Soutenance de Thèse de Mohammad CHORFA (IBS/Groupe Synchrotron)
2026-03-30 09:00 - 11:00 (Europe/Paris) | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Effets de la dynamique structurale d’une famille de protéines fluorescentes infrarouges sur leurs propriétés de fluorescence
Résumé :
Ce travail de thèse consiste en une étude structurale approfondie d’une famille de protéines fluorescentes infrarouges (IFP) développées à partir du bactérophytochrome d’une bactérie Gram-négative du genre Bradyrhizobium, constituée de la protéine mIFP et de ses variants décalés vers le bleu iBlueberry et iBlueberry2. Les IFP présentent un fort intérêt en imagerie de corps entier en raison de l’existence d’une fenêtre optique des tissus entre 650 et 900 nm, au-dessus du domaine de longueur d’onde dans lequel l’hémoglobine et la déoxi-hémoglobine absorbent, et en-dessous du domaine dans lequel l’eau et les lipides absorbent et diffusent la lumière. Les protéines étudiées ici présentent un pic d’émission de fluorescence entre 660 et 720 nm.
Le bactériophytochrome et les IFP qui en sont dérivées utilisent la biliverdine, un produit du catabolisme des hèmes, comme chromophore afin d’absorber la lumière entre 640 et 690 nm. L’étude structurale a permis de montrer qu’une boucle localisée au voisinage de la biliverdine pouvait aborder un grand nombre de conformations, à la différence des autres phytochromes et IFP étudiés jusqu’à présent, où cette boucle ne semble posséder qu’une seule conformation. La conséquence de cette fluctuation conformationnelle est la présence d’une configuration du chromophore jamais encore observée menant à une conformation compacte du macrocycle formé par les quatre cycles pyrroles de la biliverdine, distincte de la conformation linéaire, ou étendue, habituellement observée. Les spectroscopies d’absorption UV-Visible et d’émissions de fluorescence in crystallo, c’est-à-dire directement appliquées aux cristaux, ont permis de montrer que la conformation compacte du chromophore menait à un pic d’émission de fluorescence au-delà de 760 nm pour iBlueberry et iBlueberry 2, et de 800 nm pour mIFP. Cette conformation semble être favorisé par l’empilement cristallin, et être seulement très faiblement peuplée en solution.
L’analyse des séquences de bactériophytochromes et d’IFP a permis de mettre en évidence la conformation particulière du coude beta au début de la boucle en question. L’ingénierie de ce coude beta chez un membre d’une autre famille de protéines fluorescentes a montré qu’elle permettait effectivement d’augmenter la plasticité de la boucle.
Ce travail donne des pistes pour modifier la configuration du chromophore au sein de la protéine par ingénierie rationnelle, notamment en utilisant des méthodes basées sur l’intelligence artificielle, et ainsi permettre d’obtenir de nouvelles IFPs avec des maxima d’émission en plein milieu de la fenêtre optique des tissus, afin de mieux utiliser celle-ci dans des expériences de marquage à plusieurs couleurs en imagerie tissulaire ou de corps entier.
Contact :ibs.seminaires@ibs.fr

