Dear colleagues, The start of the New Year offers opportunity to overview the most important changes, events, and news from the second half of the year 2019.

www.ciisb.org  |  1/2020
Sent 7 Feb 2020, 13:24

Newsletter

Editorial

 

Dear colleagues,

The start of the New Year offers opportunity to overview the most important changes, events, and news from the second half of the year 2019.

The funding of Large Research Infrastructure for the period 2016-2019 came to the end in December 2019 and with this, also the project LM2015043. Thanks for the judicious decision of the Government funding of Large Research Infrastructures will continue also in the years 2020-2022. CIISB will receive substantial operational budget within the new project LM2018127. All papers published in the upcoming financial period should include acknowledgement to this new project.

Also, the project UP CIISB 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 during the years 2020-2022. This funding will allow CIISB to stay competitive on the European scale and will reinforce its position within the European Infrastructure consortium Instruct-ERIC as one of the leading Instruct Centers providing transnational access to its flagship technologies.

Number of excellent papers published in high-quality journals is steadily increasing. Out of 81 papers published in 2019, 14 appeared in the journals listed in Nature index, and increased thus the total number since 2016 to 47. The most significant results are described in Research Highlights. Results of other important publications can be found in the section Publications written with support of CIISB on the CIISB web.

In the attempt to enhance the information content of our web www.ciisb.org, new sections have been added. A new page “Who is Who in Czech Structural Biology” has been added to the web site of Czech Infrastructure of integrative Structural Biology with the intention to map the landscape of Czech Structural Biology, facilitate communication, and stimulate collaborations within our scientific community. As of Summer 2019, a new section Reader’s Corner - literature to read, science to follow has been added to our web. On the home page bellow Research Highlights, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. To bring to your attention gratifying ideas of the past, Quote of the months has been added to the end of the front web page. Enjoy refreshing thoughts of great minds of the past.

To conclude, please, pay attention to the upcoming meeting of the Czech Structural Biology Society and 4rdUser Meeting of CIISB in Nové Hrady, March 19-21, 2020 and the meeting of the NMR colleagues in Valtice, April 19-22, 2020.

I wish you enjoyable and successful year 2020.

Vladimír Sklenář

New grants

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. The results were announced on October 31, 2019. Among others, new scanning transmission cryo-electron microscope with a detector for electron diffractions studies on microcrystals, fluorescence cryo-electron microscope, and new direct detectors for the existing instruments Titan Krios and Talos Arctica will be purchased. The Josef Dadok National NMR Center will benefit with upgrades of the instruments electronics and purchase of new probeheads for the high-field NMR spectrometers 500-950 MHz. Substantial acquisition of upgrades and new devices will keep up also Core Facilities for X-ray diffraction and Bio-SAXS, Crystallization of Proteins and Nucleic Acids, Biophysical Techniques, Nanobiotechnology, Proteomics and Structural Mass Spectrometry. This funding will allow CIISB to stay competitive on the European scale and will reinforce its position within the European Infrastructure consortium Instruct-ERIC as one of the leading Instruct Centers providing transnational access to its flagship technologies.

News

New Pilot Version of On-line Submission System for Open Access requests to CIISB Core Facilities

So far, all requests for Open Access to CIISB Core facilities required submission of filled paper forms via email. Since January 2020, new on-line submission system offers simplified protocol for submission of requests for open access to all ten CIISB Core Facilities. All received project proposals of potential users are immediately forwarded to the evaluation process. If the proposals are evaluated positively the applicants are instantly invited to conduct their experiments. This modification speeds up the evaluation process and greatly facilitate communication between the applicants and staff of the CIISB Core Facilities.

At the moment this system is in a pilot version and it will we be fully functional soon.

New combined AFM-Raman microscope at CEITEC MU

Combined AFM-Raman microscope, consisting of Bruker Dimension Icon and Renishaw Raman microscope, was installed in the Nanobio CF labs. This unique combination extends high resolution of AFM microscopy with localization specificity of Raman spectroscopy. Complex characterization of amyloid fibers can be seen as an interesting example in this way.

Source of image: Science Advances 16 Nov 2018: Vol. 4, no. 11, eaat7715.

UP CIISB Kick-Off Meeting

On 2nd December 2019 CIISB Core Facility Heads, Executive Committee members, and administration staff of CEITEC and BIOCEV gathered to discuss the starting OP VVV investment project UP CIISB. Within this project,  CIISB will receive funding to reinvest into the existing equipment and to purchase new instrumentation in the amount of 22 mil. EUR. 

