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1. Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Author

M. Gomes, A. Fleck, A. Degaugue, F. Gourmelon, C. Léger, M. Aumont-Nicaise, A. Mesneau, H. Jean-Jacques, G. Hassaine, A. Urvoas, P. Minard, and M. Valerio-Lepiniec

Subjects
Medicine, Science
Abstract

Abstract Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approach to select the ensemble of folded proteins from an initial library. The thermostable CheY protein from Thermotoga maritima was chosen as scaffold. Four loops of CheY were diversified to create a new binding surface. The subset of the library giving rise to folded proteins was first selected using a natural protein partner of the template scaffold. Then, a gene shuffling approach based on a single restriction enzyme was used to recombine DNA sequences encoding these filtrated variants. Taken together, the filtration strategy and the shuffling of the filtrated sequences were shown to enrich the library in folded and stable sequences while maintaining a large diversity in the final library (Lib-Cheytins 2.1). Binders of the Oplophorus luciferase Kaz domain were then selected by phage display from the final library, showing affinities in the μM range. One of the best variants induced a loss of 92% of luminescent activity, suggesting that this Cheytin preferentially binds to the Kaz active site.

Published
2023
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7. Insight into microtubule nucleation from tubulin-capping proteins

Author

Campanacci, Valérie, Urvoas, Agathe, Cantos-Fernandes, Soraya, Aumont-Nicaise, Magali, Arteni, Ana-Andreea, Velours, Christophe, Valerio-Lepiniec, Marie, Dreier, Birgit, Plückthun, Andreas, Pilon, Antoine, Poüs, Christian, Minard, Philippe, and Gigant, Benoît

Published
2019

9. Geodetic Seafloor Positioning Using an Unmanned Surface Vehicle—Contribution of Direction-of-Arrival Observations

Author

Pierre Sakic, Clémence Chupin, Valérie Ballu, Thibault Coulombier, Pierre-Yves Morvan, Paul Urvoas, Mickael Beauverger, and Jean-Yves Royer

Subjects
seafloor geodesy, GNSS/acoustics, underwater positioning, unmanned surface vehicle, direction of acoustic ray arrivals, direction of arrival, Science
Abstract

Precise underwater geodetic positioning remains a challenge. Measurements combining surface positioning (GNSS) with underwater acoustic positioning are generally performed from research vessels. Here we tested an alternative approach using a small Unmanned Surface Vehicle (USV) with a compact GNSS/Acoustic experimental set-up, easier to deploy, and more cost-effective. The positioning system included a GNSS receiver directly mounted above an Ultra Short Baseline (USBL) module integrated with an inertial system (INS) to correct for the USV motions. Different acquisition protocols, including box-in circles around transponders and two static positions of the USV, were tested. The experiment conducted in the shallow waters (40 m) of the Bay of Brest, France, provided a data set to derive the coordinates of individual transponders from two-way-travel times, and direction of arrival (DOA) of acoustic rays from the transponders to the USV. Using a least-squares inversion, we show that DOAs improve single transponder positioning both in box-in and static acquisitions. From a series of short positioning sessions (20 min) over 2 days, we achieved a repeatability of ~5 cm in the locations of the transponders. Post-processing of the GNSS data also significantly improved the two-way-travel times residuals compared to the real-time solution.

Published
2021
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13. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools

Author

Figueroa, Maximiliano, Sleutel, Mike, Vandevenne, Marylene, Parvizi, Gregory, Attout, Sophie, Jacquin, Olivier, Vandenameele, Julie, Fischer, Axel W., Damblon, Christian, Goormaghtigh, Erik, Valerio-Lepiniec, Marie, Urvoas, Agathe, Durand, Dominique, Pardon, Els, Steyaert, Jan, Minard, Philippe, Maes, Dominique, Meiler, Jens, Matagne, André, Martial, Joseph A., and Van de Weerdt, Cécile

Published
2016
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15. Design, synthesis, and characterization of protein origami based on self-assembly of a brick and staple artificial protein pair

