Protein Engineering and Modeling

Bousmah, Yasmina, Magali Noiray, Hadrien Jalaber, Hélène Pasquier, Marie Béatrice Valerio-Lepiniec, Agathe Urvoas, and Marie Erard. 2024. “PH Sensitivity of YFPs Is Reduced upon AlphaRep Binding: Proof of Concept in Vitro and in Living Cells.” Chembiochem: A European Journal of Chemical Biology, July, e202400287. https://doi.org/10.1002/cbic.202400287.

Gay, Rémy, Yannick Masson, Wadih Ghattas, Guillermo A. Oliveira Udry, Christian Herrero, Agathe Urvoas, Jean-Pierre Mahy, and Rémy Ricoux. 2024. “Binding and Stabilization of a Semiquinone Radical by an Artificial Metalloenzyme Containing a Binuclear Copper (II) Cofactor.” Chembiochem: A European Journal of Chemical Biology, April, e202400139. https://doi.org/10.1002/cbic.202400139.

Rump, Airi, Kristel Ratas, Tuuli Katarina Lepasepp, Jaanus Suurväli, Olli-Pekka Smolander, Katrin Gross-Paju, Toomas Toomsoo, Jean Kanellopoulos, and Sirje Rüütel Boudinot. 2023. “Sex-Dependent Expression Levels of VAV1 and P2X7 in PBMC of Multiple Sclerosis Patients.” Scandinavian Journal of Immunology 98 (2): e13283. https://doi.org/10.1111/sji.13283.

Moreaud, Laureen, Sébastien Viollet, Agathe Urvoas, Marie Valerio-Lepiniec, Agnès Mesneau, Inès Li de la Sierra-Gallay, Jessalyn Miller, et al. 2023. “Design, Synthesis, and Characterization of Protein Origami Based on Self-Assembly of a Brick and Staple Artificial Protein Pair.” Proceedings of the National Academy of Sciences of the United States of America 120 (11): e2218428120. https://doi.org/10.1073/pnas.2218428120.

Gomes, M., A. Fleck, A. Degaugue, F. Gourmelon, C. Léger, M. Aumont-Nicaise, A. Mesneau, et al. 2023. “Design of an Artificial Phage-Display Library Based on a New Scaffold Improved for Average Stability of the Randomized Proteins.” Scientific Reports 13 (1): 1339. https://doi.org/10.1038/s41598-023-27710-4.

Udry, Guillermo A. Oliveira, Laura Tiessler-Sala, Eva Pugliese, Agathe Urvoas, Zakaria Halime, Jean-Didier Maréchal, Jean-Pierre Mahy, and Rémy Ricoux. 2022. “Photocatalytic Hydrogen Production and Carbon Dioxide Reduction Catalyzed by an Artificial Cobalt Hemoprotein.” International Journal of Molecular Sciences 23 (23): 14640. https://doi.org/10.3390/ijms232314640.

Onésime, Djamila, Léa Vidal, Stéphane Thomas, Céline Henry, Véronique Martin, Gwenaëlle André, Piotr Kubiak, Philippe Minard, Ewelina Celinska, and Jean-Marc Nicaud. 2022. “A Unique, Newly Discovered Four-Member Protein Family Involved in Extracellular Fatty Acid Binding in Yarrowia Lipolytica.” Microbial Cell Factories 21 (1): 200. https://doi.org/10.1186/s12934-022-01925-y.

Mellouk, Amine, Tom Hutteau-Hamel, Julie Legrand, Hanaa Safya, Mohcine Benbijja, Françoise Mercier-Nomé, Karim Benihoud, Jean M. Kanellopoulos, and Pierre Bobé. 2022. “P2X7 Purinergic Receptor Plays a Critical Role in Maintaining T-Cell Homeostasis and Preventing Lupus Pathogenesis.” Frontiers in Immunology 13 (September). https://www.frontiersin.org/articles/10.3389/fimmu.2022.957008.

Thébault, Stéphanie, Nathalie Lejal, Alexis Dogliani, Amélie Donchet, Agathe Urvoas, Marie Valerio-Lepiniec, Muriel Lavie, et al. 2022. “Biosynthetic Proteins Targeting the SARS-CoV-2 Spike as Anti-Virals.” PLOS Pathogens 18 (9): e1010799. https://doi.org/10.1371/journal.ppat.1010799.

Campanacci, Valérie, Agathe Urvoas, Liza Ammar Khodja, Magali Aumont-Nicaise, Magali Noiray, Sylvie Lachkar, Patrick A. Curmi, Philippe Minard, and Benoît Gigant. 2022. “Structural Convergence for Tubulin Binding of CPAP and Vinca Domain Microtubule Inhibitors.” Proceedings of the National Academy of Sciences 119 (19): e2120098119. https://doi.org/10.1073/pnas.2120098119.

