulation Technology)
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Demet Sirim |
Modelling of laccases
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| Benjamin Juhl |
Biochemical profiling by high-throughput docking
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Alexander Steudle |
Molecular modelling of antibodies
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| Tobias Kulschewski |
Simulation of protein solutions
(DFG-Sonderforschungsbereich 716, sub-project C.1)
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Do Anh Tuan |
Molecular modeling of the binding of peptides and proteins to ceramic surfaces
(DFG - PAK 410 "Biologische Erzeugung von Oxidkeramiken)
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| Sascha Rehm |
Simulation of conformational transitions in lipases (DFG-Sonderforschungsbereich 716, sub-project C.1)
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Michael Widmann |
Modelling of thiamine diphosphate dependent enzymes (DFG-Forschergruppe 1296)"
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Systematic analysis of sequence, structure, and function:
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Information on sequence, structure and function of large enzyme families are compiled, analyzed, and made publicly available. Currently we provide the following family-specific databases:
A systematic analysis of enzymes is exploited for applications in white biotechnology: identifiy optimal biocatalysts in sequence databases or design enzymes with improved activity, specificity, selectivity, or stability red biotechnology: understand the molecular basis of drug detoxification (cytochrome P450 monooxygenases) or antibiotic resistance (lactamases)
Software and hardware: design and implementation of a relational database (SQL), multisequence alignment, phylogenetic trees, analysis tools in Perl/CGI.
Ongoing projects:
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| Benjamin Juhl |
Lipase Engineering Database (LED)
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Demet Sirim |
Cytochrome 450 Engineering Database (CYPED)
Laccase and Multicopper Oxidase Engineering Database (LccED)
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| Silvia Racolta |
Triterpene Engineering Database
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At the moment the bioinformatics group has the following members:
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Post-Docs: PhD Students: |
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