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Biomolecular Interactions and Crystallization

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Head of Core Facility
Researcher ID
Phone: +420 54949 3805, +420 54949 8166
E-mail:
Office:

Official Email: bic@ceitec.muni.cz


Main Activity

The core facility provides services leading to structure characterization of biomolecules and to study (bio)molecular interactions in a real time using mainly biosensor and calorimetry-based methods. It is equipped with the instrumentation to set up crystallization conditions of biomolecules and their complexes, basic characterization of physical properties of the molecules (analytical ultracentrifugation, dynamic light scattering, CD spectroscopy, differential scanning calorimetry), and to study thermodynamics and/or kinetics of interactions (isothermal titration calorimetry, surface plasmon resonance, CD spectroscopy, analytical ultracentrifugation).

Unique Features

  • Set-up of crystallization screens using commercial-available kits
  • Automatic inspection of crystals  - remote access to results for users
  • UV imaging to distinguish a protein from a salt
  • Set-up of optimization screens
  • Estimation of the precipitation diagram
  • Production of crystals for structural determination
  • Quality improvement of crystals for structural determination
  • Isothermal titration microcalorimetry
  • Differential scanning calorimetry
  • Surface plasmon resonance
  • Particle size analysis
  • Analytical ultracentrifugation
  • Circular dichroism spectroscopy, fluorescence measurement

Key Equipments 

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The Core Facility is part of Czech National Affiliated Centre of INSTRUCT and a member of an open pan-European network Association of Resources for Biophysical Research in Europe (ARBRE)

All CEITEC core facilities are available to external users (academia and companies). Czech and international researchers from universities and research institutes interested in accessing core facilities can benefit from support of research infrastructure CIISB, funded by the Ministry of Education, Youth and Sports of the Czech Republic.

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list / cards

Name and position

E-mail

Phone

Prof. Michaela Wimmerová, Ph.D.
Research Group Leader
+420 54949 3805, +420 54949 8166
Eva Dubská
Specialist
+420 54949 2527
Josef Houser, Ph.D.
Researcher
+420 54949 2527
Jan Komárek
Researcher
+420 54949 6011
Jana Kosourová
Specialist
+420 54949 8201, +420 54949 8314
Lenka Malinovská, Ph.D.
Researcher
+420 54949 7646, +420 54949 2527
Marie Pokorná
Specialist
+420 54949 5901
Jitka Ždánská
+420 54949 2527

SELECTED PUBLICATIONS

2016

  • KUMAR, A; SYKOROVA, P; DEMO, G; DOBES, P; HYRSL, P; WIMMEROVA, M, 2016:A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure. JOURNAL OF BIOLOGICAL CHEMISTRY 291 (48), p. 25032 - 25049.
  • NORTON, P; COMUNALE, MA; HERRERA, H; WANG, MJ; HOUSER, J; WIMMEROVA, M; ROMANO, PR; MEHTA, A, 2016:Development and application of a novel recombinant Aleuria aurantia lectin with enhanced core fucose binding for identification of glycoprotein biomarkers of hepatocellular carcinoma. PROTEOMICS 16 (24), p. 3126 - 3136.

2015

  • HOUSER, J; KOMAREK, J; CIOCI, G; VARROT, A; IMBERTY, A; WIMMEROVA, M, 2015:Structural insights into Aspergillus fumigatus lectin specificity: AFL binding sites are functionally non-equivalent. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 71 , p. 442 - 453.
  • SEHNAL, D; VAREKOVA, RS; PRAVDA, L; IONESCU, CM; GEIDL, S; HORSKY, V; JAISWAL, D; WIMMEROVA, M; KOCA, J, 2015:ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. NUCLEIC ACIDS RESEARCH 43 (D1), p. D369 - D375.

2014

  • ADAMOVA, L; MALINOVSKA, L; WIMMEROVA, M, 2014:New Sensitive Detection Method for Lectin Hemagglutination using Microscopy. MICROSCOPY RESEARCH AND TECHNIQUE 77 (10), p. 841 - 849.
  • DEMO, G; PAPOUSKOVA, V; KOMAREK, J; KADERAVEK, P; OTRUSINOVA, O; SRB, P; RABATINOVA, A; KRASNY, L; ZIDEK, L; SKLENAR, V; WIMMEROVA, M, 2014:X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase. JOURNAL OF STRUCTURAL BIOLOGY 187 (2), p. 174 - 186.
  • KRIZ, Z; ADAM, J; MRAZKOVA, J; ZOTOS, P; CHATZIPAVLOU, T; WIMMEROVA, M; KOCA, J, 2014:Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 28 (9), p. 951 - 960.
  • VAREKOVA, RS; JAISWAL, D; SEHNAL, D; IONESCU, CM; GEIDL, S; PRAVDA, L; HORSKY, V; WIMMEROVA, M; KOCA, J, 2014:MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. NUCLEIC ACIDS RESEARCH 42 (W1), p. W227 - W233.