Author

Moreaud, Laureen, primary, Viollet, Sébastien, additional, Urvoas, Agathe, additional, Valerio-Lepiniec, Marie, additional, Mesneau, Agnès, additional, Li de la Sierra-Gallay, Inès, additional, Miller, Jessalyn, additional, Ouldali, Malika, additional, Marcelot, Cécile, additional, Balor, Stéphanie, additional, Soldan, Vanessa, additional, Meriadec, Cristelle, additional, Artzner, Franck, additional, Dujardin, Erik, additional, and Minard, Philippe, additional

Published
2023
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16. Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation

Author

Lei Shi, Andrea Cavagnino, Jean-Luc Rabefiraisana, Noureddine Lazar, Inès Li de la Sierra-Gallay, Françoise Ochsenbein, Marie Valerio-Lepiniec, Agathe Urvoas, Philippe Minard, Ivan Mijakovic, and Sylvie Nessler

Subjects
autophosphorylation, dimerization, regulatory mechanism, crystallization chaperone, spore development, Microbiology, QR1-502
Abstract

YabT is a serine/threonine kinase of the Hanks family from Bacillus subtilis, which lacks the canonical extracellular signal receptor domain but is anchored to the membrane through a C-terminal transmembrane helix. A previous study demonstrated that a basic juxtamembrane region corresponds to a DNA-binding motif essential for the activation of YabT trans-autophosphorylation. YabT is expressed during spore development and localizes to the asymmetric septum where it specifically phosphorylates essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. Using an artificial protein scaffold as crystallization helper, we determined the first crystal structure of this DNA-dependent bacterial protein kinase. This allowed us to trap the active conformation of the kinase domain of YabT. Using NMR, we showed that the basic juxtamembrane region of YabT is disordered in the absence of DNA in solution, just like it is in the crystal, and that it is stabilized upon DNA binding. In comparison with its closest structural homolog, the mycobacterial kinase PknB allowed us to discuss the dimerization mode of YabT. Together with phosphorylation assays and DNA-binding experiments, this structural analysis helped us to gain new insights into the regulatory activation mechanism of YabT.

Published
2019
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17. Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Author

Gomes, M., primary, Fleck, A., additional, Degaugue, A., additional, Gourmelon, F., additional, Léger, C., additional, Aumont-Nicaise, M., additional, Mesneau, A., additional, Jean-Jacques, H., additional, Hassaine, G., additional, Urvoas, A., additional, Minard, P., additional, and Valerio-Lepiniec, M., additional

Published
2023
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23. Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals

Author

Thébault, Stéphanie, primary, Lejal, Nathalie, additional, Dogliani, Alexis, additional, Donchet, Amélie, additional, Urvoas, Agathe, additional, Valerio-Lepiniec, Marie, additional, Lavie, Muriel, additional, Baronti, Cécile, additional, Touret, Franck, additional, Da Costa, Bruno, additional, Bourgon, Clara, additional, Fraysse, Audrey, additional, Saint-Albin-Deliot, Audrey, additional, Morel, Jessica, additional, Klonjkowski, Bernard, additional, de Lamballerie, Xavier, additional, Dubuisson, Jean, additional, Roussel, Alain, additional, Minard, Philippe, additional, Le Poder, Sophie, additional, Meunier, Nicolas, additional, and Delmas, Bernard, additional

Published
2022
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26. Binding of a Soluble meso-Tetraarylporphyrin to Human Galectin-7 Induces Oligomerization and Modulates Its Pro-Apoptotic Activity

Author

Philippe Egesborg, Clara Lafortune, Yves St-Pierre, Nicolas Doucet, Jean-Pierre Mahy, Agathe Urvoas, David Chatenet, Yossef López de los Santos, David N. Bernard, Matthew J. Cuneo, Rémy Ricoux, Myriam Létourneau, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation et Ingénierie des Protéines (MIP), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0303 health sciences, Porphyrin binding, Chemistry, [SDV]Life Sciences [q-bio], 030302 biochemistry & molecular biology, Cell, Biochemistry, Jurkat cells, Cell biology, 03 medical and health sciences, medicine.anatomical_structure, Molecular function, Apoptosis, medicine, Protein oligomerization, Human cancer, Galectin
Abstract

