Accueil > Research > Highlights > Archives > 2020
Towards the mechanism of action of the mitochondrial Complex I assembly complex
Assembly of the mitochondrial Complex I assembly complex suggests a regulatory role for deflavination. Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saidi M, Chretien A, Bacia-Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I and Soler-Lopez M. Angewandte chemie 2020 ; doi : 10.1002/anie.202011548 Contact : Irina Gutsche (Microscopic Imaging of Complex Assemblies Group) |
Structural and functional investigations of novel microbial rhodopsins
(1) High Resolution Structural Insights into the Heliorhodopsin Family. Kovalev K., Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Bueldt G, Gordeliy V. Nature Communications 2020 Feb 25 ;11:2137. (2) Molecular mechanism of light-driven sodium pumping. Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Bueldt G, Bamberg E, Gordeliy V. Nature Communications 2020 May 1 ; 11:2137. (3) Viral Rhodopsins 1 : A Unique Family of Light-Gated Ion Channels. Zabelskii D, Alekseev A, Kovalev K, Rankovic V, Balandin T, Soloviov D, Bratanov D, Savelyeva E, Podolyak E, Volkov D, Vaganova S, Astashkin R, Chizhov I, Yutin N, Rulev M, Popov A, Eria-Oliveira AS, Rokitskaya T, Mager T, Antonenko Y, Rosselli R, Armeev G, Shaitan K, Vivaudou M, Büldt G, Rodriguez-Valera F, Kirpichnikov M, Moser T, Koonin E, Offenhäusser A, Bamberg E, Gordeliy V. Nature Communications 2020 Nov 11 2020 ;11(1):5707. Contact : Valentin Gordeliy |
How do chaperones that they transport other proteins into mitochondria distinguish between their different "cargo proteins" ?
Structural basis of client specificity in mitochondrial membrane-protein chaperones. Sucec I, Wang Y, Dakhlaoui O, Weinhaupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B and Schanda P. Science Advances 2020 ;6(51):eabd0263 Contact : Paul Schanda (Biomolecular NMR Spectroscopy group) |
The HU protein of Deinococcus radiodurans imaged by AFM
Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy. Chen SWW, Banneville AS, Teulon JM, Timmins J and Pellequer JL. Nanoscale 2020 ;12(44):22628-22638 Contact : Jean-Luc Pellequer (Methods and Electron Microscopy group) |
Paul Schanda receives Varian Young Investigator Award
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IBS in the new health context
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SARS-CoV-2 : discovery of a new mode of transmission
DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist. Thépaut M, Luczkowiak J, Vivès C, Labiod N, Bally I, Lasala F, Grimoire Y, Fenel D, Sattin S, Thielens N, Schoehn G, Bernardi A, Delgado R, Fieschi F. doi : https://doi.org/10.1101/2020.08.09.242917 Contact : Franck Fieschi, UGA professor attached to the IBS (Membrane & Pathogens group) |
Cryo-EM structure of a key enzyme in action gives insights into the replication of a human pathogenic virus
Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational change. Benoît Arragain, Grégory Effantin, Piotr Gerlach , Juan Reguera , Guy Schoehn, Stephen Cusack, Hélène Malet. Nature Communications 2020 ;11(1):3590. doi : 10.1038/s41467-020-17349-4. Contact : Hélène Malet |
Following protein aggregation in real time by neutron spectroscopy
Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy. Pounot K, Chaaban H, Foderà V, Schirò G, Weik M, Seydel T. J.Phys.Chem.Lett. 11, 15 (2020) Contact : Martin Weik |
Hélène Malet appointed Junior Member of the Institut Universitaire de France
Viral replication and transcription are key steps of the viral cycle. Hélène Malet analyses the structure of viral proteins involved in these processes, in particular viral polymerases. During her thesis, carried out under the supervision of Dr. Bruno Canard at the AFMB, Marseille, she characterized by X-ray crystallography a polymerase structure of the Flaviviridae family, to which the Dengue virus belongs. Then, eager to learn a complementary method of structural biology, she did a post-doctorate in electron microscopy in the laboratory of Pr. Helen Saibil at Birkbeck College, London. Since then, she combines her interest in electron microscopy and viral replication. She undertook a post-doctoral fellowship on the structural analysis of Peribunyaviridae polymerase in the group of Dr. Stephen Cusack at EMBL Grenoble, before being recruited as an UGA Associate Professor at IBS in the team of Dr. Guy Schoehn in the Electron Microscopy and Methods group. Her research project focuses on the structural and functional analysis of bunyavirus replication, a viral order consisting of many highly pathogenic human viruses against which no drugs or vaccines are available. The