News:

  • 2024/01/29:

    We have two ERASMUS visitors from the University of Lisbon who will work with us on FT-ICR MS. Welcome Marta and Inês!

  • 2024/01/26:

    🕷🕷🕷Our lab ZOO is growing again. Mike's successor has just arrived! Welcome ❤ Mike II.

  • 2024/01/23:

    Our group is growing. Welcome Ženya!

  • 2024/01/20:

    In 2023 we spent a lot of time working on different projects with Angel L. Pey from Uni of Grenada. Now the results are coming out. First one on AGT1 mutants is published in FEBS Lett. Thanks INSTRUCT and CIISB for support.

  • 2024/01/18:

    We are looking for PhD students! Position funded for 4 years in the field of structural MS and cool FT-MS top-down analysis - details here.

  • 2024/01/17:

    The last piece of Marok's PhD thesis puzzle is now in Anal. Chem. Well done Marok!

  • 2024/01/13:

    Welcome Honza and enjoy fun with structural mass spec!

  • 2024/01/13:

    Congratulations to Marek on his first first-author paper. Deep insight into FPOP data processing in now in J. Proteome. Res. .

  • 2023/11/03:

    Great news, Ljubi is back after maternity leave 👶 👶 !

  • 2023/10/26:

    Alan's contribution to the desing of sci-fi SPIDOC instrumentation - single particle imaging of protein complexes. Out in the Journal of Instrumentation. Cool!

Horizon 2020
EPIC-XS
EU FT-ICR MS MSCA

Important:

  • 2023/02/20:

    We are looking for java programmer. Position for two years. Collaboration with industrial partner - Bruker Daltonics! More details HERE.

  • 2022/07/22:

    Synopsis of Ales' Hippostruct MSCA project is available here.

  • 2022/04/22:

    Are you interested in structural mass spectrometry, method development ad/or membrane proteins? We are looking for Bc, MSc, PhD students and post-doc! Inquiries should be addressed to Petr Novak.

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

Current projects


  • Expanding the analytical toolbox for structural mass spectrometry

    In this proposal, we plan to develop bi-functional chemical probes with novel reactivity and functionality that will expand the palette of currently targetable amino acid residues and thus increase the spatial resolution of chemical cross-linking. The probes will be isotopically coded to enable quantitative cross-linking experiments for monitoring of the protein dynamics. The novel reactivity will target aromatic amino acid side chains and will be based on bi-functional Togni reagents. In order to increase the functionality of currently available cross-linking probes we will design, synthetize and test isotopically labeled, MS cleavable disuccinimidyl dipropionic, diimidazolyl dipropionic and dihydrazide dipropionic urea enabling unambiguous quantitative cross-linking through hydroxy and carboxyl bearing amino acids. To further streamline these cross-linking experiments, we also plan to develop specialized algorithms dedicated to data processing of isotopically labeled samples. We will also evaluate complete analytical procedure including enrichment, separation and fragmentation of the cross-linked peptides. The effect of the reagents on the protein structure and their application to selected biologically relevant systems will form the final goal of the project. All these advancements will increase the ability of structural mass spectrometry to provide valuable information addressing structural aspects and dynamics of proteins and protein complexes.

    Funded by Czech Science Foundation (22-27695S)

  • Recognition and Validation of Druggable Targets from the Response to Cognitive Behaviour Therapy in Myotonic Dystrophy type 1 patients from Integrated -Omics Networks.

    Myotonic dystrophy type 1 (DM1), the most common adult form of muscular dystrophy, affects virtually all tissues; the noncurable condition carries significant morbidity and mortality impacting patient and family quality of life and socio-economic status. The OPTIMISTIC clinical trial has shown that Cognitive Behaviour Therapy (CBT), a patient-tailored intervention to increase activity and enable patients to deal with their disease, imparts significant beneficial impact on activity and participation. We now propose a multi-omic approach to identify the molecular signatures of the response to this clinical intervention, taking advantage of the thorough clinical characterization of the enrolled patients and the comprehensive set of serum samples at baseline and two follow-up time points. Our central hypothesis is that pathways associated with the positive response to CBT can be consolidated or reinforced by conventional drug therapies targeting the same pathways. A network-based bioinformatics approach shall be used to identify drug targets in the molecular signatures. We shall repurpose clinically approved drugs measuring impact on molecular profiles of patients cells and the behaviour of DM1 mouse models. Repurposed drugs with effects similar to CBT can be evaluated in isolation or combination with other treatments in future clinical trials for DM1 and other neurological conditions. The drug repurposing strategy based on the reverse engineering of a positive response to a behavioural intervention may set the scene for future drug development trajectories for rare diseases.

    Funded by EU - E-Rare (ReCognitiON)


  • Past projects

    • Horizon 2020 (82383): EPIC-XS-European Proteomics Infrastructure Consortium providing access (2019-2023)
    • MSCA-IF (101003406): HIPPOSTRUCT-Structural insights into binding signatures of transcription factors regulated by HIPPO signalling (2020-2022) Synopsis canbe accessed here
    • Czech Ministry of Health (NV19-05-00541): Functional Assays for Rapid Microbiological Diagnostics of Selected Health-Care Associated Infections (2019-2022)
    • Horizon 2020 (731077): FT-ICR MS-European Network of Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry Centers (2018-2022)
    • Czech Science Foundation (19-16084S) Mapping the protein surface accessible area utilizing Top Down mass spectrometry and reactive radical footprinting (2019-2021)
    • Czech Science Foundation (16-24309S) Mass Spectrometric 3D Structure Analysis of DNA Response Elements / Transcription Factor Association and Modeling (2016-2018)
    • Czech Science Foundation (16-20860S) Structural and functional analysis of Hsp70/Hsp90 chaperone complexes (2016-2018)
    • Ministry of Education, Youth, and Sports (COST CZ LD15089) A new tool for structure biology: Combination of high resolution mass spectrometry, chemical cross-linking and H/D exchange (2015-2017)
    • Ministry of Education, Youth, and Sports (Kontakt II LH15010) Structural mass spectrometry analysis for complexes of transcription factors with DNA response elements (2015-2017)
    • Czech Science Foundation and FWF (Austria) (16-34818L / I 2385-N28) Electron Transfer in Cellulose Degrading Enzymes (2016-2018)