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Newsletter 1/2019
11 Feb 2019, 10:31
Newsletter
Editorial
Dear Colleagues,
Summer and Fall 2018 passed quickly and start of the year 2019 offers excellent opportunity to remind you of the most important developments at CIISB between June and December 2018.
Thanks to the funds of the OP VVV project CIISB4HEALTH the instrumentation of CIISB is being gradually upgraded. The flag ship core facility for cryo-electron microscopy and tomography at CEITEC has been equipped with the new mid-range 200keV transmission cryo-electron microscope Talos Arctica (Thermo Fisher), which allows efficient acquisition of data for single-particle analysis and structure determination of macromolecular complexes at < 4 A resolution. Subsequently, the reconstruction of the cryo-electron core facility lab space, which took place during autumn and was finished in December, allowed re-installation of the Tecnai TF20 transmission electron microscope, which is now again available to the facility users. The Tecnai TF20 is primarily used for optimization of the samples for cryo-electron microscopy and data collection on the samples prepared by negative staining.
In the BIOCEV Centre of Molecular Structure, a new state-of-the-art SAXSpoint 2.0 instrument was installed. The instrument is equipped with dedicated high flux LiquidMetal Jet C2+ X-ray source, Eiger 1M detector, in situ UV/Vis spectrophotometric probe, a high-performance sample loader, and a flow through measurement cell. It performs SAXS and WAXS measurements in the temperature range -10 °C to 120 °C. The system is designed mostly for measurements of biological samples in liquids.
Smooth operation of CIISB depends primarily on extramural funding. Two CEITEC core facilities, Structural Mass Spectrometry at BIOCEV and Proteomics at CEITEC, are among the partners providing transnational access and participating on 4 Joint Research Activities of the European Proteomics Initiative Consortium EPIC-XS. This consortium, constituted by 18 European laboratories, has been awarded 10 million EUR grant for the period of four years, starting January 1, 2019, as a part of the Work programme Horizon 2020. Excellent news came also from the Ministry of Education, Youths, and Sports of the Czech Republic. Upon the information from the Czech government, financing of our research infrastructure in the period 2020-2022 is now ensured at the level, which reaches almost the actual operational budget. Additional finances in the total amount 3 billion CZK for investments and reinvestments in the same period will be distributed based on the OP VVV research infrastructures call, which has been announced with the deadline for application submission in May 2019.
Number of papers published with the support of CIISB in journals with high impact factors is steadily increasing. According to Web of Science, compared to 55 papers in 2017, 76 papers acknowledged support of CIISB in 2018. Out of it, 17 papers were published in journals listed in Nature Index and 22 papers appeared in journals with the impact factor higher than 5. Results of the most important publications can be found in the Research Highlight Section bellow and on the CIISB web.
As every year, also in 2019 CIISB will organize a large number of training events, workshops, and users meeting. Here, I will mention just two: XVI. Discussions in Structural Biology coupled with the 3rdUser meeting of CIISB will take place in Nové Hrady from March 21 till March 23, 2019. On May 29-31, 2019, the workshop on Integrated methodologies and approaches for structural biology will take place at CEITEC, Masaryk University in Brno. This workshop is organized as a part of the Horizon 2020 project iNEXT. All other activities planned for 2019 can be found on the CIISB web.
I wish you successful year 2019.
Vladimír Sklenář
New instruments and laboratory modifications
New microscope laboratory at the Cryo-electron microscopy core facility at CEITEC MU
The reconstruction of the Cryo-electron microscopy and tomography core facility laboratories took place during autumn 2018 and was finished in December. The new laboratory harbors the Tecnai TF20 transmission electron microscope, which is now again available to the facility users. Read more here.
New cryo-TEM at CEITEC MU
New mid-range 200 kV transmission electron microscope for cryo-electron microscopy has been installed at Cryo-electron microscopy and tomography core facility CEITEC Masaryk University. Since October 1, 2018, a new cryo transmission electron microscope Talos Arctica (Thermo Scientific) is fully available to the facility users. The microscope is equipped with the Falcon3 EC direct electron detector and the Ceta camera. More you can find here.
New state-of-the-art SAXSpoint 2.0 instrument installed at the Centre of Molecular Structure
A laboratory Small Angle X-ray Scattering device has just been delivered at the CMS: SAXSpoint 2.0 instrument with dedicated high flux LiquidMetal Jet C2+ X-ray source, Eiger 1M detector and in situ UV/Vis spectrophotometric probe. The device is equipped with a high-performance sample loader and a flow through measurement cell. More you can find here.
New grants
Ten Million Euro for Access to European Proteomics Facilities
The European Union has awarded 10 million euro to a consortium of eighteen European research groups in the field of mass spectrometry-based proteomics research throughout Europe.