latest advances in electron microscopy and the presence of state-of-the-art electron microscopes at IBS and ESRF enable to determine high-resolution structures of these essential enzymes thereby revealing their modes of action, a key step for the future development of anti-virals. In the longer term, this project aims to understand the mechanisms of interactions between viral proteins and host proteins involved in the regulation of viral replication, combining high-resolution electron microscopy of isolated particles and cellular electron microscopy, allowing an integrative view of these processes. This project is financially supported by the ANR (HiPathBunya) and will make an extensive use of IBS technology platforms managed by ISBG and funded by FRISBI and Gral. The appointment at the IUF will allow her to devote more time to this project. |
Molecular insight into the transmission of avian influenza to enable human infection
Molecular basis of host-adaptation interactions between influenza virus polymerase PB2 subunit and ANP32A. Zarco AC, Kalayil S, Maurin D, Salvi N, Delaforge E, Milles S, Jensen MR, Hart DJ, Cusack S, Blackledge M. Nature Communications ; 2020 Jul 21 ;11(1):3656 Contact : Martin Blackledge |
A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction
A microfluidic device for both on-chip dialysis protein crystallization and in situ X-ray diffraction. Junius N, Jaho S, Sallaz-Damaz Y, Borel F, Salmon JB, Budayova-Spano M. Lab on a Chip ; 20(2):296-310 Contact : Monika Budayova-Spano |
How a bacterium manages to go unnoticed and increase its virulence
Deletion of the zinc transporter lipoprotein AdcAII causes hyperencapsulation of Streptococcus pneumoniae associated with distinct alleles of the Type I restriction modification system. Claire Durmort, Giuseppe Ercoli, Elisa Ramos-Sevillano, Suneeta Chimalapati, Richard D. Haigh, Megan De Ste Croix, Katherine Gould, Jason Hinds, Yann Guerardel, Thierry Vernet, Marco Oggioni, and Jeremy S Brown. Mbio ; 11, 2 e00445-20 Contact : Claire Durmort |
Fluorescent proteins dance in the dark
Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State. Elke De Zitter, Jacqueline Ridard, Daniel Thedie, Virgile Adam, Bernard Levy, Martin Byrdin, Guillaume Gotthard, Luc Van Meervelt, Peter Dedecker, Isabelle Demachy, Dominique Bourgeois. Journal of the American Chemical Society, 2020, ja-2020-01880m (10.1021/jacs.0c01880) Contact : Dominique Bourgeois |
Structural basis for the catalytic activities of the multifunctional enzyme quinolinate synthase
Several crystal structures and the corresponding X-ray diffraction data for complexes of NadA with inhibitors, substrate analogs, at least one substrate (DHAP), product and potential intermediates of QA synthesis, are available from the Protein Data Bank. Based on a systematic analysis of these structures a coherent and comprehensive view of NadA catalysis is proposed in Coordination Chemistry Reviews by researchers from the Metallproteins group. Structural basis for the catalytic activities of the multifunctional enzyme quinolinate synthase. Volbeda A, Fontecilla-Camps JC. Coordination Chemistry Reviews, Volume 417, 15 August 2020, 213370. https://doi.org/10.1016/j.ccr.2020.213370 Contact : Juan Fontecilla-Camps, Anne Volbeda |
Structural insights into the mechanism of the radical SAM carbide synthase NifB, a key nitrogenase cofactor maturating enzyme
Structural insights into the mechanism of the radical SAM carbide synthase NifB, a key nitrogenase cofactor maturating enzyme. Sosa Fajardo A, Legrand P, Payá-Tormo L, Martin L, Pellicer Martinez MT, Echavarri-Erasun C, Vernède X, Rubio LM, Nicolet Y. J Am Chem Soc. 2020 May 30 ;142(25):11006-11012. Contact : Yvain Nicolet |
Molecular mechanism of light-driven sodium pumping
Molecular mechanism of light-driven sodium pumping. Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Büldt G, Bamberg E, Gordeliy V. Nature Communications 2020, 11:2137 Contact : Valentin Gordeliy |
COVID19 : IBS infoThe IBS re-opens step by step from 25 MayFollowing the french government’s announcement to lift coronavirus lockdown, the gradual reopening of the IBS is being organised in accordance with all safety measures and regulations recommended by our operating agencies. The IBS re-opens step by step from 25 May and should reach a level of about 50% physical presence on site after 4 weeks. It implies that part of your contacts are still teleworking and may be reached by email (to know more). IBS mobilized to fighting the SARS-CoV-2 Coronavirus pandemicIn order to contribute to the international scientific effort on Covid-19, IBS scientists have launched research programmes related to the SARS-CoV-2 Coronavirus (to know more). Seminars & eventsAll scientific events until end of July are either cancelled or postponed (to know more). InternshipsThe internships due to start after 17 March have been cancelled, and according to the UGA indications, transformed into bibliographic internships. |
