Institut de Biologie StructuraleGrenoble / France

2022

2022 Scientific Day and celebration of the IBS 30th Anniversary

2022 marks the 30th anniversary of the Institut de Biologie Structural and it was celebrated on June 16, 2022. For this special occasion, our annual scientific day took place in the Minactec amphitheater with retrospectives to honor three decades of achievement, as well as a part dedicated to current issues and perspectives. A particular focus was presented on crystallography (after a focus on NMR in 2019 and electron microscopy in 2021). In order to share these presentations with our academic and industrial partners, videos of some key moments will be put online on the IBS Youtube channel by the fall.

A poster session was also proposed during lunch, and news from former PhD students were broadcasted through videos. The IBS 2022 Young Researcher Prize was awarded to Benoit Arragain who performed his thesis in the MEM group on the Structural and functional analysis of Bunyavirales replication and transcription. Elda Bauda (second yeay PhD student in the ) received the Flash/Poster Prize for her work on the architecture of SpoIIIA-SpoIIQ, a nanomachine involved in bacterial sporulation.

The closing conference "From Curiosity to Perseverance" was given by two speakers from the Observatoire des Sciences de l’Univers de Grenoble and was dedicated to a decade of research on the surface of Mars.

To celebrate this 30th anniversary in a friendly atmosphere, a festive dinner was organized on the EPN campus for the IBS staff with games and musical animations.

Happy 30th Anniversary IBS !

Présentation plénière / Plenary presentation
Perspectives pour l’IBS par W. Weissenhorn / W. Weissenhorn envisions the futur
La fresque des 30 ans et ses auteurs / 3 decades IBS fresco and its authors
E. Bauda lors de la session poster / E. Bauda during poster session
Diner anniversaire / Celbration Diner

New issue for the IBS Newsletter

Find the June 2022 issue (in french only).

Radical chemistry : how radical SAM enzymes control it

Radical chemistry uses high-energy intermediates to carry out difficult reactions or even ones impossible to perform by the so-called polar chemistry. In nature, these reactions are fine-tuned by the structural environment within dedicated enzymes. Radical SAM proteins use an iron-sulfur cluster and S-adenosyl-L-methionine to initiate several radical reactions. These metalloproteins are notably involved in the biosynthesis of numerous cofactors and in the modification of peptides with antibiotic properties. The crystal structure of ThiH, involved in the anaerobic synthesis of vitamin B1, allowed us, by combining structural analysis and theoretical calculations, to understand how the substrate is recognized by the protein and how it is activated. In particular, hydrogen atom transfer is facilitated by a tunnel effect which allows the lowering of the activation barrier.
In conclusion, this work showed how a sum of small changes allowed to modify both the substrate selectivity and the specificity of a chemical reaction within this important family of proteins, thus paving the way to future molecular engineering approaches for more extensive use of these proteins as a biotechnological tool.

L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases. Amara P, Saragaglia C, Mouesca JM, Martin L, Nicolet Y. Nature Communications ; 13(1):2284

Contact : Yvain Nicolet( IBS/Metalloproteins group)

How an enzyme makes room for its substrates

In enzymes the "1st coordination sphere" describes the binding of substrate(s) to the active site whereas protein ligands that serve to correctly orient substrate(s) are generally defined as belonging to the "2nd coordination sphere". Protein elements that are found beyond that point, and still can affect catalysis, are part of the "outer coordination sphere". Quinolinate synthase is a good example of this classification because, besides having an active site and residues that accommodates its substrates, it modulates its catalytic site volume through remarkable internal conformational changes.

Quinolinate synthase : an example of the roles of the second and outer coordination spheres in enzyme catalysis. Juan C. Fontecilla-Camps* and Anne Volbeda. Chem Rev. (2022) doi : 10.1021/acs.chemrev.1c00869.

Contact : Juan Carlos Fontecilla-Camps (IBS/Metalloproteins group)

Extracellular endosulfatase HSulf-2 harbours a polysaccharide chain that muzzles its pro-tumoral activity

Polysaccharides of the Glycosaminoglycans (GAGs) family are essential components of cell surfaces and interstitial matrices. Among them, heparan sulfates (HS) are involved in a large number of biological functions, thanks to their ability to bind and regulate a wide array of signaling proteins. These mechanisms are tightly controlled by extracellular enzymes such as HSulf-2 endosulfatase, which modify the structure of HS and their interaction properties.
Researchers from IBS (Structure and activity of Glycosaminoglycans, Vivès team) and CEA-Biosanté (IMAC team, Odile Filhol-Cochet) have shown that HSulf-2 itself carries a GAG chain that acts as a modulator of its activity. As such, its removal (by mutation or enzymatic digestion) significantly increases the activity of the enzyme in vitro, and overexpression of Sulf-2 without a GAG chain in breast cancer cells promotes cell proliferation, migration and invasion, but also tumor growth and lung metastasis in vivo (figure).
This work sheds new light on the regulation of HS by HSulf-2, and for the development of antitumor strategies targeting these enzymes.