Kanellopoulos, Jean M., and David M. Ojcius. 2022. “The Ins and Outs of T Cell Signaling.” Biomedical Journal, April. https://doi.org/10.1016/j.bj.2022.04.002.

Rieux-Laucat, Frédéric, Jean M. Kanellopoulos, and David M. Ojcius. 2021. “Scaling the Tips of the ALPS.” Biomedical Journal, August, S2319-4170(21)00102-5. https://doi.org/10.1016/j.bj.2021.08.002.

Kanellopoulos, Jean M., and David M. Ojcius. 2021. “Neither B Cell nor T Cell - The Unique Group of Innate Lymphoid Cells.” Biomedical Journal 44 (2): 112–14. https://doi.org/10.1016/j.bj.2021.04.001.

Douguet, Laetitia, Serena Janho dit Hreich, Jonathan Benzaquen, Laetitia Seguin, Thierry Juhel, Xavier Dezitter, Christophe Duranton, et al. 2021. “A Small-Molecule P2RX7 Activator Promotes Anti-Tumor Immune Responses and Sensitizes Lung Tumor to Immunotherapy.” Nature Communications 12 (January). https://doi.org/10.1038/s41467-021-20912-2.

Kanellopoulos, Jean M., Cássio Luiz Coutinho Almeida-da-Silva, Sirje Rüütel Boudinot, and David M. Ojcius. 2021. “Structural and Functional Features of the P2X4 Receptor: An Immunological Perspective.” Frontiers in Immunology 12: 645834. https://doi.org/10.3389/fimmu.2021.645834.

López de Los Santos, Yossef, David N. Bernard, Philippe Egesborg, Myriam Létourneau, Clara Lafortune, Matthew J. Cuneo, Agathe Urvoas, et al. 2020. “Binding of a Soluble Meso-Tetraarylporphyrin to Human Galectin-7 Induces Oligomerization and Modulates Its Pro-Apoptotic Activity.” Biochemistry 59 (48): 4591–4600. https://doi.org/10.1021/acs.biochem.0c00736.

Leger, Corentin, Akram Yahia-Ammar, Kimihiro Susumu, Igor L. Medintz, Agathe Urvoas, Marie Valerio-Lepiniec, Philippe Minard, and Niko Hildebrandt. 2020. “Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium–To–Quantum Dot Förster Resonance Energy Transfer.” ACS Nano 14 (5): 5956–67. https://doi.org/10.1021/acsnano.0c01410.

Fernandez, Maxence, Agathe Urvoas, Pascale Even-Hernandez, Agnès Burel, Cristelle Mériadec, Franck Artzner, Tahar Bouceba, Philippe Minard, Erik Dujardin, and Valérie Marchi. 2020. “Hybrid Gold Nanoparticle-Quantum Dot Self-Assembled Nanostructures Driven by Complementary Artificial Proteins.” Nanoscale 12 (7): 4612–21. https://doi.org/10.1039/c9nr09987e.

Kariyawasam, Kalani, Thibault Di Meo, Fabien Hammerer, Marie Valerio‐Lepiniec, Giuseppe Sciortino, Jean-Didier Maréchal, Philippe Minard, Jean-Pierre Mahy, Agathe Urvoas, and Rémy Ricoux. 2020. “An Artificial Hemoprotein with Inducible Peroxidase- and Monooxygenase-Like Activities.” Chemistry – A European Journal 26 (65): 14929–37. https://doi.org/https://doi.org/10.1002/chem.202002434.

Rump, Airi, Olli Pekka Smolander, Sirje Rüütel Boudinot, Jean M. Kanellopoulos, and Pierre Boudinot. 2020. “Evolutionary Origin of the P2X7 C-Ter Region: Capture of an Ancient Ballast Domain by a P2X4-Like Gene in Ancient Jawed Vertebrates.” Frontiers in Immunology 11: 113. https://doi.org/10.3389/fimmu.2020.00113.

Prasad, Janak, Sébastien Viollet, Kargal L. Gurunatha, Agathe Urvoas, Agathe C. Fournier, Marie Valerio-Lepiniec, Cécile Marcelot, Bulent Baris, Philippe Minard, and Erik Dujardin. 2019. “Directed Evolution of Artificial Repeat Proteins as Habit Modifiers for the Morphosynthesis of (111)-Terminated Gold Nanocrystals.” Nanoscale 11 (37): 17485–97. https://doi.org/10.1039/C9NR04497C.

