Publications

The laboratories involved in the DYNAMO programme have produced over 400 publications since 2012, with 20% in high-impact journals (Impact Factor > 11) and a dozen patents and licences. For the 80 publications woth an impact factor > 11, over 60% resulted from international collaborations with over 100 international laboratories (>50 from Europe) including some prestigious institutions like the University of Chicago (USA), University of Cambridge (UK), the Max Plack Institute and the Ludwig Maximilians University Munich (Germany), the National Cancer Institute, NIH (USA), the Icahn School of Medicine at Mount Sinai, New York (USA), the University of Liège (Belgium), Okayama University (Japan), the University of Wisconsin-Madison (USA), the University of British Columbia in Vancouver (Canada)

2021

Abdelkrim, Yosser Zina, Josette Banroques, and N. Kyle Tanner. 2021. “Known Inhibitors of RNA Helicases and Their Therapeutic Potential.” Methods in Molecular Biology (Clifton, N.J.) 2209: 35–52. https://doi.org/10.1007/978-1-0716-0935-4_3.
Boudry, Pierre, Emma Piattelli, Emilie Drouineau, Johann Peltier, Anaïs Boutserin, Maxence Lejars, Eliane Hajnsdorf, et al. 2021. “Identification of RNAs Bound by Hfq Reveals Widespread RNA Partners and a Sporulation Regulator in the Human Pathogen Clostridioides Difficile.” RNA Biology, February, 1–22. https://doi.org/10.1080/15476286.2021.1882180.
BOURASSIN, Nicolas, Florent Barbault, Marc Baaden, and Sophie Sacquin-Mora. 2021. “Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalised Gold Surfaces.” https://doi.org/10.1101/2021.07.02.450859.
Boyer, Benjamin, Benoist Laurent, Charles H. Robert, and Chantal Prévost. 2021. “Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.” Bio-Protocol 11 (14): e4097. https://doi.org/10.21769/BioProtoc.4097.
Danilowicz, Claudia, Evan Vietorisz, Veronica Godoy-Carter, Chantal Prévost, and Mara Prentiss. 2021. “Influences of SsDNA-RecA Filament Length on the Fidelity of Homologous Recombination.” Journal of Molecular Biology 433 (18): 167143. https://doi.org/10.1016/j.jmb.2021.167143.
Duboué-Dijon, E., and J. Hénin. 2021. “Building Intuition for Binding Free Energy Calculations: Bound State Definition, Restraints, and Symmetry.” The Journal of Chemical Physics 154 (20): 204101. https://doi.org/10.1063/5.0046853.
Durand, Sylvain, and Maude Guillier. 2021. “Transcriptional and Post-Transcriptional Control of the Nitrate Respiration in Bacteria.” Frontiers in Molecular Biosciences 8: 667758. https://doi.org/10.3389/fmolb.2021.667758.
Faivre, Bruno, Murielle Lombard, Soufyan Fakroun, Chau-Duy-Tam Vo, Catherine Goyenvalle, Vincent Guérineau, Ludovic Pecqueur, et al. 2021. “Dihydrouridine Synthesis in TRNAs Is under Reductive Evolution in Mollicutes.” RNA Biology, March, 1–12. https://doi.org/10.1080/15476286.2021.1899653.
Fostier, Corentin R., Laura Monlezun, Farès Ousalem, Shikha Singh, John F. Hunt, and Grégory Boël. 2021. “ABC-F Translation Factors: From Antibiotic Resistance to Immune Response.” FEBS Letters 595 (6): 675–706. https://doi.org/10.1002/1873-3468.13984.
Gato, Alexandre, Marjorie Catala, Carine Tisné, and Pierre Barraud. 2021. “A Method to Monitor the Introduction of Posttranscriptional Modifications in TRNAs with NMR Spectroscopy.” Methods in Molecular Biology (Clifton, N.J.) 2298: 307–23. https://doi.org/10.1007/978-1-0716-1374-0_19.
Gilet, Laetitia, Olivier Pellegrini, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Frédérique Braun, Sylvain Durand, and Ciarán Condon. 2021. “Analysis of Bacillus Subtilis Ribonuclease Activity In Vivo.” Methods in Molecular Biology (Clifton, N.J.) 2209: 387–401. https://doi.org/10.1007/978-1-0716-0935-4_24.
Hardiagon, Arthur, Samuel Murail, Li-Bo Huang, Arie van der Lee, Fabio Sterpone, Mihail Barboiu, and Marc Baaden. 2021. “Molecular Dynamics Simulations Reveal Statistics and Microscopic Mechanisms of Water Permeation in Membrane-Embedded Artificial Water Channel Nanoconstructs.” The Journal of Chemical Physics 154 (18): 184102. https://doi.org/10.1063/5.0044360.
