Platforms


The  Proteomics  platform combines an Ultimate 3000 nano-HPLC and an Orbitrap Fusion Tribrid system by ThermoFisher-Scientific . Optimized procedures of sample preparation and analysis enable us to work effectively with purified fractions, intact proteins, SDS-PAGE bands/spots, immunoprecipitated proteins (on/off-beads) for the identification of
–   Interacting partners
–   PTMs
–   Differences at protein level
–   Proteome/secretome studies
Special projects like Biomarker discovery, quantification (labelled/label-free) and phosphoproteome analysis are under development.


 

The  Structure modeling  platform focuses on the prediction of protein structures and of protein-protein complexes. In addition, the effect of mutations and posttranslational modifications on protein structure and interaction are investigated. These aspects are addressed by a variety of computational tools including molecular modeling, docking, and molecular dynamics simulations.

 

 

 


The  Peptide chemistry  platform involves the structure-based design, chemical synthesis and/or modification, as well as the evaluation of binding behavior of peptides and/or proteins.

The platform comprises the following techniques:
–   Structure-based peptide design
–   Automated, parallel solid phase peptide synthesis with HPLC purification and LC/MS analysis
–   Chemical modification of peptides (non-proteinogenic building blocks, cyclic and branched peptides, N- and C-terminal modification, site-selective fluorophores and other markers/tags)
–   Binding assays to measure biomolecular interactions (Biacore-SPR, fluorescence polarization, ELISA)

 


The  Protein crystallography  platform aims at deriving an experimental understanding of the atomic structures of proteins and the interactions they participate in.

The platform bundles the following techniques:
–    Protein secondary structure characterization via circular dichroism (CD) spectroscopy
–    Determination of affinities and thermodynamic parameters of protein-ligand interactions via isothermal titration calorimetry (ITC)
–   High throughput crystallization using an automated nanoliter dispenser
–    X-ray diffraction data collection on a copper rotating anode diffractometer

 


The  Analytical Ultracentrifugation  platform comprises a custom Analytical Ultracentrifuge (max. 290000 x g) equipped with a fiber-coupled multiwavelength detector (UV-VIS-NIR). It permits the multidimensional analysis of colloids and proteins and allows us to precisely determine:

–    Hydrodynamic and structure properties of colloids (molar masses, hydrodynamic diameters, effective densities, shape anisotropies)
–    Specific and non-specific interactions (concentration effects, binding constants, oligomerization states)
–    Optical properties (size dependent extinction spectra)

 


The  Nonlinear Optical Spectroscopy  platform compromises a Sum Frequency Generation (SFG) and a Second-Harmonic Light Scattering (SHS) setup. Both setups are highly sensitive to interfaces and provide the possibility to:

–    Study surfaces and interfaces with SFG (adsorption of surfactants and proteins at air/liquid interfaces, molecular order of complex self-assembled monolayers at solid/gas interfaces)
–    Probe colloidal interfaces with SHS (adsorption of molecules on nanoparticles in suspension)