Dear Colleagues, six months ago, when I wrote Editorial for the Summer CIISB Newsletter, which described changes imposed by the Covid pandemics, I sincerely hoped that the situation at the beginning of 2021 would be different.

www.ciisb.org  |  1/2021
Sent 12 Feb 2021, 9:41

Newsletter

Editorial

Dear Colleagues,

six months ago, when I wrote Editorial for the Summer CIISB Newsletter, which described changes imposed by the Covid pandemics, I sincerely hoped that the situation at the beginning of 2021 would be different. After relatively quiet summer and fall, when a number of social and scientific activities returned close to normal, the lockdown after Christmas changed the gears again. 

Nevertheless, despite of all regulations during 2020 the extent of open access to CIISB technologies was not negatively influenced by the adopted measures and remained at the level comparable or even higher to previous years. All CIISB Core facilities have been fully functional. Visits of external foreign users are regulated by the Measures concerning foreigners and border crossing of the Czech Government. Please, check the current status on the web and contact the staff for details. Typically, the samples are mailed in and handled as usual on the first-come-first-serve basis. The users are consulted using telephone or on-line web platforms such as Zoom, Skype or MS Teams. In 2020 total number of open access applications increased compared to the numbers of 2019 from 232 to 289. In total, CIISB received 183 applications from internal and 106 from external users. Only number of external users from abroad decreased as a result of the Covid pandemics regulations. Big boost and great facilitation of the open access proposal submission brought an on-line submission system introduced in February 2020. This system works well and is being continually modified and updated to meet the needs of CIISB users.

         The data obtained by CIISB contributed to 108 scientific papers published during 2020, compared to 95 in 2019 and 78 in 2018. Increase in the quantity goes along with the increase of quality of published papers, which is steadily increasing. 21 papers appeared in the Nature Index journals, including those in Science, Nature Communications, Nature Structural and Molecular biology, Angewandte Chemie. Int. Ed., Journal of the American Chemical Society, Journal of Cell Biology, etc. Two research highlights from Science and Angewandte Chemie. Int. Ed., and five selected publications from leading journals are listed below. All of them can be found on our web at the Research Highlights Archive and in the section Publications.

            During the fall, materials for the international peer-review assessment of Large Research Infrastructures on the national level, organized by Ministry of Education, Youths and Sports of the Czech Republic, were prepared and successfully submitted on December 7, 2020. The envisaged goal of the assessment exercise is to provide the Ministry of Education, Youth and Sports and the Government of the Czech Republic with an expert basis to adopt informed political decision on public funding of large research infrastructures of the Czech Republic in the multiannual financial framework 2023-2029. Its outcome will be crucial to secure the operational budget of CIISB in the mentioned period. The results will be known during summer 2021.

            The Centre of Molecular Structure at BIOCEV established a new Protein Production facility. This initiative follows the survey mapping a preliminary interest from potential users and resulted in a platform for both routine protein production and demanding development of methods in semi high-throughput format.The facility has been in a pilot mode since July 2020 to evaluate the feasibility for the long run. Now the new Protein Production facility has been added to CIISB application form and users can apply via the standard application process.

         The project UP CIISB of the OP VVV Call 02-18-046 Research Infrastructures II for the period 2020-2022 started successfully in January 2020 and the first acquisitions of new instrumentation have already been put in operation. New mass spectrometers timsToF Pro were installed in the core facilities Structural Mass Spectrometry (BIOCEV) and in Proteomics (CEITEC). Josef Dadok NMR National Centre (CEITEC) upgraded all high-field NMR spectrometers from 600 MHz to 950 MHz with new electronics Avance Neo. In addition, the liquification units called BSNL (Bruker Smart Nitrogen Liquefier), which use an excess cooling capacity of the cryogenic probe system to liquify and recycle the nitrogen evaporating from the magnet, were installed on four systems equipped with the cryo-probes (600, 700, 850, and 950 MHz). The nitrogen refill interval is thus extended from 2-3 weeks to more than 6 months. 