Hardiagon, Arthur, Samuel Murail, Li-Bo Huang, Arie van der Lee, Fabio Sterpone, Mihail Barboiu, and Marc Baaden. 2021. “Molecular Dynamics Simulations Reveal Statistics and Microscopic Mechanisms of Water Permeation in Membrane-Embedded Artificial Water Channel Nanoconstructs.” The Journal of Chemical Physics 154 (18): 184102. https://doi.org/10.1063/5.0044360.
Huang, Li-Bo, Arthur Hardiagon, Istvan Kocsis, Cristina-Alexandra Jegu, Mihai Deleanu, Arnaud Gilles, Arie van der Lee, Fabio Sterpone, Marc Baaden, and Mihail Barboiu. 2021. “Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation.” Journal of the American Chemical Society 143 (11): 4224–33. https://doi.org/10.1021/jacs.0c11952.
Huang, Li-Bo, Arthur Hardiagon, Istvan Kocsis, Cristina-Alexandra Jegu, Mihai Deleanu, Arnaud Gilles, Arie van der Lee, Fabio Sterpone, Marc Baaden, and Mihail Barboiu. 2021. “Hydroxy Channels–Adaptive Pathways for Selective Water Cluster Permeation.” Journal of the American Chemical Society 143 (11): 4224–33. https://doi.org/10.1021/jacs.0c11952.
Iorio, Antonio, Jennifer Roche, Sylvain Engilberge, Nicolas Coquelle, Eric Girard, Fabio Sterpone, and Dominique Madern. 2021. “Biochemical, Structural and Dynamical Studies Reveal Strong Differences in the Thermal-Dependent Allosteric Behavior of Two Extremophilic Lactate Dehydrogenases.” Journal of Structural Biology 213 (3): 107769. https://doi.org/10.1016/j.jsb.2021.107769.
Laalami, Soumaya, Marina Cavaiuolo, Sylvain Roque, Carine Chagneau, and Harald Putzer. 2021. “Escherichia Coli RNase E Can Efficiently Replace RNase Y in Bacillus Subtilis.” Nucleic Acids Research 49 (8): 4643–54. https://doi.org/10.1093/nar/gkab216.
Makamte, Staëlle, Amira Jabrani, Annick Paquelin, Anne Plessis, Mathieu Sanial, Aurélien Thureau, Olga Rudenko, Francesco Oteri, Marc Baaden, and Valérie Biou. 2021. “A Large Disordered Region Confers a Wide Spanning Volume to Vertebrate Suppressor of Fused as Shown in a Trans-Species Solution Study.” https://doi.org/10.1101/2021.06.14.447554.
Mboukou, Allegra, Vinod Rajendra, Renata Kleinova, Carine Tisné, Michael F. Jantsch, and Pierre Barraud. 2021. “Transportin-1: A Nuclear Import Receptor with Moonlighting Functions.” Frontiers in Molecular Biosciences 8: 638149. https://doi.org/10.3389/fmolb.2021.638149.
Mokdadi, Molka, Yosser Zina Abdelkrim, Josette Banroques, Emmeline Huvelle, Rafeh Oualha, Hilal Yeter-Alat, Ikram Guizani, Mourad Barhoumi, and N. Kyle Tanner. 2021. “The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania Infantum and Their Analyses in Yeast.” Genes 12 (2): 212. https://doi.org/10.3390/genes12020212.
Nguyen, Phuong H., Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, et al. 2021. “Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.” Chemical Reviews 121 (4): 2545–2647. https://doi.org/10.1021/acs.chemrev.0c01122.
Oerum, Stephanie, Marjorie Catala, Maxime Bourguet, Laetitia Gilet, Pierre Barraud, Sarah Cianférani, Ciarán Condon, and Carine Tisné. 2021. “Structural Studies of RNase M5 Reveal Two-Metal-Ion Supported Two-Step DsRNA Cleavage for 5S RRNA Maturation.” RNA Biology, February, 1–11. https://doi.org/10.1080/15476286.2021.1885896.
Oerum, Stephanie, Vincent Meynier, Marjorie Catala, and Carine Tisné. 2021. “A Comprehensive Review of M6A/M6Am RNA Methyltransferase Structures.” Nucleic Acids Research 49 (13): 7239–55. https://doi.org/10.1093/nar/gkab378.