2013

  • DEMO, G; FLIEDROVA, B; WEIGNEROVA, L; WIMMEROVA, M, 2013:Crystallization and preliminary X-ray crystallographic analysis of recombinant -mannosidase from Aspergillus niger. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 69 , p. 288 - 291.
  • HOUSER, J; KOMAREK, J; KOSTLANOVA, N; CIOCI, G; VARROT, A; KERR, SC; LAHMANN, M; BALLOY, V; FAHY, JV; CHIGNARD, M; IMBERTY, A; WIMMEROVA, M, 2013:A Soluble Fucose-Specific Lectin from Aspergillus fumigatus Conidia - Structure, Specificity and Possible Role in Fungal Pathogenicity. PLOS ONE 8 (12)
  • TVAROSKA, I; KOZMON, S; WIMMEROVA, M; KOCA, J, 2013:A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta 1,6-N-Acetylglucosaminyltransferase. CHEMISTRY-A EUROPEAN JOURNAL 19 (25), p. 8153 - 8162.

2012

  • AUDFRAY, A; CLAUDINON, J; ABOUNIT, S; RUVOEN-CLOUET, N; LARSON, G; SMITH, DF; WIMMEROVA, M; LE PENDU, J; ROMER, W; VARROT, A; IMBERTY, A, 2012:Fucose-binding Lectin from Opportunistic Pathogen Burkholderia ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes. JOURNAL OF BIOLOGICAL CHEMISTRY 287 (6), p. 4335 - 4347.
  • CECIONI, S; PRALY, JP; MATTHEWS, SE; WIMMEROVA, M; IMBERTY, A; VIDAL, S, 2012:Rational Design and Synthesis of Optimized Glycoclusters for Multivalent Lectin-Carbohydrate Interactions: Influence of the Linker Arm. CHEMISTRY-A EUROPEAN JOURNAL 18 (20), p. 6250 - 6263.
  • FROMMEL, J; SOURAL, M; TYLICHOVA, M; KOPECNY, D; DEMO, G; WIMMEROVA, M; SEBELA, M, 2012:Plant aminoaldehyde dehydrogenases oxidize a wide range of nitrogenous heterocyclic aldehydes. AMINO ACIDS 43 (3), p. 1189 - 1202.
  • HOUSER, J.;J. KOMAREK;N. KOSTLANOVA;G. CIOCI;A. IMBERTY;M. WIMMEROVA., 2012:Protein oligomerization in Aleuria aurantia lectin family - importance and difficulties. Materials Structure in Chemistry 19 , p. 20 - 21.
  • MARCHETTI, R; MALINOVSKA, L; LAMEIGNERE, E; ADAMOVA, L; DE CASTRO, C; CIOCI, G; STANETTY, C; KOSMA, P; MOLINARO, A; WIMMEROVA, M; IMBERTY, A; SILIPO, A, 2012:Burkholderia cenocepacia lectin A binding to heptoses from the bacterial lipopolysaccharide. GLYCOBIOLOGY 22 (10), p. 1387 - 1398.
  • MISHRA, S; ADAMOVA, L; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:Comparison of Docking Software to Predict Saccharide Binding to Proteins Combination with In silico Protein Engineering. GLYCOBIOLOGY 22 (11), p. 1648 - 1649.
  • MISHRA, SK; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (5), p. 1250 - 1261.
  • SEHNAL, D; VAREKOVA, RS; HUBER, HJ; GEIDL, S; IONESCU, CM; WIMMEROVA, M; KOCA, J, 2012:SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (2), p. 343 - 359.
  • TVAROSKA, I; KOZMON, S; WIMMEROVA, M; KOCA, J, 2012:Substrate-Assisted Catalytic Mechanism of O-GIcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (37), p. 15563 - 15571.
  • VISACKA, K; HOFR, C; WILLCOX, S; NECASOVA, I; PAVLOUSKOVA, J; SEPSIOVA, R; WIMMEROVA, M; SIMONICOVA, L; NOSEK, J; FAJKUS, J; GRIFFITH, JD; TOMASKA, L, 2012:Synergism of the Two Myb Domains of Tay1 Protein Results in High Affinity Binding to Telomeres. JOURNAL OF BIOLOGICAL CHEMISTRY 287 (38), p. 32206 - 32215.
  • WIMMEROVA, M; KOZMON, S; NECASOVA, I; MISHRA, SK; KOMAREK, J; KOCA, J, 2012:Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods. PLOS ONE 7 (10)