Campanacci, Valérie, Agathe Urvoas, Soraya Cantos-Fernandes, Magali Aumont-Nicaise, Ana-Andreea Arteni, Christophe Velours, Marie Valerio-Lepiniec, et al. 2019. “Insight into Microtubule Nucleation from Tubulin-Capping Proteins.” Proceedings of the National Academy of Sciences of the United States of America 116 (20): 9859–64. https://doi.org/10.1073/pnas.1813559116.

Campanacci, Valerie, Agathe Urvoas, Tanja Consolati, Soraya Cantos-Fernandes, Magali Aumont-Nicaise, Marie Valerio-Lepiniec, Thomas Surrey, Philippe Minard, and Benoit Gigant. 2019. “Selection and Characterization of Artificial Proteins Targeting the Tubulin Alpha Subunit.” Structure 27 (3): 497–506. https://doi.org/10.1016/j.str.2018.12.001.

Léger, Corentin, Thibault Di Meo, Magali Aumont-Nicaise, Christophe Velours, Dominique Durand, Ines Li de la Sierra-Gallay, Herman van Tilbeurgh, et al. 2019. “Ligand-Induced Conformational Switch in an Artificial Bidomain Protein Scaffold.” Scientific Reports 9 (1): 1178. https://doi.org/10.1038/s41598-018-37256-5.

Di Meo, Thibault, Kalani Kariyawasam, Wadih Ghattas, Marie Valerio-Lepiniec, Giuseppe Sciortino, Jean-Didier Marechal, Philippe Minard, Jean-Pierre Mahy, Agathe Urvoas, and Remy Ricoux. 2019. “Functionalized Artificial Bidomain Proteins Based on an Alpha-Solenoid Protein Repeat Scaffold: A New Class of Artificial Diels-Alderases.” Acs Omega 4 (2): 4437–47. https://doi.org/10.1021/acsomega.8b03448.

Minard, Philippe. 2019. “The directed evolution of proteins.” Medecine Sciences: M/S 35 (2): 169–75. https://doi.org/10.1051/medsci/2019007.

Martin, Elodie, Majid Amar, Carine Dalle, Ihsen Youssef, Celine Boucher, Caroline Le Duigou, Matthias Brueckner, et al. 2019. “New Role of P2X7 Receptor in an Alzheimer’s Disease Mouse Model.” Molecular Psychiatry 24 (1): 108–25. https://doi.org/10.1038/s41380-018-0108-3.

Shi, Lei, Andrea Cavagnino, Jean-Luc Rabefiraisana, Noureddine Lazar, Inès Li de la Sierra-Gallay, Françoise Ochsenbein, Marie Valerio-Lepiniec, et al. 2019. “Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus Subtilis Provides New Insights in Its DNA-Dependent Activation.” Frontiers in Microbiology 9: 3014. https://doi.org/10.3389/fmicb.2018.03014.

Paalme, Viiu, Airi Rump, Kati Mädo, Marina Teras, Birgit Truumees, Helen Aitai, Kristel Ratas, et al. 2019. “Human Peripheral Blood Eosinophils Express High Levels of the Purinergic Receptor P2X4.” Frontiers in Immunology 10: 2074. https://doi.org/10.3389/fimmu.2019.02074.

Grzela, Renata, Julien Nusbaum, Sonia Fieulaine, Francesco Lavecchia, Michel Desmadril, Naima Nhiri, Alain Van Dorsselaer, et al. 2018. “Peptide Deformylases from Vibrio Parahaemolyticus Phage and Bacteria Display Similar Deformylase Activity and Inhibitor Binding Clefts.” Biochimica Et Biophysica Acta 1866 (2): 348–55. https://doi.org/10.1016/j.bbapap.2017.10.007.

Chevrel, Anne, Agnes Mesneau, Dyana Sanchez, Louisa Celma, Sophie Quevillon-Cheruel, Andrea Cavagnino, Sylvie Nessler, et al. 2018. “Alpha Repeat Proteins (ΑRep) as Expression and Crystallization Helpers.” Journal of Structural Biology 201 (2): 88–99. https://doi.org/10.1016/j.jsb.2017.08.002.

Chang, Hung-Ju, Pauline Mayonove, Agustin Zavala, Angelique De Visch, Philippe Minard, Martin Cohen-Gonsaud, and Jerome Bonnet. 2018. “A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria.” ACS Synthetic Biology 7 (1): 166–75. https://doi.org/10.1021/acssynbio.7b00266.

Safya, Hanaa, Amine Mellouk, Julie Legrand, Sylvain M. Le Gall, Mohcine Benbijja, Colette Kanellopoulos-Langevin, Jean M. Kanellopoulos, and Pierre Bobé. 2018. “Variations in Cellular Responses of Mouse T Cells to Adenosine-5’-Triphosphate Stimulation Do Not Depend on P2X7 Receptor Expression Levels but on Their Activation and Differentiation Stage.” Frontiers in Immunology 9: 360. https://doi.org/10.3389/fimmu.2018.00360.

