www.ciisb.org  |  Newsletter 2/2021
Sent 12 Oct 2021, 14:10

Newsletter

Editorial

Dear Colleagues,

it is my sad duty to begin this editorial with a painful news. On July 2, 2021, Professor Jaroslav Koča, a prominent chemist and structural biologist, passed away. He was the President of Czech Science Foundation (GAČR), Emeritus Scientific Director of the CEITEC Consortium, and Director of the National Centre for Biomolecular Research at the Faculty of Science of Masaryk University. Jaroslav was a valued member of the CIISB Executive Committee during the past decade and his contributions to the CIISB development will never be forgotten. Professor Koča died after a short, insidious illness, leaving a permanent mark both on the personal lives of all who knew him, as well as on Czech and international science.

            In spring 2021 all large research infrastructures on the Roadmap of LRI of Czech Republic underwent an in-depth evaluation of their performance organized by the Ministry of Education, Youth, and Sports of the Czech Republic.  In July, we have received results of the consensus report of the international assessment committee. CIISB performance was evaluated using 13 evaluation and monitoring criteria with the overall grade 5 – excellent. This result assures CIISB a good starting position for financing in the upcoming period 2023-2029. Sincere thanks and appreciations go to all CIISB associates for their outstanding performance during the evaluation period.

            Thanks to funding provided by the OP VVV project UP CIISB new equipment was installed in several laboratories: fluorescence light microscope for imaging of fluorescently labelled samples at cryo-conditions and scanning transmission electron microscope (S/TEM)

Talos F200C at Cryo-electron microscopy core facility, AFM microscope JPK NanoWizard 4XP on a Leica DMi8 optical microscope with a fluorescence module in Nanobiotechnology core facility, and new crystallization hotel RI182 from Formulatrix in core facility for Biomolecular Interactions and Crystallization to mention just the most important new arrivals and upgrades.

            The access requests remain on the level comparable to previous years, as well as publication activity with 83 records on Web of Science till August 31, 2021. I hope that the currently optimistic numbers concerning the ongoing Covid-19 pandemics will stay at the same level and that the situation will allow return to a normal mode of our operations, with many in-person meetings and encounters, which are so essential in science and research. I wish you enjoyable autumn and I hope to meet you in person soon.

 

Vladimír Sklenář

News

Prof. Jaroslav Koča, founder of CEITEC Institute, passed away

Excellent structural biologist and founder of CEITEC Central European Institute of Technology Prof. RNDr. Jaroslav Koča, DrSc. died on Friday 2nd July 2021. His academic and scientific career is closely linked to Masaryk University, both the MU Faculty of Science and CEITEC, where he held several senior positions. He was also the founder and longtime director of the National Center for Biomolecular Research of the Faculty of Science of MU.

CIISB graded as excellent in the international peer-review assessment of Large Research Infrastructures of the Czech Republic 2021

On Monday, July 19, 2021, Masaryk university, as a coordinator of the Czech Infrastructure for Integrative Structural Biology (CIISB), received results of the consensus report of the international assessment committee. CIISB performance was evaluated using 13 evaluation and monitoring criteria with the overall grade 5 – excellent.

Widefield cryo-light microscope for correlative light and electron microscopy imaging

A fluorescence light microscope for imaging of fluorescently labeled samples at cryo-conditions has been installed at Cryo-electron microscopy core facility CEITEC MU (CEMCOF). The purchase of the instrument is a part of the facility upgrade and further development financed by UP CIISB project.

Artificial Intelligence outlines the future of structural biology

Three recent papers published on July 15, July 22, and August 20, 2021, two by DeepMind company in Nature (July) and one by David Baker and coworkers in Science (August), bring a breakthrough in structural biology comparable to previous major instrumental and methodological innovations.

New equipment in CF Nanobio

With funding provided by the CIISB project, the NanoBio Core Facility has been equipped with new instruments that will help scientists from different disciplines to tackle their projects.

ISIDORe project approved for funding

On 22 July 2021, the EC announced that 11 projects were short-listed for funding, with total funding of €120 million. The 11 projects involve 312 research teams from 40 countries in Europe and beyond, which are addressing the emergency request to tackle the most complex societal problems.

Open call for Research Group Leader position in Life Science at CEITEC Masaryk University

We are seeking to recruit a curiosity-driven research group leader, who is keen to establish an independent research group.The position is not limited by age or research area within Life Sciences. The tender is open until the end of August 2021.

Start of MOSBRI project

On the 1st of July 2021 the molecular-scale biophysics EU programme MOSBRI commences operation. One of the principal activities of the MOSBRI project is to offer free-of-charge transnational access for researchers in academia and industry. MOSBRI offers access to laboratories of excellence working on the architecture, dynamics, and interactions of the giant molecules of life (proteins, DNA, RNA, polysaccharides, lipids) at the crucial intermediate level between atomic-resolution structural descriptions and cellular-scale observations.