The selective targeting of protein-protein interactions remains a significant determinant for the proper modulation and regulation of cell apoptosis. Prototypic galectins such as human galectin-7 (GAL-7) are characterized by their ability to form homodimers that control the molecular fate of a cell by mediating subtle yet critical glycan-dependent interactions between pro- and anti-apoptotic molecular partners. Altering the structural architecture of GAL-7 can therefore result in resistance to apoptosis in various human cancer cells, further illustrating its importance in cell survival. In this study, we used a combination of biophysical and cellular assays to illustrate that binding of a water-soluble meso-tetraarylporphyrin molecule to GAL-7 induces protein oligomerization and modulation of GAL-7-induced apoptosis in human Jurkat T cells. Our results suggest that the integrity of the GAL-7 homodimer architecture is essential for its molecular function, in addition to providing an interesting porphyrin binding modulator for controlling apoptosis in mammalian cells.

Published
2020
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27. An Artificial Hemoprotein with Inducible Peroxidase‐ and Monooxygenase‐Like Activities

Author

Philippe Minard, Agathe Urvoas, Thibault Di Meo, Jean-Didier Maréchal, Kalani Kariyawasam, Marie Valerio-Lepiniec, Rémy Ricoux, Fabien Hammerer, Jean-Pierre Mahy, Giuseppe Sciortino, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation et Ingénierie des Protéines (MIP), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
Circular dichroism, Hemeprotein, Molecular model, oxidation, Stereochemistry, [SDV]Life Sciences [q-bio], Allosteric regulation, 010402 general chemistry, 01 natural sciences, Catalysis, Mixed Function Oxygenases, Metalloproteins, artificial metalloenzyme, biology, 010405 organic chemistry, Chemistry, Organic Chemistry, General Chemistry, Monooxygenase, artificial repeat proteins, 0104 chemical sciences, Peroxidases, Docking (molecular), Covalent bond, porphyrin biohybrid, biology.protein, inducible activity, Peroxidase
Abstract

A new inducible artificial metalloenzyme was obtained by covalent attachment of a Mn(III)-tetraphenylporphyrin to the artificial bidomain repeat protein (A3A3')Y26C. The biohybrid was characterized by MALDI-ToF MS, circular dichroism and UV-Vis spectroscopies. Its peroxidase activity was tested as well as its monooxygenase activity for the oxidation of thioanisole into sulfoxide by H 2 O 2 . Catalytic tests were performed on the original scaffold and with several co-catalysts a) additional imidazole, b) a specific αRep bA3-2 that induces the opening of the (A3A3') interdomain region and c) a αRep bA3-2 bearing a His6-Tag (His6-bA3-2), and the best activity was obtained with His6-bA3-2. The mechanism was rationalized by a molecular modeling study including protein-ligand docking and large scale molecular dynamics. It appears that: 1) the hydrophobic Mn-porphyrin fits well into the (A3A3')Y26C cavity, becomes protected by the protein and fully soluble in water; 2) the biohybrid alone does not display any catalytic activity, even in the presence of imidazole because of a closed conformation of the system; 3) opening of the binding site by bA3-2 leads to a noticeable activity and, 4) the best activity is obtained in the presence of the His6-Tag with one or two of the histidines able to coordinate to the metal acting as co-catalyst in the reactions. To the best of our knowledge, this constitutes the first example of an entirely artificial metalloenzyme with inducible peroxidase and monooxygenase activities, reminiscent of allosteric regulation of natural enzymatic pathways.

