Centre of Molecular Structure

Technologies for structural and biophysical analysis of biological molecules, including mass spectrometry and expression of recombinant proteins.

CMS users are obliged to give credit to the CIISB research infrastructure in all articles/publications/texts published on the basis of services made under the CIISB research infrastructure while using the following formulation:

CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2023042 and OP JAK project "Innovation of Czech Infrastructure for Integrative Structural Biology" (no. CZ.02.01.01/00/23_015/0008175), is gratefully acknowledged for the financial support of the measurements at the CF [name of the unit/CF].

Operational status

All instruments are operational.

Events and activities

Autumn of courses

Wide range of courses is happening in the autumn of 2025. Check the list under "Courses"

MBDB - Molecular Biophysics Database

Within the project MOSBRI, new database for raw biophysical data was established with participation of CMS: MBDB. The database currently accepts data measured using BLI, SPR, ITC and MST, but the scope will widen. Next technique, which will be covered soon is Mass photometry.

Application form

To use CMS services the project application is availble via:

  1. Czech Infrastructure for Integrative Structural Biology (CIISB)
  2. Instruct-ERIC

New equipment and services

HeliX+

Heli X+ instrument is a new generation of the switchSENSE technology allowing for biophysical characterization of proteins and protein-protein interactions. The high frequency dynamic electrical switching mode probes the hydrodynamic friction and serves to analyze the conformational change of biomolecules. The fluorescence proximity sensing mode reveals the binding of molecules in real-time through changes in the dye`s local environment. 

SONICC

The crystalization hotel RI1000 was improved with the crystal detection system SONICC, which enables visualization of protein crystals and microcrystals using nonlinear optics.

twoMP

A device to measure Mass Photometry, which provides measurement of molecular mass of proteins in the solution. The technique is ideal to study oligomerization or protein-protein complexes.

Our tissue culture room is now fully operational

We provide recombinant protein production in insect (Sf9, High Five) and mammalian (HEK293T/17SF, Expi293, Expi293F GnTI-) cells. We welcome new collaborations and look forward to supporting your research projects.

Pilot MS Metabolomics service

A limited metabolomics service is newly available - contact Geovanna de Oliviera Costa or Petr Pompach for more information.

From users

Kovaľ T., et al.: Mycobacterial HelD connects RNA polymerase recycling with transcription initiation, Nature Communications 15 (2024)
Sabo J., et al.: CKAP5 enables formation of persistent actin bundles templated by dynamically instable microtubules, Current Biology 34 (2024) 21
K. Adámková, et al.: Substrate preference, RNA binding and active site versatility of Stenotrophomonas maltophilia nuclease SmNuc1, explained by a structural study, Febs Journal, (2024) 24
O. Bulvas, et al.: Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase, Nature Communications, 15 (2024) 14.

The Centre of Molecular Structure (CMS) provides state-of-the-art equipment, expertise and services for characterization of biological molecules and for structural analysis. CMS provides services in an Open Access regime, to internal IBT users and also to any academics or industrial customers. The facilities are operated under the Czech Infrastructure for Integrative Structural Biology and belong to the Czech center of the European structural biology infrastructure Instruct-ERIC. The facility educates Czech and foreign students and young scientists in a number of workshops throughout the year.

Access

 

logo_CIISB instruct_trans

MosbriLogo_FullColour

Local & international Local & international International only

User's acknowledgement in publications

CMS users are obliged to give credit to the CIISB research infrastructure in all articles/publications/texts published on the basis of measurements made under the CIISB research infrastructure while using the following formulation:

CIISB, Instruct-CZ Centre of Instruct-ERIC EU consortium, funded by MEYS CR infrastructure project LM2023042 and OP JAK project "Innovation of Czech Infrastructure for Integrative Structural Biology" (no. CZ.02.01.01/00/23_015/0008175), is gratefully acknowledged for the financial support of the measurements at the CF [name of the unit/CF].

Or in the short forulation:

We acknowledge CMS-Biocev ("Biophysical techniques, Crystallization, Diffraction, Structural mass spectrometry, Protein Production”) of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042) and CZ.02.01.01/00/23_015/0008175.

Core facilities

CF Biophysical Techniques

The core facility Biophysical techniques enables assessment of the quality, stability and interaction properties of hundreds of biomolecular samples of many structural biology projects, be it regular checks, thorough analysis of properties or optimization of molecular constructs or handling protocols.

CF Crystallization of Proteins and Nucleic Acids

The core facility Crystallization of proteins and nucleic acids enables thousands of crystallization experiments using robotic or manual setup, automated monitoring of crystal growth, experiments at selected temperatures or under defined conditions, to prepare samples for further crystallographic studies.