2011

  • CECIONI, S; FAURE, S; DARBOST, U; BONNAMOUR, I; PARROT-LOPEZ, H; ROY, O; TAILLEFUMIER, C; WIMMEROVA, M; PRALY, JP; IMBERTY, A; VIDAL, S, 2011:Selectivity among Two Lectins: Probing the Effect of Topology, Multivalency and Flexibility of "Clicked" Multivalent Glycoclusters. CHEMISTRY-A EUROPEAN JOURNAL 17 (7), p. 2146 - 2159.
  • GILBOA-GARBER, N; ZINGER-YOSOVICH, KD; SUDAKEVITZ, D; LERRER, B; IMBERTY, A; WIMMEROVA, M; WU, AM; GARBER, NC, 2011:The Five Bacterial Lectins: PA-II, PA-III, RSL, RS-III and CV-III Interactions with Diverse Animal Cells and Glycoproteins. Advances in Experimental Medicine and Biology 705 , p. 155 - 211.
  • HAVEL, V; SVEC, J; WIMMEROVA, M; DUSEK, M; POJAROVA, M; SINDELAR, V, 2011:Bambus[n]urils: a New Family of Macrocyclic Anion Receptors. ORGANIC LETTERS 13 (15), p. 4000 - 4003.
  • REVESZ, A; SCHRODER, D; SVEC, J; WIMMEROVA, M; SINDELAR, V, 2011:Anion Binding by Bambus[6]uril Probed in the Gas Phase and in Solution. JOURNAL OF PHYSICAL CHEMISTRY A 115 (41), p. 11378 - 11386.
  • SULAK, O; CIOCI, G; LAMEIGNERE, E; BALLOY, V; ROUND, A; GUTSCHE, I; MALINOVSKA, L; CHIGNARD, M; KOSMA, P; AUBERT, DF; MAROLDA, CL; VALVANO, MA; WIMMEROVA, M; IMBERTY, A, 2011:Burkholderia cenocepacia BC2L-C Is a Super Lectin with Dual Specificity and Proinflammatory Activity. PLOS PATHOGENS 7 (9)

2010

  • KLUMPLER, T; SEDLACEK, V; MAREK, J; WIMMEROVA, M; KUCERA, I, 2010:Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 66 , p. 431 - 434.
  • LAMEIGNERE, E; SHIAO, TC; ROY, R; WIMMEROVA, M; DUBREUIL, F; VARROT, A; IMBERTY, A, 2010:Structural basis of the affinity for oligomannosides and analogs displayed by BC2L-A, a Burkholderia cenocepacia soluble lectin. GLYCOBIOLOGY 20 (1), p. 87 - 98.
  • MISHRA, NK; KRIZ, Z; WIMMEROVA, M; KOCA, J, 2010:Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. CARBOHYDRATE RESEARCH 345 (10), p. 1432 - 1441.
  • SULAK, O; CIOCI, G; DELIA, M; LAHMANN, M; VARROT, A; IMBERTY, A; WIMMEROVA, M, 2010:A TNF-like Trimeric Lectin Domain from Burkholdeda cenocepacia with Specificity for Fucosylated Human Histo-Blood Group Antigens. STRUCTURE 18 (1), p. 59 - 72.

2009

  • HANSEN, SF; BETTLER, E; WIMMEROVA, M; IMBERTY, A; LEROUXEL, O; BRETON, C, 2009:Combination of Several Bioinformatics Approaches for the Identification of New Putative Glycosyltransferases in Arabidopsis. JOURNAL OF PROTEOME RESEARCH 8 (2), p. 743 - 753.
  • HOFR, C., SULTESOVA, P., ZIMMERMANN, M., MOZGOVA, I., SCHRUMPFOVA, P. P., WIMMEROVA, M., FAJKUS, J.,, 2009:Single-Myb-histone proteins from Arabidopsis thaliana: a quantitative study of telomere-binding specificity and kinetics. BIOCHEMICAL JOURNAL 419 , p. 221 - 228.
  • CHEMANI, C; IMBERTY, A; DE BENTZMANN, S; PIERRE, M; WIMMEROVA, M; GUERY, BP; FAURE, K, 2009:Role of LecA and LecB Lectins in Pseudomonas aeruginosa-Induced Lung Injury and Effect of Carbohydrate Ligands. INFECTION AND IMMUNITY 77 (5), p. 2065 - 2075.
  • MATEJKOVA, M; ZIDKOVA, J; ZIDEK, L; WIMMEROVA, M; CHMELIK, J; SKLENAR, V, 2009:Investigation of Thermal Denaturation of Barley Nonspecific Lipid Transfer Protein 1 (ns-LTP1b) by Nuclear Magnetic Resonance and Differential Scanning Calorimetry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 57 (18), p. 8444 - 8452.
  • TESARIK, R; SEDLACEK, V; PLOCKOVA, J; WIMMEROVA, M; TURANEK, J; KUCERA, I, 2009:Heterologous expression and molecular characterization of the NAD(P)H:acceptor oxidoreductase (FerB) of Paracoccus denitrificans. PROTEIN EXPRESSION AND PURIFICATION 68 (2), p. 233 - 238.
  • WIMMEROVA, M; MISHRA, NK; POKORNA, M; KOCA, J, 2009:Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis. JOURNAL OF MOLECULAR MODELING 15 (6), p. 673 - 679.

