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The structural biology of today is the pharmacology, therapy, and biotechnology of tomorrow

A gateway to realm of structural data for biochemists, biophysicists, molecular biologist, and all scientists whose research benefits from accurate structure determination of biological macromolecules, assemblies, and complex molecular machineries at atomic resolution.

Open access to 10 high-end core facilities and assisted expertise in NMR, X-ray crystallography and crystallization, cryo-electron microscopy and tomography, biophysical characterization of biomolecular interaction, nanobiotechnology, proteomics and structural mass spectrometry.

A distributed infrastructure constituted by Core Facilities of CEITEC (Central European Institute of Technology), located in Brno, and BIOCEV (Biotechnology and Biomedicine Centre), located in Vestec near Prague, Central Bohemia.

CIISB Research Results

T. Machackova, et al.: Utility of RNA sequencing for transcriptome analysis of small extracellular vesicles derived from blood sera of colorectal cancer patients, Cancer Res., 83 (2023) 3, 10.1158/1538-7445.Am2023-6709

P.N. Pham, et al.: Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light, Front. Mol. Biosci., 10 (2023) 14, 10.3389/fmolb.2023.1214235

P. Pourali, et al.: Biological Production of Gold Nanoparticles at Different Temperatures: Efficiency Assessment, Particle & Particle Systems Characterization, (2023) 10, 10.1002/ppsc.202200182

P. Slavik, et al.: Synthesis of Enantiomerically Pure Bambus 6 urils Utilizing Orthogonal Protection of Glycolurils, Journal of Organic Chemistry, (2023) 9, 10.1021/acs.joc.3c00667

J. Novotny, et al.: Flipping hosts in hyperfine fields of paramagnetic guests, Cell Rep. Phys. Sci., 4 (2023) 15, 10.1016/j.xcrp.2023.101461

M. Opatikova, et al.: Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and & alpha;-tocopherol, Nat. Plants, (2023) 14, 10.1038/s41477-023-01483-0

H. Paternoga, et al.: Structural conservation of antibiotic interaction with ribosomes, Nat. Struct. Mol. Biol., (2023) 35, 10.1038/s41594-023-01047-y

More publications

CIISB Research Highlights

the best of science obtained using CIISB Core Facilities

  • Food Hydrocolloids 2023

    Food Hydrocolloids 2023

    c) Three-dimensional (3D) reconstruction showing an electron density map with γ-conglutin model in top and side views (PDB: 4pph) fitted as a ring-like hexamer assemble.

    Jaroslaw Czubinsky Research Group


    Despite extensive research carried out on lupin seed γ-conglutin neither its mechanism of action as a hypoglycaemic nutraceutical compound nor its physiological role for the plant has been unveil. This article revealed a pH-dependent reversible association/dissociation equilibrium involving monomer, dimer and hexamer of Lupinus angustifolius γ-conglutin. The interaction between different oligomeric forms of this protein is reversible, and spectroscopic studies showed that the intact structure of γ-conglutin was preserved under the tested environmental conditions tested (pH 4.5–7.5). The obtained results prove that the hexameric form was preferred under basic conditions and was stabilised by a number of bonds formed upon association of individual protomers. The simultaneous occurrence of several oligomeric forms at a given pH value was shown, and their share was strongly driven by protein concentration. The main changes in oligomerisation of γ-conglutin take place in a pH range of 4.5–6.0, correlating with the pKaR values of the amino acid residues of His (6.0), Glu (4.1), and Asp (3.9). Moreover, a structural model of the protein in hexamer assembly was obtained based on small-angle X-ray scattering (SAXS) and negative staining cryo-electron microscopy (cryo-EM) analyses. The presented study provides essential knowledge about the colloidal dynamics and stability of γ-conglutin in solution, improving our understanding of fundamental environmental factors that could affect the health-promoting activity of this lupin seed protein.

    Czubinksi, J., Kubíčková, M., et al. pH-Dependent oligomerisation of γ-conglutin: A key element to understand its molecular mechanism of action.

    Food Hydrocol. 147, Part A, 109386 (2024)

  • Nature Communications 2023 - 3

    Nature Communications 2023 - 3

    a, b Mapping the binary interaction between RSM and RPA32C by NMR titrations. 15N labeled RSM titrated with zero to fourfold molar addition of RPA32C (a) and the reverse (b).

    Kostas Tripsianes and Lumír Krejčí Research Groups


    Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.

    Papageorgiou, A.C., Pospisilova, M., Cibulka, J. et al. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase.

    Nat Commun 14, 6751 (2023).