The European Proteomics Initiative Consortium (EPIC-XS), funded as part of the Horizon 2020 Work programme, is coordinated by Albert Heck, professor of biomolecular mass spectrometry and proteomics at Utrecht University. The project has started on the first of January 2019 and will run for a period of four years. You can find more here.
Financing of CIISB research infrastructure in 2020-22
Upon the information from Czech government, financing of research infrastructures in 2020-2022 will be ensured with very small cutting which is given by the allocated budget. Operational budget of CIISB will be ensured, and additional investment will be distributed based on the call OP VVV research infrastructures II with the deadline for application submission in May 2019.
News
Instruct Training program
Instruct training courses that have been approved by the Training Committee and are supported by central Instruct funding should be implemented according to agreed standards set by the Innovative Medicines Initiative (IMI), Education and Training body funded by the European Union. Instruct is a partner in the IMI project EMTRAIN, and as such has agreed to work within their quality criteria for training courses. The Call for proposals for Instruct Centre Training Courses (to be held in 2019) is now open. You can find more here.
Instruct-ERIC Joint Research Awards: Call for proposals
Instruct is inviting applications for funding for joint research that develops new, or improves existing access services delivered by Instruct to the user community. The aim is to develop and progress technologies to a stage where they can be made available through the Instruct access programme. Within this call, Instruct has identified opportunities for focussed technical developments in areas that are outlined below. Applications are encouraged but not limited to these areas and funds may be awarded for proposals addressing other areas. You can find more here.
During the December 2018 was opened call for Instruct-ERIC Internships. The Instruct Internship Programme funds research visits of 3-6 months duration to Instruct Centres in Europe. The aim is to facilitate valuable collaborations with Instruct research groups applying techniques that are not available in the applicant’s laboratory. Applications should specifically focus on the benefit to the applicant’s research. Internships may be hosted at any institution that hosts an Instruct Centre, providing the applicant is a resident of a different full Instruct member country at the time of making the application. More you can find here.
Activities from the past six months
Novel approaches in structural and quantitative proteomics Biocev
The lecture was given by Dr. Christoph Borchers, University of Victoria. Dr. Borchers’ research is centered around the improvement, development and application of proteomics technologies with a major focus on techniques for quantitative targeted proteomics for clinical diagnostics. More you can find here.
INSTRUCT- FRISBI course on preparation and characterization of macromolecular complexes
This INSTRUCT/FRISBI practical course provided participants with an overview of strategies for preparation and biophysical characterization of macromolecular complexes in view of biochemical and structural studies. The emphasis of the workshop was placed on purification of macromolecular assemblies from endogenous sources using engineered cell lines and in reconstitution of multiprotein complexes using the baculovirus expression system. You can read more here.
SPR workshop - Applications in life-science
After the last year success of first workshop focused on Surface plasmon resonance we decided to organize another one to promote such a valuable technique. The SPR workshop was a 2-day event with 3 speakers from abroad and 1 from CF BIC attended 30 participants. You can find more here.
Lecture: Taxonomy of errors and mistakes in X-ray crystallography
Profesor Diederichs is the main author of the X-ray diffraction processing program XDS, nowadays widely used for reduction of data. Taxonomy of errors and mistakes in X-ray crystallography Crystallography lets us visualize the molecules of life - more than 130.000 structures in the PDB attest to that. But all that glitters is not gold. Read more here.
Open day of the Centre of Molecular Structure in Biocev
The Centre of Molecular Structure (CMS) encompasses several laboratories providing a complex approach to studies of three-dimensional structure, function, and biophysical properties of biological molecules. The laboratories of CMS provide services enabling research or routine measurements on proteins, nucleic acids, protein-protein, protein-nucleic acid, or protein-small molecule complexes.
What could you hear there?
Information about equipment, techniques, and expertise available at CMS, details about modes of access, guided tour of available instruments for biomolecular techniques, with details on how certain techniques are used (amount of sample, quality, etc.). An update regarding new instruments will be given. More information you can find here.
Zetasizer Ultra workshop
In this workshop attendees learned a wide range of applications of Zetasizer Ultra to characterize their samples. The new Zetasizer Ultra instrument is the most advanced system for the measurement of particle and molecular size, particle charge and particle concentration. You can find more here.
PETER Summer School
Over 90 attendees in 3 days, 7 invited speakers and plenty of good time, that was the PETER Summer school at CEITEC Science Park organised as a part of our H2020:FET-OPEN project bringing innovations in EPR and THz.