Soutenance de Thèse de Espérance AHO (IBS/Groupe Structure et Activité des Glycosaminoglycanes)
2026-03-31 14:00 - 16:00 | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Structural and Functional effect of CXCL12/Heparan Sulfate Interactions at the Cell Surface
Résumé :
The glycocalyx is a protective layer covering the surface of cells, particularly endothelial cells, and represents a major regulator of cell-environment interactions. It functions as a mechanical barrier, a mechanosensor, and a signalling platform that controls vascular permeability. In inflammatory and tumor contexts, alterations in glycocalyx structure and density promote increased cell adhesion, extravasation, and metastatic dissemination. Structurally, the glycocalyx is composed of glycolipids, glycoproteins and proteoglycans bearing glycosaminoglycan (GAG) chains, including heparan sulfate (HS). These linear polysaccharides, organized into sulfated and non-sulfated domains, interact with numerous proteins, including growth factors and chemokines, thereby modulating their bioavailability and biological activity. Notably, chemokine-HS interactions are essential for the formation of chemotactic gradients involved in leukocyte recruitment, inflammatory extravasation, and tumor progression. The chemokine CXCL12 (stromal cell-derived factor-1, SDF-1), a member of the CXC chemokine family, exists as six distinct isoforms generated by alternative splicing of the CXCL12 gene. These isoforms share a common N-terminal sequence but differ in their C-terminal extensions, which influence their interactions with HS. Among them, CXCL12γ isoform, characterized by its exceptionally high affinity for HS, represent a particularly relevant candidate.
This work builds upon previous findings from our group showing, using biophysical approaches (QCM-D, FRAP), that CXCL12 is able to induce cross-linking of HS chains on biomimetic surfaces, resulting in HS rigidification, decreased layer thickness, and reduced HS lateral mobility. These observations suggest that chemokine-HS interactions can modify the physical properties of HS beyond a simple ligand-presentation role. The central hypothesis of this project is that binding of the CXCL12γ to HS induces remodelling of the endothelial glycocalyx at the cell surface thereby changing cellular mechanical properties and promoting immune cell adhesion. Here, we investigate the impact of CXCL12γ on HS organization across molecular, nanoscale, and cellular levels by combining biomimetic surfaces, biophysical approaches, super-resolution microscopy, and cell-based assays.
We show that CXCL12γ reorganizes HS chains at the endothelial cell surface and that all HS-binding sites are required for efficient HS rigidification and network reorganization. CXCL12γ-driven remodeling of the glycocalyx reduces HS thickness and alters its nanoscale topology, thereby promoting paracellular permeability and formation of adhesive platforms that facilitate leukocyte capture, and firm adhesion.
Contact : ibs.seminaires@ibs

Karine PHILIPPOT (Laboratoire de Chimie de Coordination du CNRS (LCC-CNRS), Toulouse, France)
2026-04-02 10:30 - 11:30 | DCM – Salle C209, DCM - Bât Chimie Recherche 301 rue de la Chimie, St Martin d'Hères, 38400, France
Design of nanocatalysts following molecular chemistry principles
Résumé :
Due to their singular properties and potential applications in various fields, considerable effort is being devoted to the design of metal-based nanomaterials. The « Metal Nanoparticle Engineering » team at LCC-CNRS (Toulouse, France) has developed an effective toolkit for the synthesis of controlled metal nanoparticles using concepts from molecular chemistry. This approach is based on the hydrogenation of organometallic or metallo-organic complexes under mild conditions (ambient temperature; 3 bar H2) in the presence of ligands as stabilising agents. (1) This approach makes it possible to obtain small nanoparticles (<10 nm) with controlled composition, either monometallic or bimetallic (alloy, core-shell, surface-decorated). These nanoparticles can be deposited on a support by simple impregnation or by direct synthesis in the presence of the chosen support (polymers, ionic liquids, silica, alumina, carbonaceous materials, etc.). These metal nanoparticle systems are suitable models for fundamental research. They find applications in various fields such as catalysis. (2,3) Non exhaustive examples concern biomass valorization (4), hydrogenation catalysis (4-6) including reduction of CO2, (7) or electrocatalytic (8-11) or photocatalytic (12-13) water splitting process.
References :
1 C. Amiens, D. Ciuculescu-Pradines, K. Philippot, Coord. Chem. Rev., 2016, 38, 409-432.
2 M. R. Axet, K. Philippot, Chem. Rev 2020, Chem. Rev. 2020, 120, 2, 1085-1145.
3 Nanoparticles in Catalysis: Advances in Synthesis and Applications, Wiley-VCH, K. Philippot & A. Roucoux (Eds.), 2021.
4 M. Cardona, P. Lecante, C. Dinoi, I. del Rosal, R. Poteau, K. Philippot, M. Rosa Axet, Green Chemistry, 2021, 23, 8480-8500.
5 C. J Abou-Fayssal, C. Fliedel, R. Poli, A. Riisager, K. Philippot, E. Manoury, Materials Today Chemistry, 2023, 34, 101752 (https://doi.org/10.1016/j.mtchem.2023.101752).
6 D. Krishnan, L. Schill, M. R. Axet, K. Philippot, A. Riisager, ChemCatChem 2024,16(4) : e20230144.
7 X.-P. Fu, L. Peres, J. Esvan, C. Amiens, K. Philippot, N. Yan, Nanoscale, 2021, 13, 8931-8939.
8 J. Creus, S. Drouet, S. Suriñach, P. Lecante, V. Collière, R. Poteau, K. Philippot, J.García-Antón, X. Sala, ACS Catalysis., 2018, 8, 11094-11102.
9 L. Mallón, J. Navarro-Ruiz, C. Cerezo-Navarrete, N. Romero, I. del Rosal, J. García-Antón, R. Bofill, L. M. Martínez-Prieto, K. Philippot, R. Poteau, X. Sala, ACS Applied Materials &
Interfaces 2025, 17(4), 6198-6210.
10 Nanoscale NiCu electrocatalyst for the hydrogen evolution reaction, T. Straistari, N. Romero, J. Esvan, M. Gil Sepulcre, C. Amiens, O. Rüdiger, S. Debeer, S. Cavaliere, K. Philippot, Nanoscale 2025, 17, 17592-17603.
11 Regulating NiFeOOH oxidation states through ruthenium incorporation, L. Mallón,1, L. Peres, N. Rivas, A. Garzón Manjón, C. Scheu, M. Gil-Sepulcre, O. Rüdiger, S. DeBeer, N. Romero, J.
Esvan, J. García-Antón, L. Rodríguez-Santiago, X. Solans-Monfort, R. Bofill, K. Philippot, L. Francàs, X. Sala, J. Mater. Chem. A, 2026, in press.
12 N. Romero, F. Sabuzi, M. Forchetta, M. Natali, R. Signorini, R. Bofill, L. Francàs, M. Gil-Sepulcre, O. Rüdiger, S. DeBeer, J. García-Antón, K. Philippot, P. Galloni, A. Sartorel, X. Sala, Green Chemistry 2025, 27, 4352-4368.
13 Dyadic Ru-based Nanomaterials for Visible Light-driven Photocatalytic Hydrogen Evolution, G. Martí, M. Aliqué, I. López, L. Francàs, R. Bofill, O. Schott, G. S. Hanan, N. Romero, K. Philippot, A. Llobet, M. Natali, J. García-Antón, X. Sala, Applied Surface Science, 2026, 716, 164621
Contact : carole.duboc@univ-grenoble-alpes.fr