Extracellular endosulfatase Sulf-2 harbors a chondroitin/dermatan sulfate chain that modulates its enzyme activity. El Masri R, Seffouh A, Roelants C, Seffouh I, Gout E, Pérard J, Dalonneau F, Nishitsuji K, Noborn F, Nikpour M, Larson G, Crétinon Y, Friedel-Arboleas M, Uchimura K, Daniel R, Lortat-Jacob H, Filhol O, Vivès RR. Cell Reports ; 38(11):110516

Contact : Romain Vivès (IBS/Structure and Activity of Glycosaminoglycans Group)

Aromatic ring flipping : Solving a long-standing paradox in protein dynamics

Nuclear magnetic resonance (NMR) studies carried out in the 1970s surprisingly demonstrated that aromatic amino acids in proteins can undergo ring rotations (or so-called flips). Paradoxically, these aromatic amino acids are in many cases located in the tightly-packed protein core, where they engage in multiple interactions to maintain the protein fold and thereby function. At that time, it was proposed that large-scale protein “breathing motions” would be necessary in order to accommodate these ring rotations, however, until now the structural details of these motions have remained elusive.
By combining NMR spectroscopy and X-ray crystallography, researchers at the IBS (Protein Dynamics and Flexibility by NMR group) in collaboration with researchers at the IAB (Palencia’s group) have revealed for the first time the structural changes associated with aromatic ring rotations in the core of a protein. The study shows how a void volume is generated around the aromatic ring to allow the ring rotation to occur.
This discovery, published in Nature on february 16, has implications for both protein design and structure prediction by highlighting how even small alterations in the delicate balance of interactions stabilizing the core can lead to major changes in the protein structure.

Visualizing protein breathing motions associated with aromatic ring flipping. L. Mariño Pérez, F.S. Ielasi, L.M. Bessa, D. Maurin, J. Kragelj, M. Blackledge, N. Salvi, G. Bouvignies, A. Palencia*, M.R. Jensen*. Nature (2022). https://doi.org/10.1038/s41586-022-04417-6

Contact : Malene R. Jensen (IBS/Group Protein Dynamics and Flexibility by NMR)

An adenovirus-inspired vaccine platform to tackle COVID-19 and future pandemics

While mRNA-based vaccine solutions have emerged very quickly to manage the ’COVID-19’ crisis caused by SARS-CoV-2, they have logistical limitations (storage at -20°C, use within 6 hours) that do not allow a large-scale deployment. Moreover, a sterilizing immunity preventing a vaccinated person from transmitting the virus does not exist currently.
The IBS ’Adenovirus and Applications’ team led by Pascal Fender designed a non-infectious particle inspired by adenovirus capable of spontaneously and irreversibly displaying up to 60 copies of a glycosylated SARS-CoV-2 antigen. The structure of these new vaccines was solved by cryo-EM by the team of Guy Schoehn. In collaboration with Dalil Hannani from the TIM-C laboratory, immunizations were performed in mice with these new generation vaccines. The immune characterization by Pascal Poignard’s group showed that the display of antigens on the vaccine platform allowed a total and long-term neutralization of SARS-CoV-2.
The generation and characterization of this new vaccine technology, which can be rapidly adapted to all emerging viruses and therefore to future pandemics, are described in the journal Molecular Therapy.

Elicitation of potent SARS-CoV-2 neutralizing antibody responses through immunization with a versatile adenovirus-inspired multimerization platform. Chevillard C, Amen A, Besson S, Hannani D, Bally I, Dettling V, Gout E, Moreau CJ, Buisson M, Gallet S, Fenel D, Vassal-Stermann E, Schoehn G, Poignard P, Dagher MC, Fender P. Molecular Therapy https://doi.org/10.1016/j.ymthe.2022.02.011.

Contact : Pascal Fender (IBS/Methods and Electron Microscopy Group)

MetaboCraft : a gameplay to learn biochemical elements on your smart phone

After AminoCraft*, the entertaining application to memorize the chemical structure of the 20 amino acids, two IBS researchers, Ee de Rosny and Véronique Rossi, associate professors at Université Grenoble Alpes (UGA), in collaboration with Marie-France Breton (Cergy University) have developed MetaboCraft. The new challenge is to reconstitute the metabolic pathways of glycolysis and the Krebs cycle.
Like AminoCraft, the goal is to provide a great way for students to have fun while quickly learning biochemical elements on their smart phone, any time of the day, while commuting, in the street or on a coffee break.
MetaboCraft, which development was funded by the IDEX initiative from Grenoble Alpes University, is available for free, in French and English on Google play and App store.