Published
2020
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31. Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors

Author

Magali Aumont-Nicaise, Liza Ammar Khodja, Magali Noiray, Agathe Urvoas, Philippe Minard, Valérie Campanacci, Benoît Gigant, Sylvie Lachkar, Patrick A. Curmi, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France., Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Structure et activité des biomolécules normales et pathologiques (SABNP), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité)

Subjects
Vinca, Centriole, Protein subunit, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Microtubules, Tubulin binding, 03 medical and health sciences, Tubulin, Microtubule, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, 030302 biochemistry & molecular biology, biology.organism_classification, Small molecule, Tubulin Modulators, 3. Good health, Domain (ring theory), biology.protein, Biophysics, Protein Binding
Abstract

Microtubule dynamics is regulated by various cellular proteins and perturbed by small molecule compounds. To what extent the mechanism of the former resembles that of the latter is an open question. We report here structures of tubulin bound to the PN2-3 domain of CPAP, a protein controlling the length of the centrioles. We show that an α-helix of the PN2-3 N-terminal region binds and caps the longitudinal surface of the tubulin β subunit. Moreover, a PN2-3 N-terminal stretch lies in a β-tubulin site also targeted by fungal and bacterial peptide-like inhibitors of the vinca domain, sharing a very similar binding mode with these compounds. Therefore, our results identify several characteristic features of cellular partners that bind to this site and highlight a structural convergence of CPAP with small molecule inhibitors of microtubule assembly.

Published
2021
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32. Photocatalytic Hydrogen Production and Carbon Dioxide Reduction Catalyzed by an Artificial Cobalt Hemoprotein

Author

Guillermo A. Oliveira Udry, Laura Tiessler-Sala, Eva Pugliese, Agathe Urvoas, Zakaria Halime, Jean-Didier Maréchal, Jean-Pierre Mahy, and Rémy Ricoux

Subjects
Inorganic Chemistry, artificial metalloenzymes, cobalt porphyrin, proton reduction, CO2 reduction, catalysis, Organic Chemistry, General Medicine, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, Catalysis, Computer Science Applications
Abstract

The covalent insertion of a cobalt heme into the cavity of an artificial protein named alpha Rep (αRep) leads to an artificial cobalt hemoprotein that is active as a catalyst not only for the photo-induced production of H2, but also for the reduction of CO2 in a neutral aqueous solution. This new artificial metalloenzyme has been purified and characterized by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS), circular dichroism, and UltraViolet–Visible spectroscopy. Using theoretical experiments, the structure of this biohybrid and the positioning of the residues near the metal complex were examined, which made it possible to complete the coordination of the cobalt ion by an axial glutamine Gln283 ligand. While the Co(III)–porphyrin catalyst alone showed weak catalytic activity for both reactions, 10 times more H2 and four times more CO2 were produced when the Co(III)–porphyrin complex was buried in the hydrophobic cavity of the protein. This study thus provides a solid basis for further improvement of these biohybrids using well-designed modifications of the second and outer coordination sphere by site-directed mutagenesis of the host protein.

Published
2022
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33. Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals

Author

Stéphanie Thébault, Nathalie Lejal, Alexis Dogliani, Amélie Donchet, Agathe Urvoas, Marie Valerio-Lepiniec, Muriel Lavie, Cécile Baronti, Franck Touret, Bruno Da Costa, Clara Bourgon, Audrey Fraysse, Audrey Saint-Albin-Deliot, Jessica Morel, Bernard Klonjkowski, Xavier de Lamballerie, Jean Dubuisson, Alain Roussel, Philippe Minard, Sophie Le Poder, Nicolas Meunier, Bernard Delmas, Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Virologie UMR1161 (VIRO), and École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
SARS-CoV-2, Recombinant Fusion Proteins, Immunology, Peptidyl-Dipeptidase A, Antiviral Agents, Microbiology, Recombinant Proteins, COVID-19 Drug Treatment, Virology, Spike Glycoprotein, Coronavirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Humans, Parasitology, Angiotensin-Converting Enzyme 2, Molecular Biology, Protein Binding
Abstract

The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named αReps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent αRep form (C2-foldon) display 0.1 nM affinities and EC50 of 8-18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, αReps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment.Author SummaryThe entry of SARS-CoV-2 in permissive cells is mediated by the binding of its spike to angiotensin-converting enzyme 2 (ACE2) on the cell surface. To select ligands able to block this interaction, we screened a library of phages encoding artificial proteins (named αReps) for binding to its receptor binding domain (RBD). Two of them were able to bind the RBD with high affinity and block efficiently the virus entry in cultured cells. Assembled αReps through covalent or non-covalent linkages blocked virus entry at lower concentration than their precursors (with around 20-fold activity increase for a trimeric αRep). These αReps derivates neutralize efficiently SARS-CoV-2 β, γ, δ and Omicron virus variants. Instillation of an αRep dimer in the nasal cavity effectively reduced virus replication in the hamster model of SARS-CoV-2 and pathogenicity.

