www.ciisb.org  |  22 Feb 2022, 14:55

Newsletter

Editorial

Dear Colleagues,

my Editorial for the first CIISB Newsletter of 2022 starts with a short recollection of the past year. Despite of the ongoing Covid-19 pandemics the access requests remained on the average level of 2019 and 2020 with 166 internal, 69 external and 19 foreign users’ applications. Publication activity with 108 Web of Science entries, including 18 articles in journals listed in the Nature Index, including Nature Communications, Science Advances, ACS Nano, Angewandte Chemie Int. Ed., Cancer Research, Inorganic Chemistry and PNAS, is the same as in 2020.

Thanks to funding provided by the OP VVV project UP CIISB the acquisition of a new equipment continued smoothly with the goal to finish this project successfully by the end of 2022. Josef Dadok National NMR Centre at CEITEC obtained new cryo-probeheads of its 600, 700, 850, and 950 MHz systems, as well as a new diffusion probe for 700 MHz spectrometer. Centre of Molecular Structure at BIOCEV upgraded its D8 Venture diffractometer and system to detect the biomolecular interactions. Also, the X-ray diffractometers at the X-ray Diffraction and Bio-SAXS CEITEC core facility have been upgraded to stay at the state-of-the-art level. Cryo-EM and cryo-ET acquired a new cryo-fluorescence microscope and vitrification robot. The new instrumental additions extend the portfolio of techniques applicable for biomolecular and chemical investigations.

The current Covid-19 pandemic situation allows, after long two years, to renew the face-to-face meetings. On March 24-26, 2022, the CIISB users’ community will meet in Nové Hrady at the occasion of the XVIII Discussions in Structural Molecular Biology and the 5th User meeting of CIISB in Nové Hrady, South Bohemia. I am very much looking forward to attend this event and I hope to meet all of you there.

Vladimír Sklenář

News

Jaroslav Koča Memorial Colloquium on Computational and Structural Biology

Jaroslav Koča Memorial Colloquium on Computational and Structural Biology was organized on November 30, 2021, in a memory of our esteemed colleague, who unexpectedly passed away in July 2021, but his scientific vision and constructive ideas will remain a living legacy for next generations of researchers.

Demonstration of the Prometheus Panta for protein stability on October 12

On October 12 the Centre of Molecular Structure with experts from NanoTemper company are holding a demonstration of the Prometheus Panta for protein stability with particle size determination and of the new Monolith MST device with better temperature control for the characterization of biomolecular interaction.

XVIII Discussions in Structural Molecular Biology and the 5th User meeting of CIISB in Nové Hrady

XVIII Discussions in Structural Molecular Biology and the 5th User meeting of CIISB in Nové Hrady is planned on 24-26 March 2022. If the situation allows we would like to return to our on-site conference. Due to the uncertainty connected with the Covid-19 situation development we plan to open the full registration to the event in January 2022.

EOSC Future

Last week we announced that the EOSC Future project and the EOSC Digital Innovation Hub (DIH) are launching an expression of interest (EoI) for business pilots (which is open until 3 December 2021).

Open call for Instruct-ERIC Hub Coordinator

Instruct-ERIC is looking for a Hub Coordinator to join their team. This is a senior role working closely with the Instruct Director who is located outside the UK. You will therefore represent the Director in many of the day-to-day tasks required to run the Instruct Hub operationally, ensuring Instruct-ERIC operates legally and efficiently. The Hub team currently includes 12 team members and has a fast-working pace with multiple interconnecting projects and tasks in operation simultaneously. This role requires someone with excellent problem solving and multitasking skills and quick responsiveness to requests and questions from all stakeholders.

ICRI 2022: International Conference on Research Infrastructures: 19. – 21. October 2022

ICRI is a major worldwide event providing an opportunity for strategic discussions about international cooperation of research infrastructures. A variety of experts and stakeholders from around the world discuss challenges and emerging trends, highlighting the essential role of research infrastructures. The upcoming ICRI in 2022 will take place in Brno, Czech Republic, from October 19 until October 21. It will be possible to participate online as well. For more information, head to www.icri2022.cz and follow us on Twitter @icri2022, using hashtag #ICRI2022.

Invitation to 7th Structural Biology Club of the Czech Society for Structural Biology

You are invited to the 7th Structural Biology Club of the Czech Society for Structural Biology online on 26 January 2022 at 13:00. 

Successful Horizon Europe Project Awards

Instruct-ERIC has been awarded 4 upcoming Horizon Europe Projects, which will all be beginning in the coming months. 

