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CIISB Successfully Evaluated by Instruct-ERIC and Preparing for the National LRI Assessment
During summer, CIISB (Instruct-CZ) successfully passed an evaluation by the Instruct-ERIC Scientific Advisory Board (SAB). The SAB assessed our performance over the period 2019–2023, and the reviewers were particularly impressed by the 536 publications acknowledging CIISB facilities during this time, our capacity to support more than 550 users annually, and the training activities organized for over 250 participants each year. Based on these results, the SAB has recommended the immediate renewal of CIISB/Instruct-CZ as an Instruct-ERIC Centre. This recognition ensures that the Czech research community will continue to benefit from access to state-of-the-art structural biology services across the Instruct-ERIC network, as well as financial support for internships and R&D grants for students and early-career researchers.
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As a next step, we are preparing for the evaluation of Large Research Infrastructures organized by the Czech Ministry of Education, Youth and Sports (MEYS) — a process that is crucial for defining the future direction and funding of Czech research infrastructures for the 2027–2034 period. CIISB has consistently been ranked among the top-performing infrastructures, and we remain committed to maintaining the highest standards in this upcoming evaluation. Success in this process will be essential to sustain our capacity to provide high-quality structural biology services to our users.
We also wish to congratulate and thank all research teams who published their work (49 publications) supported by CIISB facilities between March and September 2025 (see Research Highlights section).
Finally, we are pleased to welcome two new members to the CIISB Scientific Advisory Board — Julien Orts and Martin Blackledge. We are delighted that these renowned scientists, who are experts in describing the dynamic nature of biomolecules, have accepted their nominations and will contribute to shaping the strategic direction of CIISB in the years ahead. The SAB members, all CIISB managerial bodies, and Core Facility representatives will meet on 20th November 2025 at the BIOCEV premises to review the past year’s performance and discuss strategic priorities for 2026.
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Applications 2025
- 109 internal applications
- 105 external applications (Czech)
- 50 applications from foreign users
You can find more information here.
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2022 |
2023 |
2024 |
2025 |
| Internal users |
129 |
135 |
151 |
109 |
| External users |
79 |
88 |
117 |
105 |
| Foreign users |
27 |
40 |
57 |
50 |
| Total |
235 |
263 |
325 |
264 |
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Join our practical course Protein Crystallization and Diffraction on November 3–4, 2025, hosted at the Institute of Biotechnology of the Czech Academy of Sciences (BIOCEV, Vestec). The course offers both lectures and hands-on training in protein crystallization methods and diffraction experiments, with a maximum of 10 participants for practical sessions.
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We would like to invite you and/or your students to participate in the Protein Production Hands On Workshop held in the Centre of Molecular Structure (CMS) on December 2 – 4, 2025. This three-day course offers both foundational and practical training in recombinant protein production. Participants will gain hands-on experience across the entire workflow – from cell transformation, recombinant protein expression and purification to final sample concentration and purity validation.
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The Czech national conference with focus on structural biology The XXII Discussions in Structural Molecular Biology and the 9th User meeting of CIISB will be held in Nové Hrady, South Bohemia, on 19-21 March 2026. Conference details and the registration page will appear early in January 2026 on the web page of the Czech Society for Structural Biology: https://cssb.structbio.org/.
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Meet Jan Přibyl, Head of CF Nanobiotechnology at CEITEC MU
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Why did you choose to be in the position of CF Head?
I’ve always enjoyed connecting people with technology. At CF Nabiotechnology, I saw an opportunity to make advanced tools like AFM and nanomanipulation accessible for researchers. Leading the facility means I can help others push the boundaries of their projects while shaping a collaborative environment.
What excites you the most about your job?
The diversity of ideas. One day it’s a protein interaction study, the next it’s a new material for sensors. A project I’ll never forget was helping a team visualize nanoparticles at the nanoscale for a vaccine study—it showed me how much impact precise imaging can have. More recently, I started the ALL4AFM initiative to bring together people who love working with AFM data. Seeing that community grow is incredibly rewarding.
What are the obstacles you need to overcome?
Keeping up with technology while ensuring people can actually use it. Instruments evolve fast, but training and workflows take time. My challenge is to make sure innovation doesn’t leave anyone behind.
How do you relax and clear your head?
I go outdoors—cycling around Brno or hiking in the Moravian countryside. It’s the best way to reset after a day of troubleshooting experiments. Sometimes, the best ideas come when I’m far from the lab.
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HeliX+ Biosensor instrument (BRUKER) was purchased to the Biophysical Techniques Facility of CMS
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HeliX+ Biosensor instrument from BRUKER was purchased to the Biophysical Techniques Facility of Centre of Molecular Structure.
It enables the study of molecular interactions, including kinetics, affinity and avidity and reveals conformational changes induced by analyte binding or buffer conditions with switchSENSE analysis. This DNA-lever based technology is particularly advantageous for molecules interacting with modifying oligonucleotides.