         On August 23, 2020, two years term of the renewed CIISB Executive Committee started. By the decision of CEITEC MU and IBT CAS directors, Jiří Nantl and Bohdan Schneider, the committee will work in the following composition: Chair Vladimír Sklenář (CEITEC MU), Vice-Chair Jan Dohnálek (IBT CAS), Petr Novák (IBT CAS), Pavel Plevka (CEITEC MU), Bohdan Schneider (IBT CAS), Ivana Kutá-Smatanová (CSSB), Richard Štefl (CEITEC MU), and Michaela Wimmerová (CEITEC MU). 

         Training, seminars, and workshops postponed during 2020 are only very slowly appearing in calendar for 2021, frequently still planned only as on-line meetings. The activities are listed in the section Save the date below and in Events on the CIISB web. I hope that other will follow soon. Please, check the section Events on our web frequently to stay up-to date.

         On Tuesday, February 17, 2021 at 11:00 am the Instruct-ERIC ‘Structure Meets Function’ webinar will host presentation of CIISB – Instruct-CZ Centre. The latest science advances obtained with the assistance of CIISB core facilities will be presented by Jan Dohnálek, Pavel Plevka and Lukáš Trantírek.

         Despite of all troubles connected with the current situation I wish you enjoyable spring and summer and inexhaustible energy to cope with the Covid pandemic.

Vladimír Sklenář

 

 

 

 

News

New Protein Production facility at BIOCEV

The Centre of Molecular Structure at BIOCEV established a new Protein Production facility. This initiative follows the survey mapping a preliminary interest from potential users and resulted in a platform for both routine protein production and demanding development of methods in semi high-throughput format. The facility has been in a pilot mode since July 2020 to evaluate the feasibility for the long run. Now the new Protein Production facility has been added to CIISB application form and users can apply via the standard application process.

 

Cryo-EM data decode the mechanism behind the honeybee viral infections

How does the honeybee virus behave when infecting the host cell? Does it resemble pulling a note out of a bottle or rather opening a surprise egg? Karel Škubník and his colleagues, led by structural virologist Pavel Plevka from CEITEC Masaryk University, have discovered new findings describing the mechanism of genome release of honeybee viruses. They shed a new light on the exiting believe regarding behaviour of honeybee viruses during the host cell infection process. The scientists reached this remarkable conclusion with the help of cryo-electron microscopy combined with protein simulations, which were conducted by Robert Vácha and his research group. The research results were published on 1st January 2021 in the international scientific journal Science Advances.

 

New possibilities in fight against pathogenic bacteria – structure and role of protein HelD

Using cryogenic electron microscopy, three independent teams of researchers from Australia, the Czech Republic, and Germany have described the structure of a striking new complex between bacterial RNA polymerase and an accessory protein, HelD. The groups worked with a range of different components and organisms to gain a comprehensive understanding of how HelD uses a dramatic brute-force approach to prise open RNA polymerase and dislodge the tightly bound DNA and RNA.

This discovery provides an in-depth view of the bacterial transcription apparatus, and opens up pathways for development of urgently needed new antimicrobials capable of targeting serious pathogens such as the causative agent of tuberculosis. It leads to new possibilities of development of the much needed antimicrobials against serious pathogens, including the causative agent of tuberculosis. Their discoveries have been published in the Nature Communications Journal.

New timsToF in CMS

New mass spectrometer timsToF Pro was installed in November 2020 in the Structural mass spectrometry core facility in BioCev and is now fully in operation. The mass spectrometer will be used mostly for shotgun proteomics, hydrogen-deuterium exchange and covalent labelling experiments, and native mass spectrometry with ion mobility separation.

Job opportunity - Expert in scientific programming and data management

The Institute of Biotechnology of the Academy of Sciences of the Czech Republic at the Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University in Vestec announce an open position for an expert in scientific programming with experience in scientific data processing for a European project focused on Standards for Data Archival and Exploitation.

CIISB Access

Applications 2020

  • 183 internal applications
  • 94 external applications (Czech)
  • 12 applications from foreign users

You can find more info here.

Application overview in total

  2016 2017 2018 2019 2020
Internal users 123 178 177 147 183
External users 35 50 51 58 94
Foreign users 5 14 15 27 12

Save the date

Instruct-ERIC ‘Structure Meets Function’ webinar - presentation of CIISB

17 February 2021
11:00 AM – 12:30 PM

Online

Featuring expert speakers from Instruct Centres across Europe, the Instruct-ERIC webinar series, Structure Meets Function, highlights some of the latest developments in structural biology, demonstrating how integrative methods are enabling scientists to decipher the mechanisms that underpin health and disease.