PROJECTS

  • RIAT-CZ (ATCZ40), Interreg CZ-AT, 2016 - 2018
  • CIISB4HEALTH - Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví (CZ.02.1.01/0.0/0.0/16_013/0001776), MEYS, 2017 - 2021
  • CIISB - Czech Infrastructure for Integrative Structural Biology (LM2015043), MEYS, 2016 - 2019
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Equipment Research group / CF Profile card
Biomolecular characterization and interaction
Analytical ultracentrifugation Analytical ultracentrifugation
CF: Biomolecular Interactions and Crystallization
Automated calorimetric system Auto-iTC200 Automated calorimetric system Auto-iTC200
CF: Biomolecular Interactions and Crystallization
Circular dichroism spectroscopy Circular dichroism spectroscopy
CF: Biomolecular Interactions and Crystallization
Differential scanning calorimeter VP-DSC Differential scanning calorimeter VP-DSC
CF: Biomolecular Interactions and Crystallization
Dynamic light scattering Dynamic light scattering
CF: Biomolecular Interactions and Crystallization
Isothermal titration calorimetry VP-ITC Isothermal titration calorimetry VP-ITC
CF: Biomolecular Interactions and Crystallization
Microdeposition system for biosensor arrays Microdeposition system for biosensor arrays
CF: Biomolecular Interactions and Crystallization
Multichannel SPR system Multichannel SPR system
CF: Biomolecular Interactions and Crystallization
NanoTemper Monolith NanoTemper Monolith
CF: Biomolecular Interactions and Crystallization
NanoTemper Prometheus NanoTemper Prometheus
CF: Biomolecular Interactions and Crystallization
SPR biosensor BiaCore T200 SPR biosensor BiaCore T200
CF: Biomolecular Interactions and Crystallization
Biomolecular crystalization
Automated storage and visual inspection of crystal plates (20 ° C) Automated storage and visual inspection of crystal plates (20 ° C)
CF: Biomolecular Interactions and Crystallization
Automated storage and visual inspection of crystal plates (4 ° C) Automated storage and visual inspection of crystal plates (4 ° C)
CF: Biomolecular Interactions and Crystallization
Gradient incubator for optimizing protein crystallization temperature Gradient incubator for optimizing protein crystallization temperature
CF: Biomolecular Interactions and Crystallization
Robotics for protein crystallization Robotics for protein crystallization
CF: Biomolecular Interactions and Crystallization
List of services
Biomolecular characterization and interaction
Calorimetric titration + automated software data evaluation. Calorimetric titration + automated software data evaluation. Calorimetric measurement of receptor-ligand interaction (Standard titration method, Single injection method) Data evaluation - by automated software data evaluation - complete thermodynamic profile determination (association constant, enthalpy, entropy, stoichiometry value) using curve fitting models: One set of binding site

Booking of the service is available via CEITEC intranet system
Calorimetric titration + expert data evaluation + data evaluation training AutoITC200 Calorimetric measurement of receptor-ligand interaction (Standard titration method, Single injection method) Data evaluation - manually by expert - complete thermodynamic profile determination (association constant, enthalpy, entropy, stoichiometry value) using curve fitting models: One set of binding site, Two sets of binding sites, Sequential Binding model. Determination of kinetic parameters Km and kcat. Data evaluation training.

Booking of the service is available via CEITEC intranet system
Calorimetric titration + expert data evaluation Calorimetric measurement of receptor-ligand interaction (Standard titration method, Single injection method) Data evaluation - manually by expert - complete thermodynamic profile determination (association constant, enthalpy, entropy, stoichiometry value) using curve fitting models: One set of binding site, Two sets of binding sites, Sequential Binding model. Determination of kinetic parameters Km and kcat.