CIISB Access

Applications 2019

  • 147 internal applications
  • 58 external applications
  • 27 applications from foreign users

You can find more info here.

Application overview in total

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

Save the date

Cryo-Electron Microscopy Service Platform

7 February 2020, 9:00 AM – 7:00 PM
EMBL Heidelberg

On 7th February 2020, past and future users of the EMBL Cryo-EM Platform will have an opportunity to meet, discuss and start new scientific collaborations.

This Symposium will attempt to stimulate the exchange of experience among cryo-EM users and developers, and to strengthen the cryo-EM community.  The symposium will include sessions on applications of single particle analysis as well as a session on cryo-EM grid developments, presented by eleven invited speakers. 

Besides invited speakers, all participants are welcome to present their research during the poster session. Also a tour of the EMBL Cryo-EM Platform will be provided. The meeting will be rounded out with a discussion and feedback from future users, followed by a social event.

Instruct-ERIC and ARBRE-MOBIEU Workshop: Analysis and Optimization of Sample Quality for Cryo-electron Microscopy and Other Structural Techniques

11 – 14 February 2020

University Campus Bohunice, Masaryk University Brno

This workshop is suitable for structural biologists who want to improve their skills in sample analysis and optimization for structural techniques, in particular Cryo-EM. Training will be focused on the importance to provide basic protein quality control as well as buffer and storage optimization via using quick and relatively cheap techniques to save precious Cryo-EM time.

XVII Discussions in Structural Biology and 4th Users Meeting of CIISB

NMR Valtice

19-22 April 2020

Valtice

NMR in Valtice is the annual meeting of the nuclear magnetic resonance community and serves as the principal international forum for reporting outstanding research and development on new NMR methods, techniques and tools for research and application in science and technology.

Research Highlights

the best of science obtained using CIISB Core Facilities

Science Advance

Pavel Plevka Reasearch Group

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.

You can find more at our website.

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

Proceedings of the National Academy of Sciences of the United States of America

Dieter Blaas and Michaela Schmidtke Research Groups

More than 160 rhinovirus (RV) types cause about a billion respiratory infections annually in the United States alone, contributing to influenza-like illness. This diversity makes vaccination impractical. Existing small-molecule inhibitors target RVs by binding to a hydrophobic pocket in the capsid but exhibit side effects, resistance, and/or mutational escape, impeding registration as drugs. The pyrazolopyrimidine OBR-5-340 acts like other capsid binders by preventing conformational changes required for genome release. However, by using cryo-EM, we show that OBR-5-340 inhibits the naturally pleconaril-resistant RV-B5 by attaching close to the pocket entrance in a binding geometry different from that of most capsid binders. Combinations of inhibitors with disparate binding modes might thus effectively combat RVs while reducing the risk of resistance development.

You can find more information in our Research Highlights Archive.

Wald, J.,  Pasin, M.,  Richter, M., Walther, C., Mathai, N., Kirchmair, J., Makarov, V. M., Goessweiner-Mohr, N., Marlovits, T. C., Zanella, I., Real-Hohn, A., Verdaguer, N., Blaas, D.,  and Schmidtke. M.: Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site, Proc. Natl. Acad. Sci. U.S.A.2019, 116 (38), 19109-19115.https://doi.org/10.1073/pnas.1904732116

Selected publications

R. Chaloupkova, et al.: Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts, Acs Catalysis, 9 (2019) 4810-4823, 10.1021/acscatal.9b01031

M. Kandrnalova, et al.: Hypervalent Iodine Based Reversible Covalent Bond in Rotaxane Synthesis, Angewandte Chemie-International Edition, (2019) 5, 10.1002/anie.201908953

A. Kezar, et al.: Structural basis for the multitasking nature of the potato virus Y coat protein, Sci. Adv., 5 (2019) 13, 10.1126/sciadv.aaw3808 

M. Krafcikova, et al.: Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy, Journal of the American Chemical Society, 141 (2019) 13281-13285, 10.1021/jacs.9b03031 

V. Kuban, et al.: Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase, Journal of the American Chemical Society, 141 (2019) 16817-16828, 10.1021/jacs.9b07837 

Link  www.ciisb.org

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Masaryk University