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Centre of Molecular Structure

About us

Introduction

The Centre of Molecular Structure offers services focused on the characterization of biological molecules and of their complexes with ligands, protein and nucleic acids. The services offered include structure analysis with the use of X-ray diffraction, mass spectrometry and specialized analyses of biomolecular targets (target identification, modifications, ligand binding, folding state etc).

Preferred access modes:

Through the CIISB, with information available on the proposal submission page http://www.ciisb.org/open-access/proposal-submission

CIISB_Logo2

For Instruct country members ( https://www.structuralbiology.eu/content/countries–instruct ), access including partial cover of travel expenses can be obtained by means of the INSTRUCT European Research Infrastructure Consortium through its proposal submission web page https://www.structuralbiology.eu/submit-proposal?t=instruct

Instruct

 

 

Keywords

  • BIOPHYSICAL TECHNIQUES
  • Circular dichroism
  • UV/Vis spectrophotometry
  • Surface plasmon resonance
  • Microscale thermophoresis
  • Label-free thermophoresis
  • Tyr and Trp fluorescence
  • Calorimetry
  • Isothermal titration calorimetry
  • Differential scanning calorimetry
  • Dynamic light scattering
  • Static light scattering
  • CRYSTALLIZATION OF PROTEINS AND NUCLEIC ACIDS
  • Crystallisation robot
  • Crystallisation plate set-up
  • Crystallisation hotel
  • Remote crystallisation inspection
  • DIFFRACTION TECHNIQUES
  • Crystal structure
  • Diffractometer
  • X-ray Diffraction
  • In-situ diffraction
  • STRUCTURAL MASS SPECTROMETRY
  • Electrospray
  • MALDI
  • Coupled HPLC
  • Fingerprinting
  • Hydrogen/Deuterium exchange
  • Cross-linking
  • Covalent labelling

Reservation

The preferred way of booking CMS services / use of CMS equipment is through the CEITEC on-line booking system. On-line registration to access this booking system is available as indicated below:

 

 

 

 

 

In addition, the services/equipment may be accessed through the European Instruct (Integrating Biology) network (https://www.structuralbiology.eu/ ).

Finally, reservations may also be made by contacting directly the scientists in charge of the respective Core Facilities http://www.biocev.eu/corefacilit/centrum-molekularni-struktury/#head_of_program.

Team and contacts

velliux
Místnost I1.007
Místnost
I1.003
13_Jan Dohnalek_04
  • Dr. Jan Dohnálek

  • Guarantor of the CMS
  • Biocev representative of Czech infrastructure for integrative structural biology - CIISB, Biocev representative of European infrastructure Instruct
  • +420 325 873 758
Místnost G1.048
Místnost
G1.059
Místnost
U2.002
  • RNDr. Jiří Pavlíček, Ph.D.

  • Scientist in charge of the crystallization and X-ray diffraction service
  • +420 325 873 787
Místnost
I1.005
  • RNDr. Petr Pompach, Ph.D.

  • Scientist in charge of the mass spectroscopy service
  • +420 325 873 785
Místnost
J1.004
Místnost
I1.005

Where to find us in BIOCEV center

Mapa1NP-CMS


Equipment

    Biophysical techniques

  • Applied Photophysics Chirascan Plus ™ spectrometer

    Measurement of circular dichroism spectra and absorbance as function of temperature, pH and concentration to determine the secondary structure of proteins and peptides, conformation of RNA and DNA, as well as to detect conformational changes.

    The Chirascan Plus CD spectropolarimeter with avalanche photodiode detector – provides fast scanning and high sensitivity. This instrument can simultaneously measure accurate CD, absorbance and fluorescence data.

    • Detection range: 170-1150 nm;
    • Peltier temperature control.