Looking at long non-coding RNAs from a 3D structural perspective
In a collaborative work between the European Molecular Biology Laboratory (EMBL) in Grenoble with colleagues at the Max Delbruck Center in Berlin and the Institut de Biologie Structurale (CEA/CNRS/UGA) in Grenoble, researchers used complementary well established structural biology techniques to characterize the shape of lncRNA : atomic force microscopy, which identified captured individual RNA particles and inferred their size and compactness ; and small angle X-ray scattering, which characterized the RNA 3D shape in solution. The description of this new approach has been presented in a recent issue of Nature Protocols. This protocol is likely applicable to other long RNA molecules such as the untranslated RNAs (UTR) present in large RNA genome of viruses (details). Visualizing the functional 3D shape and topography of long non coding RNAs by single-particle atomic force microscopy and in solution hydrodynamic techniques. Uroda T, Chillon I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M. Nature Protocols ; doi : 10.1038/s41596-020-0323-7 |
Tribute to Jean-Luc FerrerThe IBS pays tribute to Jean-Luc Ferrer who passed away on April 21st, 2020 in his 55th year, after a long battle against the illness. He was a real pillar of the French CRG lines at ESRF, and an internationally recognized scientist in the field of structural biology.
From the very beginning, Jean-Luc Ferrer showed great interest and skills for technical and scientific aspects, sometimes very complex, of beamline construction and protein structure determination. For the latter, he initiated a very fruitful and long-lasting collaboration with Prof. Joseph P. Noel (La Jolla, USA) on the structural biology of phenylpropanoid synthesis in plants. He established collaborations with numerous French and international teams, but also developed his own research themes (consult J-L Ferrer list of publications). After Michel Roth’s retirement in 2001, Jean-Luc became responsible for the BM30A-FIP beamline. In this position, he always showed great creativity, determination and dynamism to highlight the assets of synchrotron radiation for protein crystallography. He was a pioneer in the automated analysis of diffraction data. In addition, he anticipated the automation of crystallography beamlines and helped develop the first sample loader based on a robotic arm, the CATS robot. Later, he had the idea to use the robot arm directly as a goniometer (the G-ROB robot), which allowed for the first time to diffract crystals in their crystallization plate, paving the way to ’in situ’ crystallography, crucial for the screening of ligands in the context of drug design. He ensured the technology transfer of these various innovations by creating the start-up company NatX-ray in Grenoble and San Diego. As a national platform, the FIP beamline has become over the years an essential equipment for the French and international protein crystallography communities. Jean-Luc Ferrer has headed the Synchrotron Group (GSY) at the IBS since its creation in 2011. As part of the ESRF-EBS program, which aims to obtain a new, extremely bright X-ray source, he sought and obtained funding for the FIP beamline reconstruction and renovation project in order to provide the best service to the community. He succeeded in driving this beamline project to completion with the launch of BM07-FIP2 next fall when ESRF reopens. Jean-Luc was a brilliant scientist, but he was also a simple and caring person, always in a good mood. Although reserved, he appreciated social events and was always up for an evening with friends. California was a place in the world where he liked to go and recharge his batteries, close to his family. He especially loved amusement parks, where he always chose the tallest rides. His kindness was sincere and created rare moments. Jean-Luc Ferrer maintained full professional commitment in spite of his illness, which deserves our greatest respect. His work to develop French structural biology and bring it to the highest international standards will leave a long-lasting impression on our community. The IBS as a whole salute the memory of this brilliant, yet modest, scientist and extend their sincere condolences to his family and loved ones. |
Bioinsecticides : does biological mean safe ?