Pellegrini, Olivier, Laetitia Gilet, Aude Trinquier, Anastasia Tolcan, Delphine Allouche, Sylvain Durand, Frédérique Braun, and Ciarán Condon. 2021. “Assay of Bacillus Subtilis Ribonuclease Activity In Vitro.” Methods in Molecular Biology (Clifton, N.J.) 2209: 403–24. https://doi.org/10.1007/978-1-0716-0935-4_25.
Sayegh, Adnan, Luca A. Perego, Marc Arderiu Romero, Louis Escudero, Jérôme Delacotte, Manon Guille-Collignon, Laurence Grimaud, Benjamin Bailleul, and Frédéric Lemaître. 2021. “Finding Adapted Quinones for Harvesting Electrons from Photosynthetic Algae Suspensions.” ChemElectroChem 8 (15): 2968–78. https://doi.org/10.1002/celc.202100757.
Timr, Stepan, and Fabio Sterpone. 2021. “Stabilizing or Destabilizing: Simulations of Chymotrypsin Inhibitor 2 under Crowding Reveal Existence of a Crossover Temperature.” The Journal of Physical Chemistry Letters 12 (6): 1741–46. https://doi.org/10.1021/acs.jpclett.0c03626.
Wu, Xiaojing, Jérôme Hénin, Laura Baciou, Marc Baaden, Fabien Cailliez, and Aurélien de la Lande. 2021. “Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.” Frontiers in Chemistry 9: 650651. https://doi.org/10.3389/fchem.2021.650651.
Yoluç, Yasemin, Gregor Ammann, Pierre Barraud, Manasses Jora, Patrick A. Limbach, Yuri Motorin, Virginie Marchand, Carine Tisné, Kayla Borland, and Stefanie Kellner. 2021. “Instrumental Analysis of RNA Modifications.” Critical Reviews in Biochemistry and Molecular Biology 56 (2): 178–204. https://doi.org/10.1080/10409238.2021.1887807.
Zhou, Jingjing, Marine Lénon, Jean-Luc Ravanat, Nadia Touati, Christophe Velours, Karolina Podskoczyj, Grazyna Leszczynska, Marc Fontecave, Frédéric Barras, and Béatrice Golinelli-Pimpaneau. 2021. “Iron–Sulfur Biology Invades TRNA Modification: The Case of U34 Sulfuration.” Nucleic Acids Research 49 (7): 3997–4007. https://doi.org/10.1093/nar/gkab138.

2020

Alsayyah, Cynthia, Oznur Ozturk, Laetitia Cavellini, Naïma Belgareh-Touzé, and Mickael M. Cohen. 2020. “The Regulation of Mitochondrial Homeostasis by the Ubiquitin Proteasome System.” Biochimica et Biophysica Acta (BBA) – Bioenergetics 1861 (12): 148302. https://doi.org/10.1016/j.bbabio.2020.148302.
Beauzamy, Léna, Jérôme Delacotte, Benjamin Bailleul, Kenya Tanaka, Shuji Nakanishi, Francis-André Wollman, and Frédéric Lemaître. 2020. “Mediator-Microorganism Interaction in Microbial Solar Cell: A Fluo-Electrochemical Insight.” Analytical Chemistry 92 (11): 7532–39. https://doi.org/10.1021/acs.analchem.9b05808.
Beauzamy, Léna, Frédéric Lemaître, and Julien Derr. 2020. “Underlying Mechanisms in Microbial Solar Cells: How Modeling Can Help.” Sustainable Energy & Fuels 4 (12): 6004–10. https://doi.org/10.1039/D0SE01304H.
Bimai, Ornella, Simon Arragain, and Béatrice Golinelli-Pimpaneau. 2020. “Structure-Based Mechanistic Insights into Catalysis by TRNA Thiolation Enzymes.” Current Opinion in Structural Biology 65 (December): 69–78. https://doi.org/10.1016/j.sbi.2020.06.002.
Bujaldon, Sandrine, Natsumi Kodama, Mithun Kumar Rathod, Nicolas Tourasse, Shin-Ichiro Ozawa, Julien Sellés, Olivier Vallon, Yuichiro Takahashi, and Francis-André Wollman. 2020. “The BF4 and P71 Antenna Mutants from Chlamydomonas Reinhardtii.” Biochimica Et Biophysica Acta. Bioenergetics 1861 (4): 148085. https://doi.org/10.1016/j.bbabio.2019.148085.
Cai, Yiming, Ben Usher, Claude Gutierrez, Anastasia Tolcan, Moise Mansour, Peter C. Fineran, Ciarán Condon, Olivier Neyrolles, Pierre Genevaux, and Tim R. Blower. 2020. “A Nucleotidyltransferase Toxin Inhibits Growth of Mycobacterium Tuberculosis through Inactivation of TRNA Acceptor Stems.” Science Advances 6 (31): eabb6651. https://doi.org/10.1126/sciadv.abb6651.
