Czech Infrastructure for Integrative Structural Biology
Structural mass spectrometry (MS3D) offers various methodologies for characterization of protein structure. IBT/CMS at BIOCEV offers different labelling approaches including hydrogen/deuterium exchange, covalent labelling, chemical cross-linking and limited proteolysis. The facility is equipped with cutting-edge technologies including high-resolution mass spectrometer, HPLC system, H/D system and in-house software for data processing. The service provided includes data processing and reporting ready for publication. Besides, the platform also offers: Identification and quantification of proteins, Precise determination of protein molecular mass, Characterization of various posttranslational modifications.
The macromolecular crystallisation platform enables in-drop dynamic light scattering measurement to check the quality of the protein sample, robotic setup of 96-well crystallisation plates, incubation at selected temperature from a wide range, and automated monitoring of the crystallisation experiments. Experiments can be stored at 4-30 (or higher) deg Celsius. Dedicated rooms with stereomicroscopes for crystal manipulation are available at 20, 10 and 25 (or higher) deg Celsius. Inert atmosphere crystallisation is available. Equipment: Formulatrix NT8 Dropsetter, Art Robbins Gryphon Dropsetter, DLS Spectrolight 600, Glovebox PETG10R320T3, Formulatrix RI 1000 Crystallisation Hotel, stereomicroscopes with imaging, cooled centrifuges, nanodrop spectrophotometer.
Techniques are provided for the analysis of kinetic and thermodynamic parameters of biomolecular interaction and for the biophysical characterisation of the structure, function and stability of biological biological macromolecules like proteins, nucleic acids, lipids and their complexes (Microscale Thermophoresis, Surface Plasmon Resonance, Isothermal titration Calorimetry, Differential Scanning Fluorescence, Differential Scanning Calorimetry, Circular Dichroism, Dynamic Light Scattering, UV/Vis Spectrometry).
D8 Venture diffractometer (Bruker) with a MetalJet D2 high-flux liquid Gallium X-ray source, Photon II detector and Kappa goniometer. This diffractometer is used for X-ray diffraction studies of biomolecular crystals (macromolecular crystallography). The device is also equipped with an ISX motorised stage for in-situ X-ray diffraction experiments, enabling screening of diffraction properties in crystallisation plates (plus limited diffraction data collection). The beam size of 70 microns (FWHM) and its high brilliance enable very effective screening, automated in-plate screening and fast data collection. Typical exposure time per degree for protein crystals: 30-90 seconds.
Versatile instrument to perform SAXS or WAXS experiments on liquid samples, in the temperature range -10° C to 120° C. SAXSpoint 2.0 (Anton Paar) is equipped with the latest high brilliance source MetalJet C2+ having a liquid gallium alloy anode, and a Dectris EIGER 1M detector. Samples can be loaded using the automated high precision sampler or manually in capillaries, including a high S/N silicon nitride measurement cell. The state of the sample can be monitored online using UV-Vis spectroscopy to identify radiation damage, measure precise sample concentration and aggregation state.
CIISB - Czech Infrastructure for Integrative Structural Biology is formed by two Centers of Excellence for Structural Biology constructed within two projects: CEITEC – Central European Institute of Technology, Brno and BIOCEV - Biotechnology and Biomedicine Centre, Vestec, Prague-West. CEITEC and BIOCEV have been financed by the EU Structural Funds through the Operational Program Research and Development for Innovation, priority axis 1 – European Centers of Excellence, which is managed by the Ministry of Education, Youth and Sports of the Czech Republic. The Czech structural biology community is represented by the Czech Society for Structural Biology (CSSB), which is forming a national link to INSTRUCT. CIISB affiliation with INSTRUCT contributes to the development of human resources in research, attracts qualified national and international researchers, and enables efficient dissemination of knowledge and expertise within INSTRUCT, as well as the efficient use of the infrastructure.
The core facilities for structural biology in BIOCEV are organized under the Centre of molecular structure, run by the Institute of Biotechnology, Czech Academy of Sciences.