    Circular dichroism can be used for:

    • Determination of protein folding;
    • Characterization of protein secondary structure and DNA conformation;
    • Detection of the changes in protein structure upon mutagenesis;
    • Studying of conformational stability of proteins and DNA (pH stability, denaturant stability, temperature, buffers addition of stabilizers).

    Data processing:

    • The CDNN software package is available for detailed model-based analysis and predicting secondary structure using CD data;
    • Software Global Analysis of multiwavelength kinetic data is available to fit multi-dimensional experimental data to one of a number of specified models.

    Sample requirements:

    • Measurement of CD spectrum for the determination of secondary structure of protein requires 160 µl of 0.1 – 0.2 mg/ml protein solution;
    • Measurement of CD spectrum for the determination of DNA conformation requires 160 µl of 20 µM of solution or 1400 µl of 2 µM solution;

    Not optimal for CD solutions, containing DTT, imidazole, glycerol, DMSO, high concentrations of salts.

  • NanoTemper Monolith NT.150

    Used to study biomolecular interactions. The device allows to characterize protein-protein and protein-ligand (small molecule, DNA, RNA, peptides, sugars, lipids) interactions that can be measured under close to native conditions based on thermophoretic effect. Protein labeling is required with this device.

    The Monolith NT.115 MST device allows to detect changes in hydration shell, charge or size of molecules and thus to detect biomolecular interactions.

    MST can be used for:

    • Determination using a fluorescent dye or fluorescent protein of the affinity of interaction from 1nM to mM.

    Sample requirements:

    • Concentration of fluorescent labeled molecule: 10 nM – 10 mM;
    • Final concentration of unlabeled molecule should be at least two orders of magnitude above the expected Kd value. To perform simulations of binding events and to help choose the appropriate concentration, the “Concentration Finder” software is available on the device control panel;
    • At least 20 µl samples per capillary is needed.
  • Malvern Microcal iTC200

    Label-free solution studies of biomolecular interactions.

    The Malvern iTC200 instrument is used for the characterization of biomolecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids etc.

    The iTC200 device can be used for:

    • Direct measurement of submilimolar to nanomolar binding constants (10 3 – 10 9 M -1);
    • Thermodynamic characterization of the molecular interaction in a single experiment (stoichiometry, Kd, ∆H and ∆S values);
    • Calorimetric measurement over a range of biologically relevant conditions (temperature, salt, pH, etc.).

    Sample requirements:

    • The buffer solution, containing both the macromolecule and the ligand of interest, should be the same.
    • The volume of the sample placed in the cell must be at least 300 µl. Preferably, the solutions of macromolecules should be dialysed against the buffer solution used for the ITC measurement;
    • The ligand solution (the sample placed in the injection syringe) must have a volume at least 70.0 µl. Normally the ligand concentration should be 10 times as high as the concentration of macromolecule;
    • In the case of high affinity interactions, the minimum concentration of macromolecule (that causes measurable heat effects) is 10 µM. For low affinity interactions the macromolecule sample concentration should be at least 5 times the Kd value;
    • The buffers used should have low ionization enthalpies (e.g. phosphate, citrate, acetate);
    • If the presence of reducing agent is required for a protein stability, then ß‑mercaptoethanol (at a concentration lower than 5 mM) or TCEP (lower than 2 mM) should be used rather than DTT.

  • Malvern Zetasizer Nano ZS90

    Measurement of molecular size using Dynamic Light Scattering (DLS), zeta potential and molecular weight using Static Light Scattering.

    The Zetasizer Nano ZS90 instrument is used for the measurement of particle and molecular size using Dynamic Light Scattering, with the option of measuring zeta potential and electrophoretic mobility, and molecular weight using Static Light Scattering.

     

    • Size (diameter): from 0.3 nm to 5 microns;
    • Molecular weight measurement down to 10 kDa;
    • Temperature range 0-90°C.

     

    Established methodologies and provided services

    • Particle size analysis (hydrodynamic radius);
    • Temperature range 0-90°C.