Soutenance de Thèse de Alix HAUREZ / DCM (équipe CIRe)
2026-04-02 13:30 - 15:30 | DCM – Salle C209, DCM - Bât Chimie Recherche 301 rue de la Chimie, St Martin d'Hères, 38400, France
Electroréduction du CO2 en méthane par des nanoparticules de cuivre générées in-situ

Résumé : A venir

Contact : Nathalie.Camerino@univ-grenoble-alpes.fr

Carole ESCARTIN (directrice de recherche à NeuroPSI, CNRS, Université Paris-Saclay)
2026-04-02 16:00 - 18:30 | Laboratoire IJCLab – Auditorium Pierre Lehmann, Rue Ampère, Orsay cedex, 91898, France
Les cellules gliales dans les maladies neurodégénératives : rôles émergents et potentiel thérapeutique
Résumé :
Les neurones ne sont pas seuls dans le cerveau. A leur côté, plusieurs types de cellules, collectivement appelées « cellules gliales », remplissent de nombreux rôles essentiels pour le bon fonctionnement et la survie des neurones. Ces cellules leur apportent des substrats énergétiques, assurent la défense contre des pathogènes, éliminent certains déchets cellulaires, et même régulent la façon dont les neurones transmettent et traitent l’information nerveuse.
Au final, les cellules gliales qui restent souvent dans l’ombre des neurones, sont des partenaires actifs permettant au cerveau de fonctionner, mais aussi d’apprendre et de s’adapter.
Depuis plusieurs années, les chercheurs découvrent que ces cellules jouent aussi un rôle important dans de nombreuses maladies qui touchent le cerveau. En effet, ces cellules se transforment en contexte pathologique, elles sont dites « réactives ». Ces changements peuvent avoir des conséquences majeures – positives ou négatives – sur les neurones et leur survie.
Les cellules gliales sont l’objet d’études variées pour comprendre leurs rôles dans le cerveau sain et pathologique, ouvrant des nouvelles pistes thérapeutiques pour de nombreuses maladies cérébrales.
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Toutes les informations sont disponibles sur : https://indico.ijclab.in2p3.fr/event/12390/
Contact : louis.fayard@IJCLAB.INP3.FR

