Czech National Centre of the European Research Infrastructure Consortium INSTRUCT ERIC
Czech Infrastructure for Integrative Structural Biology – CIISB
Structure without function is a corpse, function without structure is a ghost.
Steven Vogel and Stephen A. Wainwright, 1969
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.
ARIA Workshop and User Group meeting
Instruct-ERIC is hosting an ARIA workshop and User Group meeting on 25th February in Amsterdam.
CIISB UP project approved for financing during 2020-2022
The project CIISB UP submitted to the OP VVV Call 02-18-046 Research Infrastructures II has been positively evaluated and will receive funding to reinvest into the existing equipment and to purchase new instrumentation in the amount 22 mil. EUR.
Magnetic Resonance - An Interactive Open Access Publication of the Groupement AMPERE
The AMPERE Society has decided to launch a new publication called “Magnetic Resonance, An Interactive Open Access Publication of the Groupement AMPERE” for articles on Nuclear and Electron Magnetic Resonance and Imaging.
Advanced SAXSanalysis training
The training is designed to help you with processing data collected with small angle X-ray scattering (SAXS) instrument in the Centre of Molecular Structure in the Institute of Biotechnology of the Czech Academy of Sciences in BIOCEV. The tutorials will be by application specialist Anton Paar (instrument manufacturer).
14 Feb 2020
Instruct-ERIC and ARBRE-MOBIEU Workshop: Analysis and Optimization of Sample Quality for Cryo-electron Microscopy and Other Structural Techniques
Workshop for structural biologists who want to improve their skills in sample analysis and optimisation for structural techniques, in particular Cryo-EM.
the best of science obtained using CIISB Core Facilities
J. Am. Chem. Soc. 2019
The unstructured C-terminal domain of delta subunit of bacterial RNA Polymerase is 90 aa long and highly charged. The charge distribution of this domain is distinct, with a conserved stretch of 9 residues (96−104) containing 7 positive charges followed by the rest of the domain with 51 acidic residues (K-D/E motif). A previous study demonstrated that the two parts of the motif transiently interact, and this affects the spatiotemporal properties of this domain. From the biological point of view, δ increases cell fitness and virulence of pathogens and was previously proposed to function as a nucleic acid mimic and affect RNAP− nucleic acid interactions.
Electrostatic interactions play important roles in the functional mechanisms exploited by intrinsically disordered proteins (IDPs). The atomic resolution description of long-range and local structural propensities that can both be crucial for the function of highly charged IDPs presents significant experimental challenges. Here, we investigate the conformational behavior of the δ subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering. This strategy allows the resolution of long-range and local ensemble averaged structural contributions to the experimental RDCs, and reveals that the negatively charged segment folds back onto the positively charged strand, compacting the conformational sampling of the protein while remaining highly flexible in solution. Mutation of the positively charged region abrogates the long-range contact, leaving the disordered domain in an extended conformation, possibly due to local repulsion of like-charges along the chain. Remarkably, in-vitro studies show that this mutation also has a significant effect on transcription activity, and results in diminished cell fitness of the mutated bacteria in vivo. This study highlights the importance of accurately describing electrostatic interactions for understanding the functional mechanisms of IDPs.
Kuban, V., Srb, P., Stegnerova, H., Padrta, P., Zachrdla, M., Jasenakova, Z., Sanderova, H., Vitovska, D., Krasny, L..,Koval, T., Dohnalek, J., Ziemska-Legiecka, J., Grynberg, M., Jarnot, P., Gruca, A., Jensen, M.R., Blackledge, M., and Zidek, L.: Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase, J. Am. Chem. Soc. 2019, 141, 16817-16828, DOI:10.1021/jacs.9b07837
Science Advances 2019
Virion and genome organization of phage P68. (A and B) Structures of P68 virion, (C) genome release intermediate, and (D) empty particle. The whole P68 virion is shown in (A), whereas particles without the front half are shown in (B) to (D). The structures are colored to distinguish individual types of structural proteins and DNA. (E) Schematic diagram of P68 genome organization, with structural proteins color-coded in accordance with the structure diagrams shown in (A) to (D).
Phages infecting Staphylococcus aureus can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native S. aureus phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
Hrebík, D., Štveráková, D., Škubník, K., Füzik, T., Pantůček, R., and Plevka, P.: Structure and genome ejection mechanism of Staphylococcus aureus phage P68, Sci. Adv. 2019, 5(10), eaaw7414, DOI: 10.1126/sciadv.aaw7414
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 email@example.com. The section is being updated regularly.
Principles for Integrative Structural Biology Studies
Guru of integrative structural biology computation Andrej Sali and Michale P. Rout summarize in the recent Cell Primer Principles for Integrative Structural Biology Studies.
Chemical cross-linking with mass spectrometry: a tool for systems structural biology
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. In this review, Juan D. Chavez and James E. Bruce discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
In‐Cell EPR: Progress towards Structural Studies Inside Cells
Exploring the structure and dynamics of biomolecules in the context of their intracellular environment has become the ultimate challenge for structural biology. As the cellular environment is barely reproducible in vitro, investigation of biomolecules directly inside cells has attracted a growing interest. Among magnetic resonance approaches, site‐directed spin labeling (SDSL) coupled to electron paramagnetic resonance (EPR) spectroscopy provides competitive and advantageous features to capture protein structure and dynamics inside cells. To date, several in‐cell EPR approaches have been successfully applied to both bacterial and eukaryotic cells. In this minireview, the major advances of in‐cell EPR spectroscopy are summarized, as well as the challenges this approach still poses.
A standardized citation metrics author database annotated for scientific field
Citation metrics are widely used and misused. John P. A. Ioannidis et. al. created a publicly available data-base of 100,000 top scientists that provides standardized information on citations, h-index, co-authorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator. Separate data are shown for career-long and single-year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and 176 subfields. Field- and subfield-specific percentiles are also provided for all scientists who have published at least five papers. Career-long data are updated to end of 2017 and to end of 2018 for comparison.
How structure informs and transforms chemogenetics
Chemogenetic technologies such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are widely used to remotely control neuronal and non-neuronal signaling. DREADDs exist for most of the canonical G protein-coupled receptor signaling pathways, and provide a synthetic biology platform useful for elucidating the role of neuronal signaling for brain function. Here, Bryan L. Roth presents a focused review that shows how recent insights obtained from GPCR structural studies inform our understanding of these chemogenetic tools from a structural perspective.
Emerging structural insights into glycosyltransferase-mediated synthesis of glycans
Glycans linked to proteins and lipids play key roles in biology; thus, accurate replication of cellular glycans is crucial for maintaining function following cell division. Several recent crystal structures of glycosyltransferases with bound acceptor substrates reveal that these enzymes have common core structures that function as scaffolds upon which variable loops are inserted to confer substrate specificity and correctly orient the nucleophilic hydroxyl group. K. W. Moremen and R. S. Haltiwanger in Nature Chemical Biology review argue that the varied approaches for acceptor binding site assembly suggest that an ongoing evolution of these loop regions provides templates for assembly of the diverse glycan structures observed in biology.
Quote of November
“There are two things that are infinite, the universe and man's stupidity..... And I am not sure about the universe.”Albert Einstein