Centre of Molecular Structure

Technologies for structural and biophysical analysis of biological molecules

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 LM2018127 and European Regional Development Fund-Project „UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974), is gratefully acknowledged for the financial support of the measurements at the CF [name of the unit/CF].

Operational status

All instruments are opetational.

Events and activities

ISIDORe – First Call open

Project ISIDORe - "Integrated Services for Infectious Disease Outbreak Research” was officially launched February, and now the first call for user application is open. The 21M€ EU-funded large-scale project assembles an unprecedented One Health-driven, integrated portfolio of cutting-edge research services and resources, ranging from the most fundamental to the most applied, dedicated to the study of epidemic-prone diseases including SARS-CoV-2 variants.

More details on the project and current call is available at https://isidore-project.eu

MOSBRI - A New European Research Infrastructure for Molecular Biophysics

The European Union’s Horizon 2020 INFRAIA programme has awarded a 5 M€  infrastructure grant to MOSBRI (Molecular-Scale Biophysics Research Infrastructure www.mosbri.eu), a consortium of 13 academic centres of excellence and 2 industrial partners from 11 different European countries, coordinated by Institut Pasteur (Paris, France). One of the partners is the Institute of Biotechnology of the Czech Academy of Sciences from BIOCEV.

The MOSBRI project will enable to create a research infrastructure combining the distinct instrumentation and expertise of the individual partner laboratories, thus allowing to tackle an unusually wide variety of life science research questions. It will also disseminate its knowhow through an ambitious programme of training workshops and meetings, particularly suited to early career researchers and others new to the field.

 MOSBRI will commence operations on the 1st of July of 2021.

Application form

Aplications through the standard form is now available also for the CF Protein Production at CIISB page.

New equipment

Crystallization hotel Fromulatrix RI182

Automatic crystallization screening is now available also in lower temperatures, thanks to installation the new crystallization hotel RI182. The hotel is ready to recieve users experiments. More information here.

New mass spectrometer

CF Mass Spectrometrz wasa strenghten bz addition of timsTOF Pro instrument.

General purpose pipetting robot OT-2

The instrumental portfolio in CMS was recently extended by genreal purpose pipetting robot OT-2 from Opentrons. The open platform enables wide range of applications. In CMS, the robot will help with setting up experiments mostly for CF Biophysical Methods and CF Crystallization of Proteins and Nucleic Acids.

From users

The Boura lab (IOCB Prague) collected data for their study on the SARS-CoV-2 methyltransferase complex at the Diffraction facility of CMS. Their results published in Nat Commun 11, 3717 (2020). https://doi.org/10.1038/s41467-020-17495-9, show high conservation of active site of this complex between SARS-CoV-2 and SARS-CoV viruses.

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 LM2018127 and European Regional Development Fund-Project „UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974), 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”) of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and CZ.02.1.01/0.0/0.0/18_046/0015974.

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 services covering DNA cloning and DNA plasmid preparation, protein expression in E. coli expression systems and recombinant protein purification. Our services can also include optimization of expression and purification protocols, protein identity and purity testing and determination of protein concentration.

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.

Agerschou Emil Dandanell
Dohnálek Jan, Ing., Ph.D.
Alblová Miroslava, RNDr., Ph.D.
Charnavets Tatsiana, Ph.D.
Nepokojová Tereza, Mgr.
Pavlíček Jiří, RNDr., Ph.D.
Pompach Petr, RNDr., Ph.D.
Stránský Jan, Ing., Ph.D.
Strnad Michal, Ing.
Škultétyová Ľubica, RNDr., Ph.D.
Trundová Mária, Mgr., Ph.D.
Vaňková Pavla, Mgr., Ph.D.

CF Biophysical Methods

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

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

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

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

location: I1

  • Cloning services
    • DNA plasmid preparation
    • Cloning using traditional restriction enzymes
    • Restriction-free methodology
    • Mutagenesis
    • Checking or preparation of the DNA templates
  • Recombinant protein production
    • Protein expression in E. coli expression systems
    • Small scale expression and solubility tests
  • Recombinant protein purification
    • Affinity chromatography (IMAC, StrepTactinXT)
    • Ion-exchange chromatography
    • Size exclusion chromatography
  • Optimization of expression and purification protocols
  • Protein concentration and purity testing
  • Other services
    • DNA isolation from maxipreps
    • preparation of competent cells
    • dialysis
    • protein cleavage
    • and more

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)

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)

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 AG)
  • Ecotron Incubator Shaker (INFORS HT)
  • Probe Sonicator (QSONICA)
  • ÄKTA start (GE Healthcare Bio-Sciences AB)
  • NGC Chromatography System (Bio-Rad Laboratories Inc.)
    • Superdex 75 or 200 (10/300 increase or Hiload 16/600) columns (Cytiva)
  • DS-11+ Spectrophotometer (DeNovix Inc.)

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

You can download 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