Cai, Yiming, Ben Usher, Claude Gutierrez, Anastasia Tolcan, Moise Mansour, Peter C. Fineran, Ciarán Condon, Olivier Neyrolles, Pierre Genevaux, and Tim R. Blower. 2020. “A Nucleotidyltransferase Toxin Inhibits Growth of Mycobacterium Tuberculosis through Inactivation of TRNA Acceptor Stems.” Science Advances 6 (31): eabb6651. https://doi.org/10.1126/sciadv.abb6651.
Carpentier, Philippe, Chloé Leprêtre, Christian Basset, Thierry Douki, Stéphane Torelli, Victor Duarte, Djemel Hamdane, Marc Fontecave, and Mohamed Atta. 2020. “Structural, Biochemical and Functional Analyses of TRNA-Monooxygenase Enzyme MiaE from Pseudomonas Putida Provide Insights into TRNA/MiaE Interaction.” Nucleic Acids Research 48 (17): 9918–30. https://doi.org/10.1093/nar/gkaa667.
Carpentier, Philippe, Chloé Leprêtre, Christian Basset, Thierry Douki, Stéphane Torelli, Victor Duarte, Djemel Hamdane, Marc Fontecave, and Mohamed Atta. 2020. “Structural, Biochemical and Functional Analyses of TRNA-Monooxygenase Enzyme MiaE from Pseudomonas Putida Provide Insights into TRNA/MiaE Interaction.” Nucleic Acids Research 48 (17): 9918–30. https://doi.org/10.1093/nar/gkaa667.
Caspari, Oliver D. 2020. “Introduction of a Leaky Stop Codon as Molecular Tool in Chlamydomonas Reinhardtii.” PLOS ONE 15 (8): e0237405. https://doi.org/10.1371/journal.pone.0237405.
Catala, Marjorie, Alexandre Gato, Carine Tisné, and Pierre Barraud. 2020. “1H, 15N Chemical Shift Assignments of the Imino Groups of Yeast TRNAPhe: Influence of the Post-Transcriptional Modifications.” Biomolecular NMR Assignments, April. https://doi.org/10.1007/s12104-020-09939-6.
Catala, M., A. Gato, C. Tisné, and P. Barraud. 2020. “Yeast TRNAPhe Samples Preparation for NMR Spectroscopy.” Bio-Protocol In Press.
Catala, Marjorie, Alexandre Gato, Carine Tisné, and Pierre Barraud. 2020. “Preparation of Yeast TRNA Sample for NMR Spectroscopy.” Bio-Protocol 10 (12): e3646. https://doi.org/10.21769/BioProtoc.3646.
Catala, Marjorie, Alexandre Gato, Carine Tisné, and Pierre Barraud. 2020. “1H, 15N Chemical Shift Assignments of the Imino Groups of Yeast TRNAPhe: Influence of the Post-Transcriptional Modifications.” Biomolecular NMR Assignments 14 (2): 169–74. https://doi.org/10.1007/s12104-020-09939-6.
Cavaiuolo, Marina, Carine Chagneau, Soumaya Laalami, and Harald Putzer. 2020. “Impact of RNase E and RNase J on Global MRNA Metabolism in the Cyanobacterium Synechocystis PCC6803.” Frontiers in Microbiology 11. https://doi.org/10.3389/fmicb.2020.01055.
Cavaiuolo, Marina, Carine Chagneau, Soumaya Laalami, and Harald Putzer. 2020. “Impact of RNase E and RNase J on Global MRNA Metabolism in the Cyanobacterium Synechocystis PCC6803.” Frontiers in Microbiology 11: 1055. https://doi.org/10.3389/fmicb.2020.01055.
Carpentier, Félix de, Jeanne Le Peillet, Nicolas D. Boisset, Pierre Crozet, Stéphane D. Lemaire, and Antoine Danon. 2020. “Blasticidin S Deaminase: A New Efficient Selectable Marker for Chlamydomonas Reinhardtii.” Frontiers in Plant Science 11. https://doi.org/10.3389/fpls.2020.00242.
Derreumaux, Philippe, Viet Hoang Man, Junmei Wang, and Phuong H. Nguyen. 2020. “Tau R3–R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations.” The Journal of Physical Chemistry B 124 (15): 2975–83. https://doi.org/10.1021/acs.jpcb.0c00574.
