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PD Dr. Sonja A. Dames

Chair of Biomolecular NMR-Spectroscopy

Affiliation

Group leader, Department of Chemistry, TU Munich

Contact

Department Chemie
Biomolecular NMR Spectroscopy
Technical University Munich
Lichtenbergstra├če 4
D-85747 Garching

Phone: +49 (0)89 / 2891-3292
Fax: +49 (0)89 / 2891-3869

Website: http://www.ch.tum.de/index.php?id=413&L=1
Website: http://www.nmr.ch.tum.de/home/dames/

Research Focus

The goal of our research is to elucidate the atomic details of the biomolecular signaling network that controls cellular reactions in living organisms. The knowledge of the structure, dynamics, folding, and interactions of proteins and other biomolecules that transmit cellular signals is the key to the understanding of biological processes such as embryogenesis, organ formation, or tumorigenesis.

Our experimental method of choice is nuclear magnetic resonance (NMR) spectroscopy in solution. This method allows not only to obtain high-resolution structural and dynamic information of biomolecules, but also to study their interactions over a broad range of binding affinities and in cases where one or more interaction partner is natively unfolded. In addition other biophysical (e.g., fluorescence, circular dichroism, calorimetry, crystallography, SAXS), biochemical (e.g., mutagenesis, immunoprecipitation), and biocomputational methods (e.g., ligand-docking, molecular dynamics simulations) are employed. See also below.

TOR signaling cascade

The major subject of our research is the structural characterization of the protein TOR (target of rapamycin) and of its interactions with other cellular components. TOR is a central controller of cell growth that intercepts different signaling pathways and thereby controls processes such as transcription, translation, ribosome biogenesis, autophagy, mitochondrial metabolism, apoptosis, and the reorganization of the actin cytosceleton. Regulation of cell growth is mandatory for organs and whole organisms to reach a characteristic size. Misregulation of cell growth can result in cancer, diabetes, obesity, and pathological increase or decrease in organ and body size.

dames_research

TOR proteins consist of several functional domains (Fig. 1). All family members contain a region close to the carboxy-terminus that is about ~250 residues long and that shows homology to the catalytic subunit of PI-3/4 kinases. Despite the homology to lipid kinases, the TOR kinase domain phosphorylates serine and threonine residues of target proteins. The central ~550 residue long FAT domain occurs always in tandem with the ~35 residue encompassing FATC motif at the very carboxy-terminal end. The FRB (FKBP-rapamycin binding) domain is located between the FAT and the kinase domains. Finally, TOR contains two amino-terminal regions composed of HEAT repeats that are found in many proteins, where they often mediate protein-protein interactions. Two functionally distinct TOR complexes (TORC1/2) have been identified. Only TORC1 is sensitive to the TOR-specific inhibitor rapamycin. The longterm goal is to structurally characterize all the domains of TOR as well as their interactions with regulatory proteins, lipids and membranes, and other cellular components.

Primary Technique(s):

NMR spectroscopy in solution

  • Characterization of the structure and dynamics of proteins
  • Analysis of the interactions of proteins with other proteins, membrane-mimetics, small molecules

Protein expression and purification

  • Protein expression and isotope labeling in E. coli cells
  • Purification using different techniques (affinity chromatography, reversed-phase HPLC etc.)

Preparation of membrane-mimetics

  • Micelles, bicelles, liposomes

Complementary biophysical and computational methods

  • CD & fluorescence spectroscopy, ITC
  • MD simulations

Model Organism(s): Different E.coli strains for cloning and expression of proteins from humans and other eukaryotes as well as mycobacteria