1st Instruct Remote Internships

These pilot internships are dedicated to early career researchers (PhD students or Postdocs in their first 5 years after graduation) for providing the opportunity to discuss own structural biology project(s) with one of the Instruct Centres’ leaders. This will give the intern the opportunity to train through tutoring.

Sad news - Richard R. Ernst passed away on Friday, June 4, 2021

Professor Richard Ernst, a Nobel Prize laureate 1991 in Chemistry for his contributions to the development of the methodology of high resolution nuclear magnetic resonance (NMR) spectroscopy and one of the most influential chemists and spectroscopist of past decades, died last Friday in his care home in Winterthur

New Crystallization Hotel RI182 at BIOCEV

Core Facility Crystallization of Proteins and Nucleic Acids of BIOCEV introduces new crystallization hotel RI182 dedicated to low temperatures.

The new crystallization hotel RI182 from Formulatrix was successfully tested and is now ready for all users of our crystallization facility. The hotel is able to store crystallization plates at 10 °C (SBS format, or Lipidic Cubic Phase) and image them according to the pre-set time schedule in visible light, polarized light, and UV light.

Multi-purpose S/TEM microscope installed at CEITEC MU

New scanning transmission electron microscope (S/TEM) has been recently installed at Cryo-electron microscopy core facility CEITEC MU. The purchase was carried out within infrastructural upgrade and development financed by UP CIISB project. The new ThermoScientific Talos F200C microscope will be used for both transmission electron microscopy imaging and scanning transmission electron microscopy applications. 

CIISB Access

Applications January - July 2021

  • 121 internal applications
  • 37 external applications
  • 8 applications from foreign users 

Application overwiev in total

  2016 2017 2018 2019 2020 2021
Internal users 123 178 177 147 183 121
External users 35 50 51 58 94 37
Foreign users 5 14 15 27 13 8

Save the date

CEITEC CF Day

21 October 2021 
9:00 AM – 16:00 PM

Save the date and join us during the CEITEC CF Day. Each CF will have 30 min. slot to present their services, training, user rules, new instrumentation, and other important information for users. We will prepare a hybrid format. Therefore, it will be possible to connect online via Zoom or have a physical meeting if all regulations allow. Detailed program and registration will be revealed soon, and you can indicate which CFs you will attend and in which mode (online/offline). We are looking forward to seeing you here!

Research Highlights

Nature Communications 2021

Anillin generates tens of pico-Newton forces to slide actin filaments 
a Schematic representation of the experimental setup. b Time-lapse fluorescence micrographs showing an actin bundle attached between two silica microspheres. The bundle is being stretched as the left microsphere is pulled leftwards by an optical trap. c Typical force time-trace (top) and the force-distance curve (bottom) corresponding to stretching of an anillin-actin filament bundle (experimental data points—magenta). Asymptotic forces of individual stretching steps, calculated by fitting an exponential to the force decays (as shown in d), are indicated by black crosses. These increase hyperbolically with increasing distance between the microspheres, and thus with decreasing overlap length L. The green line represents ~1/L fit to the data. d Temporal response of the construct to stretching and relaxation; the left optical trap is moved 100 nm away from the right trap and then, after ~7 s, moved back to the original position. The temporal profile of the longitudinal position of the left optical trap is shown together with the detected distance between the microspheres (top) and the detected force (bottom). e The detected force increased with decreasing overlap length before the filaments slid apart completely (distance to disconnection = 0). All events longer than six steps are plotted (n = 11 experiments indicated by different colours). Inset, anillin density in the overlap (fluorescence intensity of anillin per unit length of the overlap) at the start and the end of the bundle stretching. Grey boxplots represent raw data, green boxplots represent data after photobleaching correction (see Fig. S2e for the photobleaching estimation) (n = 10 experiments). Corresponding data points overlay the boxplots. f, g Force response of a pre-stretched actin-anillin bundle to a decrease (f) or increase (g) of anillin-GFP concentration. Schematic representation of the experiment (top) and temporal experimental data (bottom). Decrease of the concentration (n = 15 events in 14 experiments), increase of the concentration (n = 15 events in 14 experiments). Green curves are the experimental data, mean temporal profile is shown in magenta. Box and whisker plots show a significant decrease or increase in force between time points 0 and 30 s after a decrease (one-sided Wilcoxon test, p = 0.02) or increase (one-sided Wilcoxon test, p = 0.03) of anillin-GFP concentration. In e–gdata were represented as boxplots. Central marks represent median, top and bottom edges of the box indicate the 75th and 25th percentiles, respectively. Whiskers extend the most extreme points that are not considered outliers. Outliers are marked as grey circles.