Juan FONTECILLA-CAMPS (IBS/Groupe Métalloprotéines)
2026-04-03 11:00 - 12:00 | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Origin and evolution of the eukaryotic cell : the emergence of cooperation, competition and altruisme
Résumé :

The evolutionary transition from prokaryotes to eukaryotes most likely involved the fusion of an archeon with a bacterium. One important consequence of this fusion was an increase in mean gene length in protists to about 1500 nucleotides, and corresponding 500 amino acids-long proteins. The subsequent evolution of plants and metazoans resulted in a lengthening of their genes (to over 10,000 nucleotides per gene in vertebrates). However, the coded proteins remained at an average length of also about 500 amino acids. The significance of the difference in gene length but constant protein size has been the subject of some controversy.
A second result of the evolutionary transition from prokaryotes to eukaryotes was the emergence of competition, cooperation and even altruism, between cells. These interactions cover a large spectrum going from single-cell organisms to mammals like us. Indeed, recent studies have shown that cancer cells do collaborate during tumor growth.​

These two subjects will be discussed during the seminar.​​​

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Les séminaires et soutenances sont ouverts à tous, notez toutefois que l’accès au campus EPN nécessite un avis de rendez-vous. Merci de remplir ce formulaire et de l’adresser, plus de 48h à l’avance, à ce contact. Pensez à vous munir d’une pièce d’identité le jour de votre visite.

Soutenance de Thèse de Eymeline PAGEOT (IRIG / IBS)
2026-04-21 14:00 - 16:00 | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Decoding chaos : a cryo-em walk through physarum polycephalum heterogeneous cell extracts
Résumé :

Cryo-electron microscopy (cryo-EM) has become a central method in structural biology for determining high-resolution structures of macromolecular assemblies. However, most cryo-EM studies still rely on highly purified samples, which limits the range of biological systems that can be investigated. In recent years, the analysis of cell extracts by single particle cryo-EM has emerged as an alternative strategy to explore the structural diversity of cellular proteins directly from complex mixtures. Despite its potential, this approach remains technically challenging due to the high level of heterogeneity present in such samples and the difficulty of identifying proteins without complementary techniques such as mass spectrometry.

​ The work presented in this thesis investigates the feasibility of using cryo-EM as a primary discovery tool to determine and identify protein structures directly from fractionated cell extracts. The study focuses on the plasmodial slime mould Physarum polycephalum, a non-model eukaryotic organism whose structural proteome is largely unexplored. In contrast to most previous studies in the field, protein identification relied solely on structural information derived from cryo-EM reconstructions.

Cell extracts from P. polycephalum were fractionated using biochemical separation methods and analysed by cryo-EM. Because such samples contain a wide range of proteins with different sizes, shapes, and abundances, dedicated image processing strategies were developed to address the challenges posed by particle heterogeneity and flexibility. Particular attention was given to 2D classification, particle sorting, and iterative particle picking strategies to improve the recovery of multiple particle orientations and increase the number of particles contributing to 3D reconstructions.

Using these approaches, fourteen macromolecular assemblies were identified and solved directly from the heterogeneous samples. In cases where the cryo-EM maps reached sufficient resolution, atomic models could be built ab initio. For lower-resolution structures, identification relied on structural comparison with known protein folds and structures predicted by generative tools. This work demonstrates that protein identity and putative function can be inferred directly from the structural information, opening the possibility of structure-based genome annotation in poorly characterised organisms.

Beyond the individual structures determined in this study, this work also outlines the methodological challenges associated with large-scale structural exploration of complex biological mixtures. The largely manual nature of several steps in the workflow currently limits the throughput of the approach. Strategies to automate key stages of the pipeline, including particle classification, initial model generation, and structural identification, are therefore discussed as important directions for future development.​

Finally, this work highlights the importance of community-driven analysis and open data sharing for the continued development of large-scale structural exploration approaches. Making both the raw cryo-EM data and the solved structures publicly available enables other researchers to further investigate the dataset, potentially identifying additional structures and improving the analysis using new computational methods, as well as enabling the development of the methods themselves. In the longer term, combining such « shotgun » cryo-EM approaches with advances in computational modelling and high-throughput data analysis may contribute to the systematic structural characterisation of cellular proteomes.

