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.
S. Vogel and S. A. Weinwright, 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.
New webpage on ciisb.org
A new page “Who is Who in Czech Structural Biology” has been added to the web site of CIISB
Save the date
Save the date – March 19-21, 2020
The XVII. Discussions in Structural Biology and 4th Users Meeting of Czech Infrastructure for Integrative Structural Biology (CIISB) jointly organized by Czech Society for Structural Biology and CIISB will take place in Nové Hrady, March 19 - March 21, 2020.
EOSC Early Adopter Programme
The second call for the EOSC Early Adopter Programme is now open!
the best of science obtained using CIISB Core Facilities
ANAL. CHEM. 2019
Utility of phenylhydrazine (PHN) labeling for structural studies of fucosylated N-glycans by tandem MALDI mass spectrometry (MS) in the positive ion mode is proposed. PHN-tag influences the production of specific ion types, and the MS/MS fragmentation pattern provides useful structural information.
Fucosylation is a common modification, and its site in glycans refers to different normal and pathological processes. Despite intensive research, there is still a lack of methods to discriminate unambiguously the fucose position in one-step. In this work, we propose utility of phenylhydrazine (PHN) labeling for structural studies of fucosylated N-glycans by tandem MALDI mass spectrometry (MS) in the positive ion mode. PHN-tag influences the production of specific ion types, and the MS/MS fragmentation pattern provides useful structural information. All types of core fucosylated N-glycans have produced two abundant ions consistent with B- and C-glycosidic cleavages corresponding to the loss of the FucGlcNAcPHN residue with a mass 457 and 441 Da from the parent ions. These types of fragment ions in N-glycans without a core fucose were associated with the loss of the GlcNAcPHN unit (311 and 295 Da), and fucose cleavage followed the loss of the chitobiose residue. Since diagnostic useful cleavages produce peaks with significant intensities, this approach is also beneficial for rapid recognition of antenna from core fucosylation in glycans detected with low abundances. The practical applicability of the approach is demonstrated on the analysis of multifucosylated N-glycans detected with lower abundances in lung cancer samples
Lattová, E., Skřičková, J., and Zdráhal, Z.: Applicability of Phenylhydrazine Labeling for Structural Studies of Fucosylated N-Glycans, Anal. Chem. (2019) 91(13),7985-7990. https://doi.org/10.1021/acs.analchem.9b01321
SCIENCE ADVANCES 2019
Potato virus Y (PVY) belongs to the most economically important pathogens. The collaborative research project of the National Institute of Chemistry (Ljublana, Slovenia) and Cryo-Electron Microscopy Core Facility at CEITEC MU reveals the structure of the PVY coat protein (CP) and the PVY virus like particle at near-atomic resolution. The data show a novel luminal interplay between the extended carboxy-terminal CP regions in the virion and describe RNA-CP interactions important for helical conformation and stability of the virus.
PVY is ranked as fifth in the top 10 most economically important plant viruses and is the most important viral pathogen of potato worldwide. The virus causes potato tuber necrotic ringspot disease, which can result in up to 70% yield reduction, and severely affects other economically important solanaceous crops. Despite extensive availability of data on PVY’s genome and pathogenicity, there has been no high-resolution structuralinformation for this virus. Because of the extreme economic importance of PVY, and the urgent need for structural data to better understand mechanisms of viral infectivity, we have examined in detail the structure of the PVY virion and its CP. We have determined the high-resolution electron cryo-microscopy structures of the PVY virion and a recombinant PVY-based RNA-free virus-like particle (VLP). This provides a new and detailed insight into the RNA-supported helical viral capsid architecture featuring an extended C-terminal region of CP, which is tightly packed in a unique fashion in the virion lumen. In addition, using extensive biochemical, biophysical, and computational characterization, as well as structure-based mutagenesis, we identified regions of CP that affect VLP filament assembly. Moreover, the biological activities of the CP’s N- and C-terminal regions for virus infectivity were explored by measuring the accumulation of viral RNA and systemic movement of selected PVY mutants in plants.
Kežar, A., Kavčič, L., Polák, M., Nováček, J., Gutiérrez-Aguirre, I., Tušek Žnidarič, M., Coll, A., Stare, K., Gruden, K., Ravnikar, M., Pahovnik, D., Žagar, E., Merzel, F., Anderluh,G., and Podobnik, M.: Structural basis for the multitasking nature of the potato virus Y coat protein, Sci. Adv. (2019) 5(7), eaaw3808, DOI: 10.1126/sciadv.aaw3808
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 firstname.lastname@example.org. 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.
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.
Aminoacyl-tRNA synthetases as therapeutic targets
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for protein synthesis with evolutionarily conserved enzymatic mechanisms. Recent genomic, proteomic and functionomic advances have unveiled unexpected disease-associated mutations and altered expression, secretion and interactions in human ARSs, revealing hidden biological functions beyond their catalytic roles in protein synthesis. These studies have also brought to light their potential as a rich and unexplored source for new therapeutic targets and agents through multiple avenues, including direct targeting of the catalytic sites, controlling disease-associated protein–protein interactions and developing novel biologics from the secreted ARS proteins or their parts. Sunghoon Kim et. al. in Nature Reviews Drug Discovery address the emerging biology and therapeutic applications of human ARSs in diseases including autoimmune and rare diseases, and cancer.
Atomic Force Microscopy Based Tip-Enhanced Raman Spectroscopy in Biology
Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, can provide not only the topography characterization with high resolution, but also can deliver the chemical or molecular information of a sample beyond the optical diffraction limitation. In this review, Bo Liu et. al. mainly focus on the applications of AFM-TERS in three biological systems: nucleic acids, proteins and pathogens. From the TERS characterization to the data analysis, this review demonstrates that AFM-TERS has great potential applications to visually characterizing the biomolecular structure and crucially detecting more nano-chemical information of biological systems.
Compressive Force Spectroscopy: From Living Cells to Single Proteins
One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. A less recognized variation of this method, the application of compressive force, allows studies from large samples (living cells) to smaller, multi-molecular complexes (viruses) down to single protein molecules. These studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, Daniel Mark Czajkowsky et. al. briefly review some of the recent achievements and highlight exciting areas of its future development.
RNA Dynamics by NMR Spectroscopy
To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate dynamics in RNA with atomic resolution. In this review, Katja Petzold et. al. provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours.
Quote of September
“A journey of a thousand miles starts with a single step.”Chinese philosopher Laozi (604 - 531 BC)