  • ACS Catalysis 2023

    ACS Catalysis 2023

    Crystal structures of DhaA223 and DhaA231. (a) Cartoon representations of DhaA223 (8OE2, red) and DhaA231 (PDB ID: 8OE6, dark blue) crystal structures aligned to the DhaA115 (PDB ID: 6SP5, gray). Residues of the catalytic pentad are shown as sticks. Stabilizing mutations are shown as spheres (pink spheres indicate mutations suggested by both FireProt and PROSS). (b) The structural context of selected stabilizing mutations. Newly formed stabilizing interactions involving other residues or water molecules (red spheres) are depicted by yellow dashed lines.

    Zbyněk Prokop and David Bednář Research Groups


    Thermostability is an essential requirement for the use of enzymes in the bioindustry. Here, we compare different protein stabilization strategies using a challenging target, a stable haloalkane dehalogenase DhaA115. We observe better performance of automated stabilization platforms FireProt and PROSS in designing multiple-point mutations over the introduction of disulfide bonds and strengthening the intra- and the inter-domain contacts by in silico saturation mutagenesis. We reveal that the performance of automated stabilization platforms was still compromised due to the introduction of some destabilizing mutations. Notably, we show that their prediction accuracy can be improved by applying manual curation or machine learning for the removal of potentially destabilizing mutations, yielding highly stable haloalkane dehalogenases with enhanced catalytic properties. A comparison of crystallographic structures revealed that current stabilization rounds were not accompanied by large backbone re-arrangements previously observed during the engineering stability of DhaA115. Stabilization was achieved by improving local contacts including protein–water interactions. Our study provides guidance for further improvement of automated structure-based computational tools for protein stabilization.

    Kunka, A., Marques, S. M., Havlásek, M., Vašina, M,, Velátová, N., Cengelová, L., Kovář, J., Damborský, J., Marek, M., Bednář*. D., and Prokop*, Z. Advancing Enzyme’s Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning

    ACS Catal. 2023, 13, 19, 12506–12518,

More publications Research Highlights archive

Reader’s Corner

literature to read, science to follow

In this section, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. It is our hope that links to exciting science, which deserves attention of the structural biology community, will help you to locate gems in the steadily expanding jungle of scientific literature. You are welcome to point out to any paper you found interesting by sending a link or citation to The section is being updated regularly.


7 Dec

Celebrating 30 years of Structure

Journal Structure was launched in 1993 as the first journal exclusively dedicated to structural biology by our founding academic chief editors, Wayne A. Hendrickson and Carl-Ivar Br€ande´ n, who were later joined by Alan Fersht. Christopher Lima and Andrej Sali became academic chief editors of Structure in 2003, and they were at the helm of the journal for 18 years until stepping down in the autumn 2021.

Structure is now celebrating its 30th birthday with this special anniversary issue. Editors commissioned reviews to highlight recent developments in different areas of structural biology. Sabine Botha and Petra Fromme provide an overview of the current state of serial femtosecond crystallography (SFX) research, the impact COVID-19 had on the SFX community, and how scientists adapted to these challenges. Koji Yonekura and his co-workers describe their contributions toward the development of electron 3D crystallography/microcrystal electron diffraction (MicroED) and highlight applications and current limitations of this method. Vaibhav KumarShukla, Gabriella Heller, and Flemming Hansen discuss the impact of artificial intelligence (AI) on biomolecular nuclear magnetic resonance (NMR) spectroscopy. Tuo Wang and his colleagues report how solid-state NMR is used to study the structures of fungaland plant cell walls. Syma Khalid and her co-workers define the term ‘‘computational microbiology’’ and describe state-of-the-art molecular dynamics imulations of bacterial systems.

21 Nov

Intrinsic structural dynamics dictate enzymatic activity and inhibition (PNAS)

Enzymes are known to sample various conformations, many of which are critical for their biological function. However, structural characterizations of enzymes predominantly focus on the most populated conformation. As a result, single-point mutations often produce structures that are similar or essentially identical to those of the wild-type enzyme despite large changes in enzymatic activity. Here, we show for mutants of a histone deacetylase enzyme (HDAC8) that reduced enzymatic activities, reduced inhibitor affinities, and reduced residence times are all captured by the rate constants between intrinsically sampled conformations that, in turn, can be obtained independently by solution NMR spectroscopy. Thus, for the HDAC8 enzyme, the dynamic sampling of conformations dictates both enzymatic activity and inhibitor potency. Our analysis also dissects the functional role of the conformations sampled, where specific conformations distinct from those in available structures are responsible for substrate and inhibitor binding, catalysis, and product dissociation. Precise structures alone often do not adequately explain the effect of missense mutations on enzymatic activity and drug potency. Our findings not only assign functional roles to several conformational states of HDAC8 but they also underscore the paramount role of dynamics, which will have general implications for characterizing missense mutations and designing inhibitors.

Reader’s Corner Archive

Quote of December

“Science is the systematic classification of experience.”

George Henry Lewes

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