News:

Important:

  • 2017/11/08:

    Several bachelor and master theses are available in the lab. Areas of structrual biology, cutting edge mass spectrometry and cell signalling are awaiting new students. Check the tab Teaching.

Research

Focus

Structural mass spectrometry

method development

  • novel covalent labeling and cross-linking chemistry of proteins /nucleic acids
  • new acid proteases as a tool for protein digestion
  • automation of HDX-MS and CX-MS workflow including software design
and application to selected biological problems (medicinally or biotechnologically important proteins), membrane proteins, dynamic and heavily modified proteins and their complexes

Functionalized surfaces for mass spectrometry

  • ambient ion landing protein immobilization
  • surface Immuno-affinity substrates for clinical diagnostics
  • biochemically active plates for desorption mass spectrometry

Projects


  • European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers

    EU_FT-ICR_MS proposal aims to establish a European network of FT-ICR (Fourier Transform Ion Cyclotron Resonance) mass spectrometry (MS) centers in association with a manufacturer and a SME software company. Mass spectrometry (MS) has become the most ubiquitous analytical techniques in use today, providing more information on the composition and the structure of a substance from a smaller amount of sample than any other techniques. Unlike other analytical techniques, such as NMR, which mainly rely on a unique technology, MS is characterized by the existence of a large range of mass analyzers. FT-ICR MS is the most powerful MS technique. It offers up to 100 fold higher mass resolving power and mass accuracy than any other MS technique. On the contrary to NMR community with which the FT-ICR MS shares several features, FT-ICR MS has never been involved in a European INFRA network and so will be a legitimate candidate to the Integrating Activities for Starting Communities call. The EU_FT-ICR_MS network includes 10 FT-ICR MS centers from 8 different European countries (Belgium, Czech Republic, Finland, France, Germany, Italy, Portugal, and United Kingdom) and 1 third country (Russia), a European FT-ICR MS manufacturer and 2 SMEs. It includes centers equipped with up-to-date FT-ICR MS and expertise which will cover most of the field in which FT-ICR mass spectrometry is involved: BioOrganic & BioInorganic, Cultural heritage, Glycomics, Environment, Imaging, InfraRed Spectroscopy of Ions in the Gas Phase, Lipidomics, Medicine, Petroleum & Coal Oil, Nanoparticles, Organic chemistry, Physical chemistry, Proteomics, Structural biology. The EU_FT-ICR_MS proposal contains six work-packages which cover all the aspects of the INFRAIA-02-2017 (RIA) Integrating Activities for Starting Communities (WP1 Transnational access; WP2 Training and Education; WP3 Open Data and e-Infrastructure; WP 4 Joint Research Action; WP 5 Dissemination; WP6 Consortium management).

    Funded by EU (EU_FT-ICR_MS)

  • Mass Spectrometric 3D Structure Analysis of DNA Response Elements / Transcription Factor Association and Modeling

    The structural analysis of heterogeneous native biomolecular interactions in vivo is hampered by the lack of suitable fast and high-throughput methods with an appropriate resolving power. The 2D proteomic mass spectrometric (MS)-based analysis of the interactome currently represents the gold standard for the target identification and novel drug screening. A cohort of new structural mass spectrometric methods (MS3D) supported by molecular dynamics (MD) modeling algorithms is fully complementary to the existing high-resolution but non-native structural methods. The goal of this project is to develop the MS3D method of biomolecular interaction pairs of the transcription factor (TF) and its DNA response element, both in vitro and in vivo models. The low-resolution analysis of the individual structures and their interaction landscapes will deliver experimental data feedback to the predictive MD computation of native heterogeneous complexes. The ultimate mission is to establish the MS3D native structural analysis as a novel standard of biomolecular analysis for the rational drug design.

    Funded by Czech Science Foundation (16-24309S)

  • Structural and functional analysis of Hsp70/Hsp90 chaperone complexes

    Project is focused on the analysis of interactions between chaperones Hsp90 and Hsp70 and their co-chaperones. Combination of structural mass spectrometry with functional assays will be used to describe the interactions sites as well as parts of the molecules influenced by the formation of chaperone complexes. This approach should reveal new factors influencing the activity of Hsp70 and Hsp90, uncover new protein interaction sites suitable for designing new low molecular weight inhibitors and bring insights into the dynamic behaviour of the chaperone complexes. The new findings related to assembly and functioning of chaperone complexes can also uncover the mechanisms that underlie several human diseases including cancer or neurodegenerative diseases. Besides the contribution to basic research, the results of the project can be exploited in biotechnology industry including rational drug design or folding of recombinant proteins.

    Joint project with Dr. Petr Muller, RECAMO, Brno, Czech Republic

    Funded by Czech Science Foundation (16-20860S)

  • A new tool for structure biology: Combination of high resolution mass spectrometry, chemical cross-linking and H/D exchange

    The aim of this project is to nucleate a group of researchers with a common interest, namely developing and applying new biomolecular mass spectrometry (MS) methods in order to make the characterisation of protein structure and dynamcis more rapid and routine. Methods include non-denaturing MS approaches in combination with ion mobility, as well as 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.

    Funded by Ministry of Education, Youth, and Sports (COST CZ – LH15010)

  • Structural mass spectrometry analysis for complexes of transcription factors with DNA response elements

    The proposed project is aimed to in-vitro and in-vivo identification of DNA response elements using chemical cross-linking and hydrogen/deuterium exchange combined with high resolution mass spectrometry. The next goal is participation of young scientists in the international frame of this research project.

    New knowledge will lead not only to valuable insight into regulation transcription and gene expression, but also into the structure-function relationship of complexes transcription factor/DNA.

    Joint project with Prof Daniele Fabris, State University of New York, Albany, U.S.A.

    Funded by Ministry of Education, Youth, and Sports (Kontakt II – LH15010)

  • Electron Transfer in Cellulose Degrading Enzymes

    The proposed project is aimed at elucidation of interactions between cellobiose dehydrogenase (CDH) and its putative redox partner – lytic polysaccharide monooxygenase (LPMO) – in solution and in their cellulose bound state. Our research strategy is based on the combined expertise of both research partners. The Austrian group will perform protein engineering and production as well as in-solution spectrophotometry and calorimetry to monitor CDH-LPMO electron transfer rates and interactions. The Czech team will employ structural mass spectrometry techniques based on protein isotopic exchange and chemical cross-linking to investigate the structural details of the protein-protein and protein-substrate interactions. The results will answer the questions if CDH functions as an “LPMO reductase” and if specific interactions are involved in their interprotein electron transfer. This will expand our understanding of biocatalytic redox processes of cellulose depolymerization, which may help increasing the efficiency of biofuel production or degradation processes in biorefineries.

    Collaboration with Petr Halada - joint project with prof. Roland Ludwig, University of Natural Resources and Life Sciences, Vienna, Austria

    Funded by Czech Science Foundation and Fonds zur Förderung der wissenschaftlichen Forschung (Austira) – (I 2385-N28)