CF Diffraction techniques

The core facility devoted to diffraction analysis offers crystal quality screening, in situ crystal testing, single crystal data collection and processing, small angle X-ray scattering (SAXS) experiments with robotic sample loading and online UV-VIS spectrometry, and SAXS data processing. Hundreds of samples are processed per year in the self-assisted mode or with full staff support.

CF Structural Mass Spectrometry

The core facility Structural mass spectrometry provides analyses of hundreds of samples and supports many internal and external structural biology projects. The main focus of the services lies in monitoring of proteins structural changes and protein-protein interaction by chemical cross-linking and hydrogen-deuterium exchange.

CF Protein Production

The core facility for protein production provides comprehensive services, covering every step from DNA to purified protein. These include gene cloning into expression vectors using various techniques and heterologous expression in Escherichia coli for bacterial expression, HEK293T, Expi293, and Expi293F™ GnTI- for mammalian expression, and the baculoviral system in Sf9 or High Five™ insect cells. The expression is followed by multistep protein purification.

Acknowledgement

The Centre of Molecular Structure is financially supported by the MEYS project LM2018127 Czech Infrastructure for Integrative Structural Biology (CIISB), CIISB4HEALTH (CZ.02.1.01/0.0/0.0/16_013/0001776), UP CIISB (CZ.02.1.01/0.0/0.0/18_046/0015974), and ELIBIO (CZ.02.1.01/0.0/0.0/15_003/0000447)

Additional information

How to apply for the measurement: https://stigmator.ceitec.muni.cz/project_form/

Czech Infrastructure for Integrative Structural Biology https://www.ciisb.org/

BIOCEV web pages of CMS https://www.biocev.eu/cs/infrastruktury-a-servisni-laboratore/centrum-molekularni-struktury.3

Instruct-ERIC infrastructure web pages https://www.instruct-eric.eu/centre/biocev/

Please contact Ing. Jan Dohnálek, Ph.D. for more information.

Alblová Miroslava, RNDr., Ph.D.
Dohnálek Jan, Ing., Ph.D.
Černovec Táňa, Ph.D.
de Oliveira Costa Geovanna
Holá Lenka, Ing.
Kadlec Tim, MgA.
Klápšťová Veronika, Mgr., Ph.D.
Kolarčíková Tereza, Mgr.
Pavlíček Jiří, RNDr., Ph.D.
Plucarová Jitka, Mgr., Ph.D.
Pompach Petr, RNDr., Ph.D.
Prchalová Terezie
Pyrihová Eva, Ph.D.
Rasl Jan, Mgr., Ph.D.
Stránský Jan, Ing., Ph.D.
Szmitkowska Agnieszka, Ph.D.
Strnad Michal, Ing.
Škultétyová Ľubica, RNDr., Ph.D.
Vaňková Pavla, Mgr., Ph.D.
Vidrnová Lenka, Bc.

CF Biophysical Methods

contact: Tatsiana Charanavets

location: I1

  • Characterisation of intermolecular interactions
    • Calorimetry (affinity, enthalpy, and the stoichiometry of interaction)
    • Microscale thermophoresis (affinity of binding)
    • BioLayer interferometry (affinity and kinetic of interaction)
    • Surface plasmon resonance (dissociation constant, association and dissociation rates)
  • Characterisation of molecular state in solution
    • Circular dichroism spectrometry (secondary structure of proteins, conformation of oligonicleotides)
    • Dynamic light scattering (size of molecule/complex, monodispersity/polydispersity, aggregation)
    • Differential scanning calorimetry (thermodynamic parameters of thermal denaturation of proteins or oligonicleotides)
    • Mass photometry (molecular mass of proteins)
    • Differential scanning fluorescence (thermostability of proteins)
    • Fluorescence spectroscopy (excitation and emission spectra, absorption,  kinetic measurements, steady-state and time-resolved fluorescence anisotropy)
    • Fourier transform infrared spectroscopy (secondary structure of proteins, spectral fingerprints of different chemical structures, quantification structural changes) 
  • Sample quality assessment
    • Dynamic light scattering (monodispersity/polydispersity, aggregation)
    • UV-Vis spectroscopy (concentration estimate, aggregation)
    • Mass photometry (polydispersity)
    • Small angle X-ray scattering (aggregation, particle size estimate, folding; see CF Diffraction techniques)
    • Circular dichroism spectrometry (folding)
  • High throhput sample condition screening
    • Dynamic light scattering (monodispersity/polydispersity, aggregation)
    • Differential scanning fluorescence (thermostability of proteins, aggregation)

Links:

CMSwiki (Biocev network only)