Hadpech, Sudarat, Sawitree Nangola, Koollawat Chupradit, Kanda Fanhchaksai, Wilhelm Furnon, Agathe Urvoas, Marie Valerio-Lepiniec, et al. 2017. “Alpha-Helicoidal HEAT-like Repeat Proteins (ΑRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation.” Scientific Reports 7 (1): 16335. https://doi.org/10.1038/s41598-017-16451-w.

Suurväli, Jaanus, Pierre Boudinot, Jean Kanellopoulos, and Sirje Rüütel Boudinot. 2017. “P2X4: A Fast and Sensitive Purinergic Receptor.” Biomedical Journal 40 (5): 245–56. https://doi.org/10.1016/j.bj.2017.06.010.

Di Meo, Thibault, Wadih Ghattas, Christian Herrero, Christophe Velours, Philippe Minard, Jean-Pierre Mahy, Rémy Ricoux, and Agathe Urvoas. 2017. “ΑRep A3: A Versatile Artificial Scaffold for Metalloenzyme Design.” Chemistry (Weinheim an Der Bergstrasse, Germany) 23 (42): 10156–66. https://doi.org/10.1002/chem.201701518.

Figliuolo, Vanessa R., Luiz Eduardo Baggio Savio, Hanaa Safya, Hayandra Nanini, Cláudio Bernardazzi, Alessandra Abalo, Heitor S. P. de Souza, et al. 2017. “P2X7 Receptor Promotes Intestinal Inflammation in Chemically Induced Colitis and Triggers Death of Mucosal Regulatory T Cells.” Biochimica Et Biophysica Acta 1863 (6): 1183–94. https://doi.org/10.1016/j.bbadis.2017.03.004.

Gurunatha, Kargal L., Agathe C. Fournier, Agathe Urvoas, Marie Valerio-Lepiniec, Valérie Marchi, Philippe Minard, and Erik Dujardin. 2016. “Nanoparticles Self-Assembly Driven by High Affinity Repeat Protein Pairing.” ACS Nano 10 (3): 3176–85. https://doi.org/10.1021/acsnano.5b04531.

Ghattas, Wadih, Lur Cotchico-Alonso, Jean-Didier Maréchal, Agathe Urvoas, Maëva Rousseau, Jean-Pierre Mahy, and Rémy Ricoux. 2016. “Artificial Metalloenzymes with the Neocarzinostatin Scaffold: Toward a Biocatalyst for the Diels-Alder Reaction.” Chembiochem: A European Journal of Chemical Biology 17 (5): 433–40. https://doi.org/10.1002/cbic.201500445.

Figueroa, Maximiliano, Julie Vandenameele, Erik Goormaghtigh, Marie Valerio-Lepiniec, Philippe Minard, André Matagne, and Cécile Van de Weerdt. 2016. “Biophysical Characterization Data of the Artificial Protein Octarellin V.1 and Binding Test with Its X-Ray Helpers.” Data in Brief 8: 1221–26. https://doi.org/10.1016/j.dib.2016.07.036.

Figueroa, Maximiliano, Mike Sleutel, Marylene Vandevenne, Gregory Parvizi, Sophie Attout, Olivier Jacquin, Julie Vandenameele, et al. 2016. “The Unexpected Structure of the Designed Protein Octarellin V.1 Forms a Challenge for Protein Structure Prediction Tools.” Journal of Structural Biology 195 (1): 19–30. https://doi.org/10.1016/j.jsb.2016.05.004.

Kanellopoulos, Jean. 2015. “Natural Killer T Cells.” Biomedical Journal 38 (6): 469. https://doi.org/10.1016/j.bj.2016.01.007.

Chevrel, A., A. Urvoas, I. L. de la Sierra-Gallay, M. Aumont-Nicaise, S. Moutel, M. Desmadril, F. Perez, et al. 2015. “Specific GFP-Binding Artificial Proteins ( Rep): A New Tool for in Vitro to Live Cell Applications.” Bioscience Reports 35 (4): e00223–e00223. https://doi.org/10.1042/BSR20150080.

Valerio-Lepiniec, M., A. Urvoas, A. Chevrel, A. Guellouz, Y. Ferrandez, A. Mesneau, I. L. de la Sierra-Gallay, et al. 2015. “The ΑRep Artificial Repeat Protein Scaffold: A New Tool for Crystallization and Live Cell Applications.” Biochemical Society Transactions 43 (5): 819–24. https://doi.org/10.1042/BST20150075.