The webinar will be hosted by Czech Infrastructure for Integrative Structural Biology (CIISB) with presentations of Pavel Plevka, Jan Dohnálek, and Lukáš Trantírek.

Advanced methods in macromolecular crystallization IX

9 – 15 May 2021

Nové Hrady, Czech Republic

Course, originally planned for May 2020, is postponed to May 9-15 2021.

The main aim of this course is consideration of theoretical aspects of crystal growth process as well as practical work: there will be a healthy mix of advanced discussions of the theory and of laboratory experiments and the possibility for participants to crystallize their own proteins.

 

Research Highlights

the best of science obtained using CIISB Core Facilities

Science 2020

Leonid A. Sazanov Research Group

Complex I is the first and, with 45 subunits and a total mass of ~1 MDa, the most elaborate of the mitochondrial electron transfer chain enzymes. Complex I converts energy stored in chemical bonds into a proton gradient across the membrane that drives the synthesis of adenosine triphosphate (ATP), the universal energy currency of the cell. In each catalytic cycle, the transfer of two electrons from nicotinamide adenine dinucleotide (NADH) to a hydrophobic electron carrier quinone, which happens in the peripheral arm of the enzyme, is coupled to the translocation of four protons across the inner mitochondrial membrane in the membrane arm. The exact mechanism of this energy conversion currently presents an enigma because of complex I’s size and the spatial separation between the two reactions.

To understand the coupling mechanism of complex I, we solved its cryo–electron microscopy (cryo-EM) structures in five different conditions, including the substrate- and inhibitor-bound states and during active turnover, unlocking the various conformations that the enzyme goes through during the catalytic cycle. We also improved the resolution to up to 2.3 to 2.5 Å, allowing us to directly observe water molecules critical for proton pumping.

Kampjut, D.and Sazanov, L.A. The coupling mechanism of mammalian respiratory complex I, Science, 2020, 370, eabc4209, https://doi.org/10.1126/science.abc4209

Angew. Chem. Int. Edit. 2020

Lukáš Trantírek and Harald Schwalbe Research Groups

L. Trantírek and H. Schwalbe research groups report here the in-cell NMR-spectroscopic observation of the binding of the cognate ligand 2’-deoxyguanosine to the aptamer domain of the bacterial 2’-deoxyguanosine-sensing riboswitch in eukaryotic cells, namely Xenopus laevis oocytes and in human HeLa cells. The riboswitch is sufficiently stable in both cell types to allow for detection of binding of the ligand to the riboswitch. Most importantly, they show that the binding mode established by in vitro characterization of this prokaryotic riboswitch is maintained in eukaryotic cellular environment. Data also bring important methodological insights: Thus far, in-cell NMR studies on RNA in mammalian cells have been limited to investigations of short (< 15 nt) RNA fragments that were extensively modified by protecting groups to limit their degradation in the intra-cellular space. Here, they show that the in-cell NMR setup can be adjusted for characterization of much larger (~ 70 nt) functional and chemically non-modified RNA.

Broft, P., S. Dzatko, S., Krafcikova, M., Wacker, A., Hänsel-Hertsch, R., Dötsch, V., Trantirek, L., and Schwalbe, H.: In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells, Angew. Chem. Int. Edit. 2020, 59, 2-11 doi.org/10.1002/anie.202007184

Selected publications

P. Bardy, et al.: Structure and mechanism of DNA delivery of a gene transfer agent, Nature Communications, 11 (2020) 13, 10.1038/s41467-020-16669-9 

P. Broft, et al.: In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells, Angewandte Chemie-International Edition,  10, 10.1002/anie.202007184 

D. Kampjut, et al.: The coupling mechanism of mammalian respiratory complex I, Science, 370 (2020) 547-+, 10.1126/science.abc4209 

K. Škubník, et al.: Capsid opening enables genome release of iflaviruses, Sci. Adv., 7 (2021) eabd7130, 10.1126/sciadv.abd7130 

Link  www.ciisb.org

© 2021
Masaryk University