Internship Call Open

The 9th Instruct-ERIC Internship Call is now open. PhD Students and Postdoctoral Fellows are invited to apply for the call, which funds transnational visits for 3-6 months to Instruct centres.

Bertini Award

The call is open for the Ivano Bertini Award. Submit your nominations here to recognise a significant achievement in any area of the biological sciences.

Anonymous survey on Biophysical Data Standards and Accessibility

We would like to know your experience and views on the current status and needs for data standardization and availability of databases for the individual techniques of molecular biophysics. You are invited to contribute to this world-wide survey and have your voice heard!

CIISB Access

Applications 2021

  • 166 internal applications
  • 69 external applications (Czech)
  • 16 applications from foreign users

You can find more info here.

Application overwiev in total

  2016 2017 2018 2019 2020 2021
Internal users 123 178 177 147 183 166
External users 35 50 51 58 94 69
Foreign users 5 14 15 27 13 16

 

Save the date

XVIII Discussions in Structural Molecular Biology and the 5th User meeting of CIISB in Nové Hrady

24 – 26 March 2022

NOVÉ HRADY

XVIII Discussions in Structural Molecular Biology and the 5th User meeting of CIISB in Nové Hrady is planned on 24-26 March 2022. If the situation allows we would like to return to our on-site conference. Due to the uncertainty connected with the Covid-19 situation development we plan to open the full registration to the event in January 2022.
We will provide updates if there are changes to these plans. For the latest information see the website of the Czech Society for Structural Biology: https://cssb.structbio.org/. Please, mark the dates in your diaries and be ready to register in January.

Research Highlights

EMBO Journal 2022

Cryo-EM structures of CspA27 inside the exit tunnel

  1. Structure and nascent chain contacts in the exit tunnel for CspA27-1.
  2. Structure and nascent chain contacts in the exit tunnel for CspA27-2.
  3. Structure and nascent chain contacts in the exit tunnel for CspA27-3.

Marina V. Rodnina Research Group

Significance

Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a β-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a β-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity.

Agirrezabala, X., Samatova, E., Macher, M., Liutkute, M., Maiti, M., Gil-Carton, D., Novacek, J., Valle. M., and Rodnina, M.V.: EMBO J. (2022) e109175, https://doi.org/10.15252/embj.2021109175

 

ACS Nano 2021

Snapshots from simulations representing the release pathways. The rapid pathway category (R1–R3) was divided into (R1) burst genome release, where capsids disintegrate into fragments; (R2) rupture genome release, where capsids split open (most often into two halves); and (R3) bloom genome release, where capsids open wide in one hemisphere without breaking the other. In the rupture and bloom pathways, a majority of the capsid reassembles after the genome release. Occasionally, pentamers of capsid proteins may be detached. The subcategory leaky release (L) started with a slow release and ended with a rapid release. The slow pathway (S1–S3) category was divided into (S1) release through a pore on a twofold axis, (S2) release through a pore on a threefold axis, and (S3) release through multiple pores. Note that slow release was only observed for the noncompact genome. All release examples are shown with the noncompact genome. Color coding: Beads forming the body of the capsid are orange on the outside and purple on the inside of the capsid. The genome is represented by blue beads. Red and green beads represent attractive beads between pentamers.

Robert Vácha Research Group

Significance

Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/ genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery.

 

Sukeník, L., Mukhamedova, L., Procházková, M., Škubník, K., Plevka, P., and Vácha, R.:

Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation, ABC Nano 2021, 15, 12, 19233–19243, https://doi.org/10.1021/acsnano.1c04814

 

Research Highlights Archive

Selected publications

L.J. Bailey, et al.: PLK1 regulates the PrimPol damage tolerance pathway during the cell cycle, Sci. Adv., 7 (2021) 15, 10.1126/sciadv.abh1004

H. Covelo-Molares, et al.: The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features, Nucleic Acids Res., 49 (2021) 10895-10910, 10.1093/nar/gkab900

J. Holubova, et al.: Selective Enhancement of the Cell-Permeabilizing Activity of Adenylate Cyclase Toxin Does Not Increase Virulence of Bordetella pertussis, International Journal of Molecular Sciences, 22 (2021) 18, 10.3390/ijms222111655

I. Ilikova, et al.: Towards spruce-type photosystem II: consequences of the loss of light-harvesting proteins LHCB3 and LHCB6 in Arabidopsis, Plant Physiology, 187 (2021) 2691-2715, 10.1093/plphys/kiab396

P. Jarosova, et al.: Alkaloid Escholidine and Its Interaction with DNA Structures, Biology-Basel, 10 (2021) 16, 10.3390/biology10121225

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