Published
2022
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38. Geodetic Seafloor Positioning Using an Unmanned Surface Vehicle—Contribution of Direction-of-Arrival Observations

Author

Valérie Ballu, Paul Urvoas, Pierre-Yves Morvan, Thibault Coulombier, Clémence Chupin, Jean-Yves Royer, Pierre Sakic, Mickael Beauverger, GeoForschungsZentrum - Helmholtz-Zentrum Potsdam (GFZ), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), iXBLUE, Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Ultra-short baseline, 010504 meteorology & atmospheric sciences, Positioning system, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], Direction of arrival, Geodetic datum, direction of acoustic ray arrivals, 010502 geochemistry & geophysics, Geodesy, 01 natural sciences, direction of arrival, Data set, GNSS/acoustics, GNSS applications, unmanned surface vehicle, General Earth and Planetary Sciences, underwater positioning, lcsh:Q, seafloor geodesy, Underwater, lcsh:Science, Geology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Transponder
Abstract

International audience; Precise underwater geodetic positioning remains a challenge. Measurements combining surface positioning (GNSS) with underwater acoustic positioning are generally performed from research vessels. Here we tested an alternative approach using a small Unmanned Surface Vehicle (USV) with a compact GNSS/Acoustic experimental set-up, easier to deploy, and more cost-effective. The positioning system included a GNSS receiver directly mounted above an Ultra Short Baseline (USBL) module integrated with an inertial system (INS) to correct for the USV motions. Different acquisition protocols, including box-in circles around transponders and two static positions of the USV, were tested. The experiment conducted in the shallow waters (40 m) of the Bay of Brest, France, provided a data set to derive the coordinates of individual transponders from two-way-travel times, and direction of arrival (DOA) of acoustic rays from the transponders to the USV. Using a least-squares inversion, we show that DOAs improve single transponder positioning both in box-in and static acquisitions. From a series of short positioning sessions (20 min) over 2 days, we achieved a repeatability of ~5 cm in the locations of the transponders. Post-processing of the GNSS data also significantly improved the two-way-travel times residuals compared to the real-time solution.

Published
2021
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39. Binding of a Soluble

Author

Yossef, López de Los Santos, David N, Bernard, Philippe, Egesborg, Myriam, Létourneau, Clara, Lafortune, Matthew J, Cuneo, Agathe, Urvoas, David, Chatenet, Jean-Pierre, Mahy, Yves, St-Pierre, Rémy, Ricoux, and Nicolas, Doucet

Subjects
Binding Sites, Galectins, Apoptosis, In Vitro Techniques, Recombinant Proteins, Article, Molecular Docking Simulation, Jurkat Cells, Mesoporphyrins, Solubility, X-Ray Diffraction, Scattering, Small Angle, Humans, Protein Interaction Domains and Motifs, Protein Multimerization, Protein Structure, Quaternary, Nuclear Magnetic Resonance, Biomolecular, Protein Binding
Abstract

The selective targeting of protein-protein interactions remains a significant determinant for the proper modulation and regulation of cell apoptosis. Prototypic galectins such as human galectin-7 (GAL-7) are characterized by their ability to form homodimers that control the molecular fate of a cell by mediating subtle yet critical glycan-dependent interactions between pro- and anti-apoptotic molecular partners. Altering the structural architecture of GAL-7 can therefore result in resistance to apoptosis in various human cancer cells, further illustrating its importance in cell survival. In this study, we used a combination of biophysical and cellular assays to illustrate that binding of a water soluble meso-tetraarylporphyrin molecule to GAL-7 induces protein oligomerization and modulation of GAL-7-induced apoptosis in human Jurkat T cells. Our results suggest that the integrity of the GAL-7 homodimer architecture is essential for its molecular function, in addition to providing an interesting porphyrin binding modulator to control apoptosis in mammalian cells.