    Sample requirements:

    • 25 µl of sample and the same volume of “empty“ buffer ;
    • For protein solutions, concentrations of at least 0.2 mg/ml;
    • For the measurements of zeta potential in folded capillary cells, 0.75 ml of sample is required.

     

  • NanoTemper NT.LabelFree

    Characterization of protein-ligand interactions based on thermophoretic effect, using the intrinsic tryptophan fluorescence. No sample modification is required with this device.

    The NT.LabelFree MST instrument uses intrinsic tryptophan fluorescence for microscale thermophoresis detection, thereby allowing label-free and immobilization-free experiments.

    MST can be used for:

    • The label and immobilization free determination of protein binding to Ions, nucleic acids, small molecules and sugars (with an affinity of interaction in the range of 10 nM to mM).

    Sample requirements:

     

      • Concentration range of tryptophan-containing protein: 100 nM-10 µM;
      • Final concentration of unlabeled molecule should be at least an order of magnitude or more above the expected Kd value ;
      • Molecular weight range: 10-107 Da;

    Minimum sample volume used: 10 µl per sample

  • NanoTemper Prometheus NT.48

    Measurement of protein stability using tyrosine and tryptophan fluorescence.

    The Prometheus NT.48 instrument measure native DFS to determine protein thermal transition temperatures and stability of 48 up to samples at a time.

    No dye is required, tryptophan fluorescence at 330 nm and 350 nm is detected;

    Temperature range: from 15 °C to 95 °C.

    DFS can be used for:

    • Determination of thermal transition temperatures and stability of proteins.

    Sample requirements:

    • Protein must contain tryptophans in order to detect protein unfolding;
    • Sample concentration range: from 5 µg/ml to 250 mg/ml;
    • Prepare at least 20 µl of your samples;
    • For thermal unfolding experiments no assay development or special sample preparation is needed
  • AnalyticJena SPECORD® 50 PLUS i

    Molecular absorption spectroscopy with ultraviolet and visible radiation in the spectral range 190 to 1100 nm.

    The AnalyticJena SPECORD 50 PLUS device is a UV/Vis double-beam spectrophotometer with split-beam technology that combines high energy throughput with good stability.

    • 190-1100 nm;
    • 50-1500 µl of sample;
    • Scanning, dual beam
    • Temperature control with Peltier element, scan-range 5-95ºC.

    The spectrometer can be used for:

    • Proteins and DNA thermostability measurements;

    With or without stirrer can be used for enzyme kinetics.

  • Malvern Microcal VP-DSC

    Direct measurement of intramolecular stability of biological macromolecules, as well as the intermolecular stability of biologically-relevant complexes such as oligomeric proteins, nucleic acid duplexes, and micellar systems (lipid and detergent micelles).

    The MicroCal VP-DSC instrument measures the temperature of thermally-induced structural transitions of molecules in solution. A complete thermodynamic profile is generated to understand the factors that affect conformation and stability of proteins, nucleic acids, micellar complexes and other macromolecular systems.

    • The operating temperature range is of -10°C to 130°C;
    • Maximum scan rates are 90°C/hr in the upscan mode and 60°C/hr in the downscan mode.

     

    DSC can be used for:

    • The determination of transition midpoint, enthalpy (ΔH) of unfolding due to heat denaturation and change in heat capacity (ΔCp);
    • The study of factors that contribute to the folding and stability of native biomolecules, including hydrophobic interactions, hydrogen bonding, conformational entropy, and physical environment.