CF Crystallization of Proteins and Nucleic Acids

contact: Jiří Pavlíček

location: I1

  • Crystallization of proteins and nucleic for atomic structure resolution
  • Robotic setup of crystallization plates (high throughput screening, condition optimization)
  • Manual setup of crystallization plates (scaling to higher volumes, condition optimization)
  • Lipidic cubic phase (crystallization of membrane proteins)
  • Crystal seeding (crystal growth control and improvement)
    • Robotic (optimization, screening for new conditions)
    • Manual (optimization, crystal quality improvement)
  • Automated monitoring of crystallization experiments (imaging over time, remote web access)
    • Visible, Cross polarized, UV Fluorescence, Second harmonic generation, TPE-UVF (crystal detection techniques)
  • Manual monitoring (assessing and imaging of plates in compatible with automated imaging; mostly done by users)
    • Visible, Cross polarized, UV Fluorescence (crystal detection techniques)
  • Crystal harvesting and vitrification (preparation for diffraction experiments)
  • Anaerobic crystallization (manual setup and crystal harvesting in nitrogen atmosphere using glovebox)
  • Preparation for synchrotron trips (sample transfer to synchrotron-compatible holders - UniPuck, SPINE puck)
  • Vitrification and blotting of cryoEM grids (sample preparation for cryoEM)
  • Long term storage in LN2 (sample storage before diffraction or cryoEM experiments)
    • canes or UniPuck

Links:

CMSwiki (Biocev network only)

RockMakerWeb (remote crystallogenesis monitoring)

CF Diffraction Methods

contact: Jan Stránský

location: I1

  • Single crystal X-ray diffraction
    • Testing of diffraction quality
    • Data collection (determination of atomic structures)
    • Cryo conditions
    • Room temperature
    • Controlled humidity or crystal dehydration (improvement of diffraction quality, room temperature experiments)
    • In-situ in crystallization plates (testing of diffraction quality without crystal manipulation)
    • X-ray fluorescence (atomic element identification)
  • Small angle X-ray scattering
    • Characterization in solution (sample quality, particle size, particle flexibility)
    • Low resolution structure (estimation of molecular shape without prior knowledge)
    • Atomic model validation (confirmation of models from AlphaFold, crystallography, cryoEM, NMR, etc.)
    • Characterization of flexible or disordered systems (assessing flexibility, estimate of conformational populations, ...)
    • Analysis of mixtures (assessing of oligomerization, ratio of different particles, particle size and shape distributions)
    • Automatic measurements (high throughput experiments)
    • In-situ UV-Vis spectroscopy (concentration validation, sample quality monitoring, chemistry changes)
    • SEC-SAXS (separation of problematic samples before or during the experiment)
  • Assistance with data processing

Links:

CMSwiki (Biocev network only)

CF Structural Mass Spectrometry

contact: Petr Pompach

location: G1

  • Separation of protein mixtures
  • Intact protein analysis
  • Peptide/protein/metabolite profiling
  • Protein identification
  • Characterization of protein modifications
  • Protein/metabolite quantification
  • Protein surface covalent labeling
  • Chemical cross-linking
  • H/D exchange
  • Data processing and interpretation of mass spectrometric data

Links:

CMSwiki (Biocev network only)

CF Protein Production

contact: Miroslava Alblová

location: I1

  • Cloning services

    • Design of expression vectors

    • DNA template control by whole plasmid sequencing

    • Ordering gene fragments from an external company

    • Cloning using traditional restriction enzymes

    • Restriction-free methodologies (RF, KLD, In-Fusion)

    • Site-directed mutagenesis

    • Plasmid DNA preparation (minipreps, midipreps, maxipreps)

    • Preparation of competent cells

  • Recombinant protein production in E. coli

    • Small-scale expression and solubility tests in various E. coli strains

    • Large-scale protein expression

    • Protein production in minimal media

  • Recombinant protein production in insect cells

    • BacPAK™ (TaKaRa) and FlexiBAC baculovirus systems

    • Small-scale cell transfection and expression verification by Western blot

    • Baculovirus amplification

    • Large-scale production in Sf9 or High Five™ cells

  • Recombinant protein production in mammalian expression systems

    • Expression in HEK293T/17SF, Expi293™, Expi293F™ GnTI- cells

    • Small-scale cell transfection and expression verification by Western blot

    • Large-scale cell transfection and protein production

  • Recombinant protein purification

    • Affinity chromatography (HiTrap HP, Ni-INDIGO, Strep-Tactin®XT, GST, cobalt)

    • Ion-exchange chromatography

    • Size exclusion chromatography

    • Protein concentration and dialysis

    • Tag removal (TEV, SUMO, 3C protease)

    • Optimization of expression and purification protocols

Links:

CMSwiki (Biocev network only)