Booking of the service is available via CEITEC intranet system
Sedimentation velocity Sedimentation velocity Sedimentation velocity method can be used for determination of sample dispersity, oligomeric state of proteins, the shape of the particle and it is also suitable for analysis of aggregates and a study of biomolecular interactions.

Booking of the service is available via CEITEC intranet system
Sedimentation equilibrium Sedimentation equilibrium Sedimentation equilibrium method can be used for accurate determination of molecular weights of various biomolecules and the study of their interactions.

Booking of the service is available via CEITEC intranet system
Microdeposition system for biosensor arrays - standard service Microdeposition system for biosensor arrays - standard service Compact automated non-contact dispensing system of ultra-low volumes of biomolecules and bioreagens.

Booking of the service is available via CEITEC intranet system
Microdeposition system for biosensor arrays - advanced optimization service Microdeposition system for biosensor arrays - advanced optimization service Compact automated non-contact dispensing system of ultra-low volumes of biomolecules and bioreagens. Advanced service involves advanced optimization of instrument settings in case of more complex and viscous samples and reagens.

Booking of the service is available via CEITEC intranet system
Crystallization of biomolecules
Standard crystallization screen set-up Standard crystallization screen set-up Set-up of crystallization screens (drop volume 200-300 nl) using commercial kits (including kits for membrane proteins, protein complexes and nucleic acids) - Sitting drop crystallization method, Crystallization under oil

Booking of the service is available via CEITEC intranet system
Customized crystallization Customized crystallization Setting-up multidimensional gradients for optimization (from up to 5 different solutions). Set-up of optimization screens - Hanging drop crystallization method, Sitting drop crystallization method, Crystallization under oil.

Booking of the service is available via CEITEC intranet system
Advanced crystallization techniques Advanced crystallization techniques Optimization of protein crystal production in large scale (manual setting) - Membrane protein crystallization techniques, Crystallization by dialysis or using capilaries Note: Service price is calculated individually. Contact the responsible person for details.

Booking of the service is available via CEITEC intranet system
Customized crystallization, Plate storage and inspection Customized crystallization, Plate storage and inspection Setting-up multidimensional gradients for optimization (from up to 5 different solutions). Set-up of optimization screens - Hanging drop crystallization method, Sitting drop crystallization method, Crystallization under oil. Storage of the screening plates for 3 months at a constant temperature 4°C or 20°C. Automatic screening of crystals - Regular automatic inspection within the period of one month, UV imaging to distinguish a protein from a salt. Online access to the images 24/7 Storage of the screening plates for extended period of time (6 months) at a constant temperature 4°C or 20°C with a possibility of a demanded extra inspection.

Booking of the service is available via CEITEC intranet system
Standard crystallization Screen Set-up, Plate Storage and Inspection Standard crystallization Screen Set-up, Plate Storage and Inspection Set-up of crystallization screens (drop volume 200-300 nl) using commercial kits (including kits for membrane proteins, protein complexes and nucleic acids). Sitting drop crystallization method, crystallization under oil. } Storage of the screening plates for 3 months at a constant temperature 4°C or 20°C Automatic screening of crystals . Regular automatic inspection within the period of one month. UV imaging to distinguish a protein from a salt. Online access to the images. Storage of the screening plates for extended period of time (6 months) at a constant temperature 4°C or 20°C with a possibility of a demanded extra inspection

Booking of the service is available via CEITEC intranet system
Plate storage and inspection Plate storage and inspection Storage of the screening plates for 3 months at a constant temperature 4°C or 20°C. Automatic screening of crystals. Regular automatic inspection within the period of one month. UV imaging to distinguish a protein from a salt. Online access to the images 24/7. Storage of the screening plates for extended period of time (6 months) at a constant temperature 4°C or 20°C with a possibility of a demanded extra inspection.

Booking of the service is available via CEITEC intranet system
Others
Consulting - assistance Service includes consulting with specialist, expert data evaluation, advanced experimental design or personal user support during measurement.

Booking of the service is available via CEITEC intranet system
Initial training for instruments in user mode (operated by users him-herself) Initial training for instruments which are operated by users him/herself. This includes Biacore T200 (SPR), multichannel SPR imaging system, DelsaMax Core (DLS), Jasco J-815 (CD), VP-ITC, VP-DSC, Monolith NT.115 Nano (MST), Prometheus (DSF), microdeposition system for biosensor arrays and gradient incubator for optimizing protein crystallization temperature. Training is performed by CF: BIC staff - responsible person for each instrument. Without this training users cannot operated the instruments on their own.

Booking of the service is available via CEITEC intranet system
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