    Sample requirements:

     

    • Sample buffer and buffer in the reference cell should be exactly the same;
    • The sample solutions should be dialysed against the buffer solution used for the DSC measurements.
    • Sample and reference cell volumes are 200 µl;
    • Typical sample concentration: 0.2 – 2.0 mg/ml;
    • If the presence of reducing agent is required for the sample, the use of up to 5 mM ß-mercaptoethanol or TCEP instead of DTT is recommended;
    • Since fluoride-containing samples cause irreparable damage to the VP-DSC cell, their use is prohibited.
  • BioRad ProteOn XPR36

    Label-free quantitative analysis of biomolecular interactions by the technique of surface plasmon resonance (SPR). The ProteOnTM XPR36 protein interaction array system enables label-free quantitative analysis of biomolecular interactions in real time using SPR technology. The ProteOn system allows to screen analytes simultaneously against 36 different targets of interest, enabling rapid comparison among large numbers of interactions.

    SPR can be used for:

    • Quantification of binding affinity and kinetics;
    • Determination of binding specificity and the number of binding sites;
    • Characterization of membranes, lipids, nucleic acids and micellar systems.

    Sample requirements:

    • Concentration of ligand depends on the level of immobilization desired, generally 10–200 μg/ml. For kinetic analysis the best results are obtained by using a 100-fold range of analyte concentrations, 0.1–10xKd;
    • Immobilization of one interacting partner is essential. The service can provid with a sensor chip, or with the user bringing own chip;
    • The ProteOn acetate buffer (at pH 4.0, 4.5, 5.0, or 5.5) is recommended as immobilization buffer;

    The recommended running buffer for most applications is the ProteOn phosphate buffered saline, pH 7.4 (10 mM sodium phosphate and 150 mM sodium chloride with 0.005% Tween 20).

    Crystallization of proteins and nucleic acids

  • Formulatrix RI 1000 crystallisation hotel

    Crystallisation plate storage and automated crystallization monitoring enclosure allowing remote access to crystallization images. Crystallisation drop images can be taken using visible light, polarized light and UV.

    A service offered is the remote (web-based) access to crystallisation droplet images, and automated preliminary evaluation of crystallisation experiments.

  • ArtRobbins Gryphon dropsetter

    A multi-channel (96 channels) pipetting robot for the easy set-up of nanodrop crystallisation plates.

    This crystallisation robot equipment allows the robotic setup of 96-well crystallisation plates, for screening of crystallisation conditions (and also for “routine crystal production”)  -  for proteins, nucleic acids, complexes of biological macromolecules;

  • SpectroLight 600

    In drop dynamic light scattering measurements in Terasaki 72-well plates. This equipment allows to check the monodispersity of the macromolecule in drops, thereby allowing to check the suitability of the sample for crystallisation.

    Diffraction techniques

  • Bruker D8 Venture diffractometer

    Bruker D8 Venture diffractometer with a high-flux liquid Gallium X-ray source MetalJet D2, Photon II detector and Kappa goniometer. The diffractometer is used (at CMS) for X-ray diffraction of biomolecular crystals.

    ISX stage for D8 Venture – motorized stage for in-situ X-ray diffraction experiments, enabling screening of diffraction properties in crystallization trays.

    This equipment allows to offer the following services:

    • In-situ (in the crystallisation plates) testing of crystal diffraction using the ISX stage;
    • Testing of diffraction using mounted crystals and / or measurement of X-ray diffraction data;
    • Diffraction data processing, providing a data file (such as an MTZ file);
    • Assistance / advice to solve a 3D structure (including a full 3D structure determination service on request);

    Upon request: Measurement of X-ray diffraction data sets at synchrotron radiation sources.

    Structural mass spectrometry

  • Bruker Daltonics 15T-Solarix XR FT-ICR mass spectrometer (associated with Agilent Technologies 1200 HPLC system)

    Bruker Daltonics 15T-Solarix XR FT-ICR mass spectrometer, with electrospray and MALDI ion sources. This ultra-high resolution mass spectrometer is used mostly for the determination of the precise mass of biological macromolecules, and the characterization of their posttranslational modifications. Further possibilities include peptide mass fingerprinting, detection of small molecule/metabolites, monitoring of protein structural changes and protein-protein interactions under physiological conditions by hydrogen-deuterium exchange, chemical cross-linking and covalent labelling.