On November 27, 2025 Biophysical Techniques Facility of Centre of Molecular Structure will hold a workshop “Studying of molecular interactions by HeliX biosensor”. Will be represented instrument principle and applications, followed up by conducting of kinetic measurement on HeliX+ and protein-DNA conjugation using the proFIRE technology.
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CIISB Research Highlights
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Nucleic Acid Research 2025-2
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MALDI-TOF/TOF tandem mass spectra recorded for the precursor ions with m/z 560.08 (MH+) from protein sample treated for 30 min with SVP.
L. Tomaska Research Group
Significance
Poly (ADP-ribose) polymerases (PARPs) are enzymes catalyzing the post-translational addition of chains of ADP-ribose moieties to proteins. In most eukaryotic cells, their primary protein targets are involved in DNA recombination, repair, and chromosome maintenance. Even though this group of enzymes is quite common in both eukaryotes and prokaryotes, no PARP homologs have been described so far in ascomycetous yeasts, leaving their potential roles in this group of organisms unexplored. Here, we characterize Pyl1 protein of Yarrowia lipolytica as the first candidate of PARP in yeasts. We show that the expression of PYL1 gene is increased in mutants lacking either subunit of telomerase and identified several of its candidate protein targets in vivo. We demonstrate that Pyl1p is a functional PARP that undergoes auto-PARylation and PARylates YlKu70/80 complex. We also show that overexpression of PYL1 in Y. lipolyticacells results in dissociation of YlKu80 from telomeres in vivo, supporting the role of Pyl1p in telomere protection and maintenance. Based on our observations, we propose Pyl1p and its homologs identified in other yeast species represent a distinct class of PARPs, thus substantiating a more detailed investigation of their roles in these organisms.
Sepsiova R. et al.: Poly (ADP-ribose) polymerase in yeasts: characterization and involvement in telomere maintenance
NAR 2025, 10.1093/nar/gkaf837
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Data processing in mzmine.
T. Pluskal Research Group
Significance
Untargeted high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery and exposomics, with compound identification remaining the major bottleneck. Currently, the standard workflow applies spectral library matching against tandem mass spectrometry (MS2) fragmentation data. Multi-stage fragmentation (MSn) yields more profound insights into substructures, enabling validation of fragmentation pathways; however, the community lacks open MSn reference data of diverse natural products and other chemicals. Here we describe MS(n)Lib, a machine learning-ready open resource of >2 million spectra in MSn trees of 30,008 unique small molecules, built with a high-throughput data acquisition and processing pipeline in the open-source software mzmine.
Brungs C. et al.: MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries
Nature Methods 2025, 10.1038/s41592-025-02813-0
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The cryo-EM reconstruction of the TTLL11/MT complex.
C. Barinka Research Group
Significance
Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification targeting unstructured tubulin C-terminal tails-plays a pivotal role in defining the tubulin code. Here, we describe a mechanism by which tubulin tyrosine ligase-like 11 (TTLL11) expands and diversifies the code. Cryo-electron microscopy revealed a unique bipartite MT recognition strategy wherein TTLL11 binding and catalytic domains engage adjacent MT protofilaments. Biochemical and cellular assays identifiedpreviously uncharacterized polyglutamylation patterns, showing that TTLL11 directly extends the primary polypeptide chains of alpha- and beta-tubulin in vitro, challenging the prevailing paradigms emphasizing lateral branching. Moreover, cell-based and in vivo data suggest a cross-talk between polyglutamylation and the detyrosination/tyrosination cycle likely linked to the TTLL11-mediated elongation of the primary alpha-tubulin chain. These findings unveil an unrecognized layer of complexity within the tubulin code and offer mechanistic insights into the molecular basis of functional specialization of MT cytoskeleton.
Campbell J. et al.: Mechanistic insights into TTLL11 polyglutamylase-mediated primary tubulin chain elongation
Science Advances 2025, 10.1126/sciadv.adw1561
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Angewandte Chemie Int. Ed. 2025
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Chiral Pd6L8 or Pd12L16 cages.
O. Jurcek Research Group
Significance
The rational design and selective self-assembly of flexible and unsymmetric ligands into large coordination complexes is an eminent challenge in supramolecular coordination chemistry. Here, we present the coordination-driven self-assembly of natural ursodeoxycholic-bile-acid-derived unsymmetric tris-pyridyl ligand (L) resulting in the selective and switchable formation of chiral stellated Pd6L8 and Pd12L16 cages. The selectivity of the cage originates in the adaptivity and flexibility of the arms of the ligand bearing pyridyl moieties. The interspecific transformations can be controlled by changes in the reaction conditions. The orientational self-sorting of L into a single constitutional isomer of each cage, i.e., homochiral quadruple and octuple right-handed helical species, was confirmed by a combination of molecular modelling and circular dichroism. The cages, derived from natural amphiphilic transport molecules, mediate the higher cellular uptake and increase the anticancer activity of bioactive palladium cations as determinedin studies using in vitro 3D spheroids of the human hepatic cells HepG2.