Published
2020

40. Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer

Author

Agathe Urvoas, Philippe Minard, Niko Hildebrandt, Igor L. Medintz, Corentin Leger, Kimihiro Susumu, Marie Valerio-Lepiniec, Akram Yahia-Ammar, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation et Ingénierie des Protéines (MIP), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), NanoBioPhotonics (NANO), Naval Research Laboratory (NRL), Chimie Organique et Bioorganique : Réactivité et Analyse (COBRA), Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Organique Fine (IRCOF), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE09-0015,NEUTRINOS,Suivi des interactions biologiques par détection optique ultrasensible à base de nanoparticules(2016), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Optical Sciences Division, Departments of Cell Biology and Chemistry, The Scripps Research Institute, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Organique Fine (IRCOF), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Scaffold protein, Conformational change, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 02 engineering and technology, Biosensing Techniques, 010402 general chemistry, 01 natural sciences, molecular diagnostics, Protein structure, Quantum Dots, Fluorescence Resonance Energy Transfer, [CHIM]Chemical Sciences, lanthanides, General Materials Science, protein structure, Terbium, binding assay, [PHYS]Physics [physics], Chemistry, Ligand binding assay, General Engineering, molecular ruler, 021001 nanoscience & nanotechnology, Acceptor, 0104 chemical sciences, Förster resonance energy transfer, Semiconductors, Quantum dot, FRET, Biophysics, 0210 nano-technology, Biosensor
Abstract

Publisher: American Chemical Society; International audience; Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprised of small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET-switches were used in a separation-free solution-phase assay to quantify different protein targets at subnanomolar concentrations and measure the conformational changes with subnanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live cell imaging of ligand-receptor interactions.

Published
2020
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43. Geodetic Seafloor Positioning Using an Unmanned Surface Vehicle—Contribution of Direction-of-Arrival Observations

Author

Sakic, Pierre, Chupin, Clémence, Ballu, Valérie, Coulombier, Thibault, Morvan, Pierre-yves, Urvoas, Paul, Beauverger, Mickael, Royer, Jean-yves, Sakic, Pierre, Chupin, Clémence, Ballu, Valérie, Coulombier, Thibault, Morvan, Pierre-yves, Urvoas, Paul, Beauverger, Mickael, and Royer, Jean-yves

Abstract

Precise underwater geodetic positioning remains a challenge. Measurements combining surface positioning (GNSS) with underwater acoustic positioning are generally performed from research vessels. Here we tested an alternative approach using a small Unmanned Surface Vehicle (USV) with a compact GNSS/Acoustic experimental set-up, easier to deploy, and more cost-effective. The positioning system included a GNSS receiver directly mounted above an Ultra Short Baseline (USBL) module integrated with an inertial system (INS) to correct for the USV motions. Different acquisition protocols, including box-in circles around transponders and two static positions of the USV, were tested. The experiment conducted in the shallow waters (40 m) of the Bay of Brest, France, provided a data set to derive the coordinates of individual transponders from two-way-travel times, and direction of arrival (DOA) of acoustic rays from the transponders to the USV. Using a least-squares inversion, we show that DOAs improve single transponder positioning both in box-in and static acquisitions. From a series of short positioning sessions (20 min) over 2 days, we achieved a repeatability of ~5 cm in the locations of the transponders. Post-processing of the GNSS data also significantly improved the two-way-travel times residuals compared to the real-time solution.

Published
2021
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47. Binding of a Soluble meso-Tetraarylporphyrin to Human Galectin-7 Induces Oligomerization and Modulates Its Pro-Apoptotic Activity

Author

López de los Santos, Yossef, primary, Bernard, David N., additional, Egesborg, Philippe, additional, Létourneau, Myriam, additional, Lafortune, Clara, additional, Cuneo, Matthew J., additional, Urvoas, Agathe, additional, Chatenet, David, additional, Mahy, Jean-Pierre, additional, St-Pierre, Yves, additional, Ricoux, Rémy, additional, and Doucet, Nicolas, additional

Published
2020
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