    Agilent Technologies 1200 HPLC system (usually coupled to the 15T-SolariX XR mass spectrometer) for the separation of complex peptide mixtures, proteins and metabolites.

    This equipment allows to provide the following services:

    • Protein molecular weight determination by ultra-high resolution FT-ICR mass spectrometer with sequence confirmation by Top-down approach using different fragmentation techniques (collision induced dissociation, electron transfer/capture dissociation);
    • Peptide mass fingerprinting – identification of proteins from gel or solution including larger protein mixtures by using MALDI or ESI ;
    • Characterization of posttranslational modification such as phosphorylation, glycosylation or disulphide bonds ;
    • Structural mass spectrometry: limited proteolysis, hydrogen/deuterium exchange, chemical cross-linking, covalent labelling;
    • HPLC separation of peptides, proteins and small molecules (metabolites) coupled with mass spectrometric detection by FT-ICR;
    • Processing and interpretation of mass spectrometric data.

Our Services

Three-dimensional structure determination by macromolecular crystallography (protein/NA crystallization, X-ray diffraction structure determination)

Core Facility Services

The available state-of-the-art equipment for the biophysical characterization of biomacromolecules enables to perform studies on proteins, nucleic acids or complexes thereof for a wide range of molecular biology or structural biology research projects. Individual techniques are provided either as full service including analysis, or as the supply of dedicated machine time to trained users.

Biophysical core research facilities offer a range of services, including investigations of biomolecular interactions, of structure, stability and conformation of DNA and proteins, determination of hydrodynamic radii, zeta potential and electrophoretic mobility of molecules, together with crystallization screens.

The protein and nucleic acid crystallization facility provides the technologies for successful macromolecular crystallization, and subsequent steps (monitoring of the crystallization plates, crystal cryo-cooling (vitrification) in liquid nitrogen and long-term storage. The facility welcomes guests to use either complex approach to target crystallization with the use of all options available at CMS, or individual access to the facility equipment: “normal” (room) temperature, plus high and low temperature crystallisation (with dedicated high quality stereomicroscopes available for these temperatures), pre-crystallization characterization of samples by sub-microliter dynamic light scattering, time-line observation of macromolecular crystallization in combined UV/VIS and DLS monitoring for difficult projects, automated crystallization monitoring with remote access (in a crystallization hotel), crystal cryo-cooling (vitrification) equipment.

The X-ray diffraction facility enables in situ (i.e. in crystallisation trays) automated screening of crystals for X-ray diffraction without disturbing the crystallization drop and its precise condition, single crystal diffraction quality screening and X-ray diffraction data collection at room temperature and at cryo-temperatures (80-300 K). Diffraction data processing and structure solution and refinement can be provided on request. The facility can also provide regular synchrotron data collection and data analysis. Services are provided either as access to dedicated machine time for trained users, as partial services (for example up to data processing) and, to a limited extent, also as a full service.

The Structural Mass Spectrometry facility provides access to novel biomolecular mass spectrometry (MS) methods in order to make the characterization of protein structure and dynamics more rapid and routine. Methods include non-denaturing mass spectrometric approaches in combination with hydrogen-deuterium exchange, chemical crosslinking and other labeling techniques together with computational approaches. This toolbox will be made available to the broader scientific community, and will greatly enhance our ability to design new drugs and ensure the quality and efficacy of biopharmaceuticals, thereby benefiting human health.

References and Publications

CONNECTION TO INTERNATIONAL RESEARCH INFRASTRUCTURES OR CONSORTIA

The Centre of Molecular Structure belongs to the Czech Infrastructure for Integrative Structural Biology (CIISB) – an affiliate center of the European infrastructure for structural biology Instruct (ESFRI). Members of CIISB represented the Czech structural biology community and the Czech Republic as one of the countries at the establishment of the Instruct consortium.