*Since its release in September 2016, AminoCraft has been downloaded by over 100,000 users mainly aged between 18 and 24 years old. Most users are from France, followed by Algeria and the United States (february 2022 figures).

A new SARS CoV-2 spike lipid nanoparticle vaccine candidate provides efficient protection

The SARS-CoV-2 pandemic causes an ongoing global health crisis, which requires efficient and safe vaccination programs. In this study, researchers at the IBS (EBEV, CAID, MEM et M&P groups), in collaboration with IDMIT, Amsterdam University and Institut Pasteur, develop synthetic SARS-CoV2 S glycoprotein-coated liposomes that resemble virus-like particles. Soluble S glycoprotein trimers were stabilized by formaldehyde cross-linking and coated onto lipid vesicles (S-VLP). Immunization of cynomolgus macaques with the S-VLP nanoparticles induced high antibody titers with potent neutralizing activity against the vaccine strain, Alpha, Beta, and Gamma variants and TH1 CD4+ biased T cell responses.Upon the first and second immunization, antibodies were most mostly generated against the receptor binding domain (RBD), which is immunodominant, while the third immunization boosted non-RBD antibody titers. Sera from immunized animals showed potent neutralization against the vaccine strain and the Alpha variant after two immunizations and robust neutralization of Beta and Gamma strains after teh third immunization. Challenge of animals with SARS-CoV-2 shows a complete protection through sterilizing immunity, which may correlate with the detectio of mucosal immune antibody titers.
Thus, the S-VLP nanoparticle vaccine candidate is efficient and safe, based on a proven classical approach for further development and clinical testing.

Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects Macaques from infection. Guidenn Sulbaran, Pauline Maisonnasse, Axelle Amen, Gregory Effantin, Delphine Guilligay, Nathalie Dereuddre-Bosquet, Judith A. Burger, Meliawati Poniman, Marlyse Buisson, Sebastian Dergan Dylon, Thibaut Naninck, Julien Lemaître, Wesley Gros, Anne-Sophie Gallouët, Romain Marlin, Camille Bouillier, Vanessa Contreras, Francis Relouzat, Daphna Fenel, Michel Thepaut, Isabelle Bally, Nicole Thielens, Franck Fieschi, Guy Schoehn, Sylvie van der Werf, View ORCID ProfileMarit J. van Gils, Rogier W. Sanders, Pascal Poignard, Roger Le Grand, Winfried Weissenhorn. Cell Reports Medicine doi : 10.1016/j.xcrm.2022.100528

Contact : Winfried Weissenhorn (IBS/Entry and Budding of Enveloped Viruses group)

An essential interaction folds the nucleoprotein of the SARS-CoV-2 virus around its viral partner nsp3a

While vaccines target the molecular mechanisms responsible for infection of the cell via the Spike protein, it is equally important to target the viral replication machinery in patients already infected with the virus.
Researchers at the IBS (Protein Dynamics and Flexibility by NMR Group) characterised the nucleoprotein (N) of SARS-CoV-2, the most abundant protein produced by the virus. This protein has numerous functions that are essential for viral infection, including protection of the viral genome against the intracellular host immune system.
This natural target for the development of antiviral inhibitors comprises long intrinsically disordered domains which confer a high degree of flexibility – essential for its biochemical activity – but which also renders it particularly difficult to characterize using classical structural biology. IBS researchers used NMR (nuclear magnetic resonance) spectroscopy - used this technique to determine the structure and dynamics of the protein N and to describe its interaction with the viral partner nsp3a – an interaction that is essential for viral function.
The interaction implicates two distinct “linear motifs” within the central disordered domain of the protein N, which wrap the disordered domain around the partner nsp3a. This results in a substantial collapse of the dimensions of N, forming a highly compact, but still dynamic molecular assembly, which is also shown to regulate the ability to bind viral RNA.
The first molecular description of an essential interaction between two proteins from SARS-CoV-2 provides new insight which could inspire innovative inhibitory strategies to combat COVID-19. Press release (currently only available in French).

The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a, Science Advances ;8(3):eabm4034. doi : 10.1126/sciadv.abm4034

Contact : Martin Blackledge (IBS/Protein Dynamics and Flexibility by NMR Group)