Chattopadhyay S. et al.: Flexibility-Aided Orientational Self-Sorting and Transformations of Bioactive Homochiral Cuboctahedron Pd12L16
Angew. Chem. Int. Ed. 2025, 10.1002/anie.202513902
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Cryo-EM structures of the as-isolated and reduced CODH–ACS.
P. Wendler Research Group
Significance
Catalytic metal clusters play critical roles in important enzymatic pathways such as carbon fixation and energy conservation. However, how ligand binding to the active-site metal regulates conformational changes critical for enzyme function is often not well understood. One carbon fixation pathway that relies heavily on metalloenzymes is the reductive acetyl-coenzyme A (acetyl-CoA) pathway. In this study, we investigated the catalysis of the last step of the reductive acetyl-CoA pathway by the CO-dehydrogenase (CODH)-acetyl-CoA synthase (ACS) complex from Carboxydothermushydrogenoformans, focusing on how ligand binding to the nickel atom in the active site affects the conformational equilibrium of the enzyme. We captured six intermediate states of the enzyme by cryo-electron microscopy, with resolutions of 2.5-1.9A, and visualized reaction products bound to cluster A (an Ni,Ni-[4Fe4S] cluster) and identified several previously uncharacterized conformational states of CODH-ACS. The structures demonstrate how substrate binding controls conformational changes in the ACS subunit to prepare for the next catalytic step.
Ruickoldt J. et al.: Ligand binding to a Ni-Fe cluster orchestrates conformational changes of the CO-dehydrogenase-acetyl-CoA synthase complex
Nature Catalysis 2025, 10.1038/s41929-025-01365-y
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A. S. Chaudhari, et al.: Light-dependent flavin redox and adduct states control the conformation and DNA-binding activity of the transcription factor EL222, Nucleic Acids Research. 53 (2025) 6, 10.1093/nar/gkaf215
K. P. Khakurel, et al.: Ultrafast Dynamics in Flavocytochrome C by Using Transient Absorption and Femtosecond Fluorescence Lifetime Spectroscopy, The Journal of Physical Chemistry B, 129 (2025) 15, 10.1021/acs.jpcb.4c05496
N. Senthilnathan, et al.: Magneto-Fluorescent Microrobots with Selective Detection Intelligence for High-Energy Explosives and Antibiotics in Aqueous Environments, ACS Applied Materials & Interfaces, 2025, 10.1021/acsami.5c02259
O. Bulvas, et al.: Conformational landscape of the mycobacterial inosine 5′-monophosphate dehydrogenase octamerization interface, Journal of Structural Biology, 2025, 10.1016/j.jsb.2025.108198
R. Coufal, et al.: Fluorescent Nanoporous Materials from Polypropylene-Based Covalent Adaptable Networks, ACS Omega, 2025, 10.1021/acsomega.4c10168
J. Kučera, et al.: Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency, Journal of Proteome Research, 2025, 10.1021/acs.jproteome.4c00527
M. Skaličková, et al.: Interaction of Selected Anthracycline and Tetracycline Chemotherapeutics with Poly(I:C) Molecules, ACS Omega, 2025, 10.1021/acsomega.4c05483
M. Javanainen, et al.: Lipid Scrambling Pathways in the Sec61 Translocon Complex, Journal of the American Chemical Society, 2025, 10.1021/jacs.4c11142
E. Paulenová, et al.: The insight into the biology of five homologous lectins produced by the entomopathogenic bacterium and nematode symbiont Photorhabdus laumondii, Glycobiology, 2025, 10.1093/glycob/cwaf033
P. Ryzhaya, et al.: Arg-C Ultra Simplifies Histone Preparation for LC-MS/MS, Analytical Chemistry, 2025, 10.1021/acs.analchem.5c02238
M. Janosev, et al.: Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins, Nature Communications, 2025, 10.1038/s41467-025-60207-4
M. A. Marzabad, et al.: Cyclodextrin-Based Metal–Organic Framework as an Application Platform for Bioactive Ruthenium(III) Complexes, Inorganic Chemistry, 2025, 10.1021/acs.inorgchem.5c00813
D. Liu, et al.: Optineurin-facilitated axonal mitochondria delivery promotes neuroprotection and axon regeneration, Nature Communications, 2025, 10.1038/s41467-025-57135-8
V. Svojanovský, et al.: Digital Immunoassay for Biomarker Detection Based on Single-Particle Laser Ablation ICP MS, Analytical Chemistry, 2025, 10.1021/acs.analchem.5c00641
F. Scollo, et al.: Unraveling the GM1 Specificity of Galectin-1 Binding to Lipid Membranes, ACS Bio & Med Chem Au, 5 (2025) 3, 10.1021/acsbiomedchemau.5c00040
K. Raulf, et al.: The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1–17), Nucleic Acids Research, 2025, 10.1093/nar/gkaf324
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