Zdeněk Lánský Research Group

 Significance

Constriction of the cytokinetic ring, a circular structure of actin filaments, is an essential step during cell division. Mechanical forces driving the constriction are attributed to myosin motor proteins, which slide actin filaments along each other. However, in multiple organisms, ring constriction has been reported to be myosin independent. How actin rings constrict in the absence of motor activity remains unclear. Here, we demonstrate that anillin, a non­motor actin crosslinker, indispensable during cytokinesis, autonomously propels the contractility of actin bundles. Anillin generates contractile forces of tens of pico-Newtons to maximise the lengths of overlaps between bundled actin filaments. The contractility is enhanced by actin disassembly. When multiple actin filaments are arranged into a ring, this contractility leads to ring constriction. Our results indicate that passive actin crosslinkers can substitute for the activity of molecular motors to generate contractile forces in a variety of actin networks, including the cytokinetic ring.

Kučera, O., Siahaan, V., Janda, D.,  Dijkstra, S.H.,Pilátová, E.,  Zatecka, E.,  Diez, S., Braun, M., and Lansky, Z.: Anillin propels myosin-independent constriction of actin rings, Nature Comm. (2021)12:4595 | https://doi.org/10.1038/s41467-021-24474-1

Nature Communications 2021

Nature Index Journal

EH domains of AtEH1/Pan1 differ in their Ca2+-binding capacities. a Domain organization of AtEH1/Pan1 and AtEH2/Pan1. Both proteins contain two Eps15 homology domains (EH), a coiled-coil domain (CC), and an acidic (A)-motif. A schematic representation of a multiple sequence alignment (MSA) - shows strong conservation of the EH domains (blue lines) across the plant kingdom. Percentages indicate the relative number of identical amino acids. bg Cartoon representation of the X-ray structure of EH1.1 and NMR/all-atom molecular dynamics structure of EH1.2. Ions are shown as orange (Ca2+) or grey (Na+) spheres. Insets show the ion coordination in each EF-hand loop. Ca2+ coordinating residues and water molecules (W) are indicated in (c, d) and (f, g).

Savvas N. Savvides, Kostas Tripsianes, Roman Pleskot, and Daniel Van Damme Research Groups

Significance

Clathrin-mediated endocytosis (CME) is the gatekeeper of the plasma membrane. In contrast to animals and yeasts, CME in plants depends on the TPLATE complex (TPC), an evolutionary ancient adaptor complex. The mechanistic contribution of the individual TPC subunits to plant CME remains however elusive. In this study, we used a multidisciplinary approach to elucidate the structural and functional roles of the evolutionary conserved N-terminal Eps15 homology (EH) domains of the TPC subunit AtEH1/Pan1. By integrating high-resolution structural information obtained by X-ray crystallography and NMR spectroscopy with all-atom molecular dynamics simulations, we provide structural insight into the function of both EH domains. Both domains bind phosphatidic acid with a different strength, and only the second domain binds phosphatidylinositol 4,5-bisphosphate. Unbiased peptidome profiling by mass-spectrometry revealed that the first EH domain preferentially interacts with the double N-terminal NPF motif of a previously unidentified TPC interactor, the integral membrane protein Secretory Carrier Membrane Protein 5 (SCAMP5). Furthermore, we show that AtEH/Pan1 proteins control the internalization of SCAMP5 via this double NPF peptide interaction motif. Collectively, our structural and functional studies reveal distinct but complementary roles of the EH domains of AtEH/Pan1 in plant CME and connect the internalization of SCAMP5 to the TPLATE complex.

Yperman, K., Papageorgiou, A. C., Merceron, R., De Munck, S., Bloch, Y., Eeckhout,D., Jiang, Q., Tack, P., Grigoryan, R., Evangelidis, T., Van Leene, J., Vincze, L., , Vandenabeele, P., Vanhaecke, F., Potocký, M., De Jaeger, G., Savvides, S. N. , Tripsianes , K., Pleskot, R.  & Van Damme D.: Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding, Nature Comm. (2021) **, **  https://doi.org/10.1038/s41467-021-23314-6

 

Research Highlights Archive

Selected publications

D.B. Grabarczyk, et al.: HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain, Nat. Chem. Biol.,  20, 10.1038/s41589-021-00831-5 

M.P. Cheng, et al.: Thermal and pH Stabilities of i-DNA: Confronting in vitro Experiments with Models and In-Cell NMR Data, Angewandte Chemie-International Edition,  10, 10.1002/anie.202016801 

Perez-Illana, et al.:Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses,Sci. Adv., 7 (2021) 14, 10.1126/sciadv.abd9421 

M.S. Svetlov, et al.: Context-specific action of macrolide antibiotics on the eukaryotic ribosome, Nature Communications, 12 (2021) 14, 10.1038/s41467-021-23068-1 

Yperman, et al.:Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding,Nature Communications, 12 (2021) 11, 10.1038/s41467-021-23314-6 

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Masaryk University