CF Crystallisation: operational since January 2016
Key equipment: robot for nanovolume crystallization drop setup with automated setup screening (Gryphon), crystallization hotel for automated monitoring of crystallization experiments (Formulatrix RI1000 with UV imaging), dedicated rooms with controlled temperature enabling crystal manipulation without temperature disturbance, several high resolution stereomicroscopes for crystal manipulation, equipment for crystallization under defined atmosphere (e.g. oxygen-free), in-drop dynamic light scattering Spectrolight 600.
Expertise: Classical and robotic crystallogenesis with remote experiment monitoring in three dedicated laboratories with strictly controlled temperature regimes with full backup. Automated screening of variation of crystallization conditions and its effects. Anaerobic crystallization and manipulation of biomacromolecules.
Open-access: Assisted use of all experimental equipment for crystallogenesis, limited capacity for service crystallogenesis.
CF X-ray diffraction: operational since January 2016
Key equipment: X-ray diffractometer D8 Venture for precise measurements with the MetalJet D2 X-ray source detector Photon 2, kappa goniometer, and in-situ motorized stage ISX; SAXSpoint 2.0 instrument with dedicated high flux LiquidMetal Jet C2+ X-ray source, Eiger 1M detector and in situ UV/Vis spectrophotometric probe; cryo-bench.
Expertise: Manual and robotic screening for X-ray diffraction of macromolecular and small molecule samples, automated evaluation of suitability for structural studies. In-house data collection and processing, in-situ evaluation of sensitive crystallisation targets, experimental phasing experiments – evaluation for MIR, SAD and MAD approaches, synchrotron-based data collection and processing, structure solution from small molecules to large protein-protein or protein-nucleic acid complexes, structure finalization and interpretation. Small Angle X-ray Scattering measurements of biological macromolecules in solution, data processing and analysis leading to sample characterisation (sample purity, aggregation and dispersity state, low resolution molecular envelope calculation).
Open-access: Assisted use of all experimental equipment, hosting prolonged experiments (in-house experimental phasing), “service” data collection at synchrotron sources of radiation in individual cases, capacity dedicated to methods development, long-term documented cryo-storage.
CF Biophysical techniques: fully operational since January 2016.
Key equipment: Biorad ProteOn surface plasmon resonance, Microscale thermophoresis, Differential scanning fluorimeter, Isothermal titration calorimeter, UV CD spectrometer, Dynamic light scattering equipment
Expertise: Characterisation of intermolecular interactions by calorimetry, surface plasmon resonance, CD spectrometry, microscale thermophoresis, DFS, light scattering. Identification of ligands for macromolecular targets based on determination of binding constants and kinetic profiles of interacting molecules.
Open-access: Assisted use of all experimental equipment and “service” characterisation of interactions.
CF High resolution mass spectrometry: operational since January 2016.
Key equipment: High-resolution mass spectrometer (MALDI/ESI 15T solarix XR) and multidimensional ultra power liquid chromatography system; Autoflex speed mass spectrometer (MALDI); Excimer laser.
Expertise: Qualitative characterization of molecules/molecular assemblies – from small organic molecules (metabolites) over biomolecules (oligosaccharides, nucleic acids, proteins) to supramolecular biopolymer complexes. The utilization of high resolution mass spectrometry (15T FT-ICR MS) to determine the composition of molecules (metabolites, nucleic acid, proteins, and carbohydrates) based on accurate mass measurements and fragment pattern. FT-ICR MS will be equipped with atmospheric pressure ionization technique (electrospray) and various types of vacuum ionization techniques (laser desorption, matrix-assisted laser desorption). Also FT-ICR MS will be able to perform sustained off-resonance irradiation, collision-induced and electron transfer/capture dissociations. Mass spectrometric cutting-edge analysis of post-translational modifications, and of structural states of proteins and complexes in solution. Combination of covalent surface labelling, isotope (H/D) exchange, chemical cross-linking, mass spectrometry and protein structure modelling are used for protein conformational studies and the characterization of protein/ligand non-covalent interactions.
Open-access: Separation of protein mixtures • intact protein analysis • Peptide/protein/metabolite profiling • Protein identification • Characterization of protein modifications • Protein/metabolite quantification • protein surface covalent labelling • chemical cross-linking • H/D exchange • Data processing and interpretation of mass spectrometric data • Teaching courses, hands-on courses • Consulting services, specific intra- and intermolecular interactions.
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