CF Biophysical Methods

contact: Tatsiana Charnavets

  • Surface Plasmon Resonance (SPR) system ProteOn XPR36 (BioRad)
  • Circular dichroism (CD) spectrometer Chirascan Plus (Applied Photophysics)
  • Monolith microscale thermophoresis (MST) NT.115 (Nano Temper)
  • Monolith microscale label free thermophoresis NT.LabelFree (Nano Temper)
  • Isothermal titration calorimeter MicroCal iTC200 (Malvern Panalytical)
  • Dynamic light scattering (DLS) technique  Zetasizer Nano ZS90 (Malvern Panalytical)
  • Multi-angle dynamic light scattering (MADLS) technique Zetasizer Ultra (Malvern Panalytical)
  • Differential scanning fluorescense (DSF) assay Prometheus NT.48 (Nano Temper)
  • UV/Vis Spectrometer Specord 50 Plus (Analytica Jena)
  • Modular fluorescence spectrometer FLS1000 (Edinburgh Instruments)
    • with SuperK EXTREME, a supercontinuum white light laser (NKT Photonics)
  • FTIR spectrometer Vertex 70v (Bruker)
  • SPARK (TECAN)
  • OCTET R8 (Sartorius)
  • Mass photometer TwoMP (Refeyn)
  • Helix+ (Bruker)
  •  

CF Crystallization of proteins and nucleic acids

contact: Jiří Pavlíček

  • Crystallization robots
    • Gryphon (Art Robbins)
    • NT8 (Formulatrix)
  • General purpose pipetting robot OT-2 (Opentrons)
  • Crystallization hotel RI1000 (Formulatrix)
  • Crystallization hotel RI182 (Formulatrix) in low temperature
  • Stereomiroscopes (Olympus)
  • Cold room
  • Cryo storage for crystals & cryoEM samples
  • Glovebox with stereomicroscope (GS)
  • SpectroLight 600 (Xtal Concepts)
  • SONICC (Formulatrix)
  • Vitrobot (Thermo Scientific)

CF Diffraction techniques

contact: Jan Stránský

  • D8 Venture (Bruker)
    • MetalJet D2+ X-ray source (Excillum)
    • 4-circle goniometer
    • Detector Photon III 28
    • CryoStream 800 (Oxford Cryoscience)
    • In-situ plate holder ISX stage (Bruker)
    • Hummidity control HClab (Arinax)
    • XFR detector Quantax 200 (Bruker)
  • SAXSpoint 2.0
    • MetalJet C2+ Xray source (Excillum)
    • Detector EIGER R 1M (Dectris)
    • ASX autosampler
    • CaryUV 60 (Agillent)
    • AktaGO (GE Healthcare)

CF Structural Mass Spectrometry

contact: Petr Pompach

  • 15T-SolariX XR FT-ICR mass spectrometer (Bruker Daltonics)
  • HPLC, UPLC (Agilent Technoligies)
  • Excimer laser (Coherent)
  • MALDI-TOF (Bruker Daltonics)
  • timsTOF Pro mass spectrometer (Bruker Daltonics)
  • HDX robot (Ophir Analytical)
  • timsTOF SCP mass spectrometer (Bruker Daltonics)
  • HPLC (Evosep)

CF Protein Production

contact: Miroslava Alblová

  • Biometra TAdvanced Twin PCR Thermal Cycler (Analytik Jena)
  • Azure 300 Imaging System (Azure Biosystems)
  • New Brunswick Innova® 44R Incubator Shaker (Eppendorf)
  • Ecotron Incubator Shaker (INFORS HT)
  • Biohazard box SafeFAST Classic S/D (class II, FASTER)
  • New Brunswick Innova® 40/40R Benchtop Orbital Shaker (Eppendorf)
  • PHCbi IncuSafe CO₂ static incubator (MCO-170AIC, PHC)
  • New Brunswick S41i - CO₂ Incubator Shaker (Eppendorf)
  • CellDrop FL Unlimited cell counter (DeNovix)
  • Nikon ECLIPSE Ts2 FL inverted microscope (Nikon)
  • Q700 Sonicator (QSONICA)
  • Avanti J-26S XP High-Speed centrifuge (Beckman Coulter)
  • ÄKTA start protein purification system (Cytiva)
  • NGC Chromatography System (Bio-Rad)
    • Superdex 75 or 200 columns (10/300 increase or HiLoad 16/600, Cytiva)
  • Trans-Blot® Turbo™ Transfer System (Bio-Rad)
  • DS-11+ Spectrophotometer (DeNovix)

Centre of Molecular Structure offers its services also to commercial users. Please, contact Jan Dohnálek for further details.

Services offered by the CMS here.

D8 HClab

D8 HClab

FLS1000

FLS1000

Formulatrix1000

Formulatrix1000

Gryphon

Gryphon

Mass Spectrometry

Mass Spectrometry

NT8

NT8

SEC-SAXS

SEC-SAXS

Specord50plus

Specord50plus

Vertex70V

Vertex70V