Czech National Centre of the European Research Infrastructure Consortium INSTRUCT ERIC

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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 Core Facilities Research Highlights 

V. Siahaan, et al.: Microtubule lattice spacing governs cohesive envelope formation of tau family proteins, Nat. Chem. Biol., 18 (2022) 1224-+, 10.1038/s41589-022-01096-2

O. Gahura, et al.: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases, Nature Communications, 13 (2022) 13, 10.1038/s41467-022-33588-z

D. Zapletal, et al.: Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell, (2022), 82(21):4064-4079.e13. doi: 1016/j.molcel.2022.10.010

X. Peng, et al.: Self-Propelled Magnetic Dendrite-Shaped Microrobots for Photodynamic Prostate Cancer Therapy, Angewandte Chemie-International Edition, 9, 10.1002/anie.202213505

M. Siborova, et al.: Tail proteins of phage SU10 reorganize into the nozzle for genome delivery, Nature Communications, 13 (2022) 13, 10.1038/s41467-022-33305-w

More publications

CIISB Research Highlights

the best of science obtained using CIISB Core Facilities

  • Nature Chemical Biology 2022

    Nature Chemical Biology 2022

    Tau cooperativity by local microtubule lattice compaction

    a, Schematics of the assay geometry. b, Quantification of cooperative binding of tau to taxol-lattice microtubules (mean ± s.d., n = 652 microtubules, 60 experiments, 95% confidence bounds, r2 = 0.9633, gray), Hill–Langmuir equation fit (green). AU, arbitrary units. c, Fluorescence time-lapse micrographs showing microtubule lattice straightening (yellow arrow) upon formation of tau envelopes (green). Twenty nanomolar tau-mCherry was added at t = 0 s. Scale bar, 2 μm.

    Zdeněk Lánský Research Group

    Significance

    Tau is an intrinsically disordered microtubule-associated protein (MAP) implicated in neurodegenerative disease. On microtubules, tau molecules segregate into two kinetically distinct phases, consisting of either independently diffusing molecules or interacting molecules that form cohesive ‘envelopes’ around microtubules. Envelopes differentially regulate lattice accessibility for other MAPs, but the mechanism of envelope formation remains unclear. Here we find that tau envelopes form cooperatively, locally altering the spacing of tubulin dimers within the microtubule lattice. Envelope formation compacted the underlying lattice, whereas lattice extension induced tau envelope disassembly. Investigating other members of the tau family, we find that MAP2 similarly forms envelopes governed by lattice spacing, whereas MAP4 cannot. Envelopes differentially biased motor protein movement, suggesting that tau family members could spatially divide the microtubule surface into functionally distinct regions. We conclude that the interdependent allostery between lattice spacing and cooperative envelope formation provides the molecular basis for spatial regulation of microtubule-based processes by tau and MAP2.

    Valerie Siahaan, Ruensern Tan, Tereza Humhalova, Lenka Libusova, Samuel E. Lacey, Tracy Tan, Mariah Dacy, Kassandra M. Ori-McKenney, Richard J. McKenney, Marcus Braun & Zdenek Lansky

    Microtubule lattice spacing governs cohesive envelope formation of tau family proteins

    Na.t Chem. Biol., 18, 1224-1235 (2022): | https://doi.org/10.1038/s41589-022-01096-2

  • Nature Communications 2022

    Nature Communications 2022

    a Front and side views of the composite model with both monomers in rotational state 1. The two F1/c10-ring complexes, each augmented by three copies of the phylum-specific p18 subunit, are tied together at a 60°-angle. The membrane-bound Fo region displays a unique architecture and is composed of both conserved and phylum-specific subunits.
    b Side view of the Fo region showing the lumenal interaction of the ten-stranded β-barrel of the c-ring (grey) with ATPTB12 (pale blue). The lipid-filled peripheral Fo cavity is indicated.
    c Close-up view of the bound lipids within the peripheral Fo cavity with cryo-EM density shown.
    d Top view into the decameric c-ring with a bound pyrimidine ribonucleoside triphosphate, assigned as UTP, although not experimentally detected. Map density shown in transparent blue, interacting residues shown.

    Alena Zíková and Alexey Amunts Research Group

    Significance

    Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-eform an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

    Gahura, O., Mühleip, A., Hierro-Yap, C., Panicucci, B, Jain, M., Hollaus, D., Slapničková, M., Zíková, A. & Amunts, A.: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases, Nature Comm. (2022) 13:5989,https://doi.org/10.1038/s41467-022-33588-z

  • Molecular Cell 2022

    Molecular Cell 2022

    Cryo-EM structures of mouse full-length Dicer alone and in complex with Dicerdpre-miRNA reveal the molecular basis of locking Dicer in the closed state
    (A) Domain architecture of full-length mouse Dicer numbered at boundaries.
    (B) Overall structure of the full-length mouse Dicer, shown as 3.8-A ̊ cryo-EM density map and ribbon representations in two orthogonal views. Interface between the HEL1 and RNase IIIb domains is highlighted by a box.
    (C) Overall structure of the full-length mouse Dicer-RNA complex, shown as 4.2-A ̊ cryo-EM density map and ribbon representations in two orthogonal views.

    Richard Štefl and Petr Svoboda Research Groups

    Significance

    MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucle- ases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is spe- cifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the com- plete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicerd–miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleav- age-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.

    Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., Much, Ch., Sebesta, M. Buccheri, V., Horvat, F., Jenickova, I., Prochazkova, M., Prochazka, J., Pinkas, M., Novacek, J., Joseph, D. F., Sedlacek R., Bernecky C., O’Carrol, D., Stefl. R., and Svoboda, P.: Structural and functional basis of mammalian microRNA biogenesis by Dicer

    Mol. Cell 2022, 82, 4064–4079, https://doi.org/10.1016/j.molcel.2022.10.010

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 readerscorner@ciisb.org. The section is being updated regularly.


 

15 Nov

Single-cell genomic variation induced by mutational processes in cancer (Nature)

How cell-to-cell copy number alterations that underpin genomic instability in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer, remains understudied. Here, by applying scaled single-cell whole-genome sequencing to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct ‘foreground’ mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

15 Nov

NMR-guided directed evolution (Nature)

Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzym. Machine learning methods have recently showed promise in predicting productive mutations, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.

Reader’s Corner Archive

Quote of December

“The virtues of science are skepticism and independence of thought.”

Walter Gilbert

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