Bti is a bioinsecticide – which means that it is produced by a living organism, the bacterium Bacillus thuringiensis subsp. israelensis. In the light of its apparent safety for non-target organisms, Bti has progressively replaced chemical insecticides that were historically used for mosquito control. In Europe, it has become in a decade the only insecticide authorized for mosquito control at the larval stage. In the context of the worldwide biodiversity crisis, the hegemony of Bti is worrying and a growing number of study question its status of a “safe” insecticide. This documentary aims at compiling the current knowledge on Bti impact on the environment and the ecosystems, notably enlightening available alternatives implemented in some countries. This reportage echoes a review article recently published in the journal Science of the Total Environment, dealing with the environmental and socioeconomic aspects of mosquito control using Bti : Environmental and socioeconomic effects of mosquito control in Europe using the biocide Bacillus thuringiensis subsp. israelensis (Bti). Brühl CA, Després L, Frör O, Patil CD, Poulin B, Tetreau G, Allgeier S. Sci Total Environ. 2020 Mar 21:137800. doi : 10.1016/j.scitotenv.2020.137800 |
A tightly controlled radical-based chemistry !
Structure-function of radical SAM enzymes ; from mechanism to biotechnological applications. Nicolet Y. Nature Catalysis ; 3 , 337–350 |
What role can Structural Biology play in the fight against Covid-19 ?
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Watching Measles virus factories at work in liquid droplets
Measles Virus Nucleo- and Phosphoproteins form Liquid-like Phase-Separated Compartments that Promote Nucleocapsid Assembly. Serafima Guseva Sigrid Milles, Malene Ringkjøbing Jensen, Nicola Salvi, Jean-Phillipe Kleman, Damien Maurin, Rob W.H. Ruigrok, Martin Blackledge. Science Advances ; Vol. 6, no. 14, eaaz7095 |
How an electron and a proton modulate protein binding to DNA
Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR. Crack JC, Amara P, Volbeda A, Mouesca JM, Rohac R, Pellicer Martinez MT, Huang CY, Gigarel O, Rinaldi C, Le Brun NE, Fontecilla-Camps JC. J Am Chem Soc, 142(11):5104-5116 (2020). |
Structural and functional insights into Cyt1Aa, a naturally crystallin insecticidal protein
Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade. Tetreau G, Banneville AS, Andreeva EA, Brewster AS, Hunter MS, Sierra RG, Teulon JM, Young ID, Burke N, Gruenewald TA, Beaudouin J, Snigireva I, Fernandez-Luna MT, Burt A, Park HW, Signor L, Bafna JA, Sadir R, Fenel D, Boeri-Erba E, Rosenthal M, Coquelle N, Burghammer M, Cascio D, Sawaya MR, Winterhalter M, Gratton E, Gutsch I, Federici B, Pellequer JL, Sauter NK, Colletier JP. Nature Communications ; 11, 1153 |
Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures
Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures. Eugenio de la Mora, Nicolas Coquelle, Charles S. Bury, Martin Rosenthal, James M. Holton, Ian Carmichael, Elspeth F. Garman, Manfred Burghammer, Jacques-Philippe Colletier, and Martin Weik . PNAS ; doi.org/10.1073/pnas.1821522117 |
Photoswitching mechanism of a fluorescent protein revealed by time-resolved serial femtosecond crystallography and transient absorption spectroscopy
Photoswitching mechanism of a fluorescent protein revealed by time-resolved serial femtosecond crystallography and transient absorption spectroscopy. Woodhouse J, Nass-Kovacs G, Coquelle N, Uriarte LM, Adam V, Barends TRM, Byrdin M,. de la Mora E, Doak RB, Feliks M, Field M, Fieschi F, Guillon V, Jakobs S, Joti Y, Macheboeuf P, Motomura K, Nass K, Owada S, Roome CM, Ruckebusch C, Schirò G, Shoeman RL, Thepaut M, Togashi T, Tono K, Yabashi M, Cammarata M, Foucar L, Bourgeois D, Sliwa M, Colletier JP, Schlichting I, Weik M. Nature Communications ; 11, 741 |