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Les séminaires et soutenances sont ouverts à tous, notez toutefois que l’accès au campus EPN nécessite un avis de rendez-vous. Merci de remplir ce formulaire et de l’adresser, plus de 48h à l’avance, à ce contact. Pensez à vous munir d’une pièce d’identité le jour de votre visite.

Anamaria NESCULEA (LBBE - Lyon)
2026-04-23 13:00 - 14:00 | IMAG – Salle de Réunion, 150 place du Torrent, St Martin d’Hères, 38400, France
Genomic correlates of convergent phenotypic evolution in birds
Contact : lucie.lamothe@univ-grenoble-alpes.fr

Soutenance de Thèse de Moritz KIRCHNER (IRIG / IBS)
2026-04-23 14:00 - 16:00 | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Molecular bases of a multiprotein assembly linking membrane biology to stress adaptation in enterobacteria
Résumé :

Enteric bacteria encounter a variety of stress factors when infecting their host. This includes but is not limited to acid stress, oxygen limitation and antibiotic stress. Bacteria counteract such stressors using various stress response systems. A central factor in the stress adaptation of enterobacteria is their cell envelope, in particular their cell membrane. A system of proteins which has been demonstrated to be involved in multiple stress adaptation pathways is the RavA-ViaA-LdcI triad in Escherichia coli. RavA and ViaA are two proteins with as of yet unknown function that have been shown to sensitise E. coli to aminoglycoside antibiotics under anaerobic conditions. RavA forms a large complex with LdcI, an inducible lysine decarboxylase which is one of the central enzymes involved in acid stress response of E. coli. Both RavA and ViaA have been shown to bind specific anionic lipids and their lipid binding capacity is strongly linked to their sensitising effect to aminoglycosides.
​This thesis presents the exploration of the connections these three proteins have to each other and their other binding partners by optical and electron microscopy in order to elucidate how their action leads to antibiotic sensitisation and what role their connection to the cell membrane and acid stress might play in this regard. It is shown that LdcI prefers to localise to the cell periphery to efficiently counteract acid stress and that mutations of its active site lead to large domain movements which might play a crucial role in its enzymatic activity. Furthermore, an investigation of liposome decoration by RavA and ViaA is presented, demonstrating the effect they have on membrane shape. In addition, the first cryo-EM structure of ViaA is presented using helical repeat proteins to stabilise the protein. Finally, predictions of RavA and ViaA protein-protein interactions in the inner E. coli membrane reveal possible functional targets of the proteins and the implications of these new possible avenues for action are discussed with regard of the microscopy investigations.

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Les séminaires et soutenances sont ouverts à tous, notez toutefois que l’accès au campus EPN nécessite un avis de rendez-vous. Merci de remplir ce formulaire et de l’adresser, plus de 48h à l’avance, à ce contact. Pensez à vous munir d’une pièce d’identité le jour de votre visite.

Mikhail ELTSOV (Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch)
2026-04-24 11:00 - 12:00 | IBS – Salle des séminaires, IBS 71 avenue des Martyrs, Grenoble, 38042, France
Seeing chromatin in situ : advances and challenges of human and machine vision
Résumé :
Using cryo-electron tomography of vitreous sections, we directly visualized nucleosomes and linker DNA trajectories in situ within flash frozen Drosophila embryos. Measurements of linker length and curvature revealed an irregular zigzag pattern of chromatin folding characterized by relatively limited linker bending. In favorable orientations, individual nucleosome particles and their structural variants could be identified without the need for structural averaging. Moreover, we detected particles containing a variable number of DNA gyres, ranging from fewer than one to up to three, resembling previously proposed non-octameric nucleosome-like particles.
To place these structural observations in the context of functional chromatin organization, we are developing computational approaches for nucleosome identification in cellular tomograms. We believe that our approach, Template Learning, based on training deep-learning networks on synthetic tomographic data, can provide a general framework for detecting small macromolecular complexes in crowded cellular environments.
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Hôte : Irina Gutsche (IBS/MICA)