BioSAXS practical course 2018
Two days practical course on basics of biological small angle x-ray scattering (SAXS) was organised on September 24-25t at CEITEC, buliding A35. Participants were introduced to the practical aspects of SAXS experiment setup during laboratory practical and excursion to the Core Facility X-ray diffraction and BioSAXS. One 2h lecture on SAXS basic principles given by Alexey Kikhney (EMBL-Hamburg) was open to broader audience. Find more here.
organized by Czech Society for Structural biology and Czech Infrastructure for Integrative Structural Biology with support of Institute of Biotechnology AS CR, Institute of Microbiology AS CR and South Bohemian University in České Budějovice.
The 4th Instruct Biennial Structural Biology Conference will take place in Alcalá de Henares, Spain. The historical Alcalá de Henares was the original location of the Universidad Complutense, founded in 1293 and one of the oldest universities in the world, as well as being the birthplace of Miguel de Cervantes. The social programme of the meeting will include a visit to the city, a gala dinner and extensive opportunities to network with the Instruct Structural Biology community.
The iNEXT workshop Integrated methodologies and approaches for structural biology, Masaryk University, Brno, jointly organized by CEITEC Masaryk University, University of Utrecht, Czech Infrastructure for Integrative Structural Biology, and Czech Society for Structural Biology, will provide a comprehensive overview of the state-of the-art progress of integrative methodologies to existing and potential users of iNEXT facilities.
The aim of this meeting is to illustrate how the big biological questions are resolved by combining key methods in structural biology (eg X-ray and neutron crystallography, cryo-EM, NMR and small angle scattering - SAXS and SANS) with other complementary approaches, enhancing our understanding of the dynamic behaviour of macromolecular complexes in the cell.
Research highlights
The Febs journal 2018
The main goal of this work is to provide the structural basis for the role of 14‐3‐3 protein binding in regulating caspase‐2 activation. Because all our previous attempts to crystallize the complex between Ser139‐ and Ser164‐ phosphorylated caspase‐2 (residues 123–452 without the CARD domain, hereafter referred to as proC2) and 14‐3‐3ζ had been unsuccessful, we decided to use small angle X‐ray scattering (SAXS) combined with NMR, with chemical cross‐linking coupled to MS and with fluorescence spectroscopy to characterize the solution structure and conformational behavior of this complex. More you can find here.
Nat. Commun. 2018
During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the Apidaecin 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome. More you can read here.
Selected publications
Acimovic, I. et al.Post-Translational Modifications and Diastolic Calcium Leak Associated to the Novel RyR2-D3638A Mutation Lead to CPVT in Patient-Specific hiPSC-Derived Cardiomyocytes. Journal of Clinical Medicine7, 22,doi:10.3390/jcm7110423 (2018).
Crowe-McAuliffe, C. et al.Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proceedings of the National Academy of Sciences of the United States of America115, 8978-8983,doi:10.1073/pnas.1808535115 (2018).
Darebna, P. et al.Detection and Quantification of Carbohydrate-Deficient Transferrin by MALDI-Compatible Protein Chips Prepared by Ambient Ion Soft Landing. Clinical Chemistry64, 1319-1326,doi:10.1373/clinchem.2017.285452 (2018).
Kaurov, I. et al. The Diverged Trypanosome MICOS Complex as a Hub for Mitochondrial Cristae Shaping and Protein Import.Current Biology 28, 3393-+, doi:10.1016/j.cub.2018.09.008 (2018).
Moulick, A. et al.Real-Time Visualization of Cell Membrane Damage Using Gadolinium Schiff Base Complex-Doped Quantum Dots.Acs Applied Materials & Interfaces10, 35859-35868,doi:10.1021/acsami.8b15868 (2018).
Munster, L. et al.Dialdehyde cellulose crosslinked poly(vinyl alcohol) hydrogels: Influence of catalyst and crosslinker shelf life.Carbohydrate Polymers198, 181-190,doi:10.1016/j.carbpol.2018.06.035 (2018).
Podhorsky, J. et al. Preparation of Heteroleptic Tin(IV) N,O-beta-Heteroarylalkenolate Complexes and Their Properties as PI-MOCVD Precursors for SnO2 Deposition.European Journal of Inorganic Chemistry, 5027-5035, doi:10.1002/ejic.201800913 (2018).
Prochazkova, M. et al.Virion structure and genome delivery mechanism of sacbrood honeybee virus.Proceedings of the National Academy of Sciences of the United States of America115, 7759-7764,doi:10.1073/pnas.1722018115 (2018).
Sharma, S. et al.Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation.Proceedings of the National Academy of Sciences of the United States of America115, E7053-E7062,doi:10.1073/pnas.1803909115 (2018).
Vojackova, P., Chalupa, D., Prieboj, J., Necas, M. & Svenda, J.Enantioselective Conjugate Additions of 2-Alkoxycarbonyl-3(2H)-furanones. Organic Letters 20, 7085-7089,doi:10.1021/acs.orglett.8b03039 (2018).