Dezaire, Ambre, Christophe H. Marchand, Marine Vallet, Nathalie Ferrand, Soraya Chaouch, Elisabeth Mouray, Annette K. Larsen, et al. 2020. “Secondary Metabolites from the Culture of the Marine-Derived Fungus Paradendryphiella Salina PC 362H and Evaluation of the Anticancer Activity of Its Metabolite Hyalodendrin.” Marine Drugs 18 (4): 191. https://doi.org/10.3390/md18040191.
Duboué-Dijon, E., M. Javanainen, P. Delcroix, P. Jungwirth, and H. Martinez-Seara. 2020. “A Practical Guide to Biologically Relevant Molecular Simulations with Charge Scaling for Electronic Polarization.” The Journal of Chemical Physics 153 (5): 050901. https://doi.org/10.1063/5.0017775.
Exner, Thomas E., Stefanie Becker, Simon Becker, Audrey Boniface-Guiraud, Philippe Delepelaire, Kay Diederichs, and Wolfram Welte. 2020. “Binding of HasA by Its Transmembrane Receptor HasR Follows a Conformational Funnel Mechanism.” European Biophysics Journal: EBJ 49 (1): 39–57. https://doi.org/10.1007/s00249-019-01411-1.
Falciatore, Angela, Marianne Jaubert, Jean-Pierre Bouly, Benjamin Bailleul, and Thomas Mock. 2020. “Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity.” The Plant Cell 32 (3): 547–72. https://doi.org/10.1105/tpc.19.00158.
Garrido, Clotilde, Oliver D. Caspari, Yves Choquet, Francis-André Wollman, and Ingrid Lafontaine. 2020. “Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles.” Cells 9 (8): 1795. https://doi.org/10.3390/cells9081795.
Gilet, Jules, Romain Conte, Claire Torchet, Lionel Benard, and Ingrid Lafontaine. 2020. “Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.” Molecular Biology and Evolution 37 (2): 365–78. https://doi.org/10.1093/molbev/msz221.
Giusti, Fabrice, Marina Casiraghi, Elodie Point, Marjorie Damian, Jutta Rieger, Christel Le Bon, Alexandre Pozza, Karine Moncoq, Jean-Louis Banères, and Laurent J. Catoire. 2020. “Structure of the Agonist 12–HHT in Its BLT2 Receptor-Bound State.” Scientific Reports 10 (1): 1–13. https://doi.org/10.1038/s41598-020-59571-6.
Hamouche, Lina, Cyrille Billaudeau, Anna Rocca, Arnaud Chastanet, Saravuth Ngo, Soumaya Laalami, and Harald Putzer. 2020. “Dynamic Membrane Localization of RNase Y in Bacillus Subtilis.” MBio 11 (1). https://doi.org/10.1128/mBio.03337-19.
Hamouche, Lina, Cyrille Billaudeau, Anna Rocca, Arnaud Chastanet, Saravuth Ngo, Soumaya Laalami, and Harald Putzer. 2020. “Dynamic Membrane Localization of RNase Y in Bacillus Subtilis.” MBio 11 (1): e03337-19. https://doi.org/10.1128/mBio.03337-19.
Henninger, Erin, and Maria T Teixeira. 2020. “Telomere-Driven Mutational Processes in Yeast.” Current Opinion in Genetics & Development, Cancer Genomics, 60 (February): 99–106. https://doi.org/10.1016/j.gde.2020.02.018.
Ignatov, Dmitriy, Karolis Vaitkevicius, Sylvain Durand, Laty Cahoon, Stefanie S. Sandberg, Xijia Liu, Birgitte H. Kallipolitis, et al. 2020. “An MRNA-MRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria Monocytogenes.” Cell Reports 30 (12): 4027-4040.e7. https://doi.org/10.1016/j.celrep.2020.03.006.
Ignatov, Dmitriy, Karolis Vaitkevicius, Sylvain Durand, Laty Cahoon, Stefanie S. Sandberg, Xijia Liu, Birgitte H. Kallipolitis, et al. 2020. “An MRNA-MRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria Monocytogenes.” Cell Reports 30 (12): 4027-4040.e7. https://doi.org/10.1016/j.celrep.2020.03.006.
Katava, M., M. Marchi, D. Madern, M. Sztucki, M. Maccarini, and F. Sterpone. 2020. “Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse.” The Journal of Physical Chemistry B 124 (6): 1001–8. https://doi.org/10.1021/acs.jpcb.9b10776.
Kawasaki, Takayasu, Viet Hoang Man, Yasunobu Sugimoto, Nobuyuki Sugiyama, Hiroko Yamamoto, Koichi Tsukiyama, Junmei Wang, Philippe Derreumaux, and Phuong H. Nguyen. 2020. “Infrared Laser-Induced Amyloid Fibril Dissociation: A Joint Experimental/Theoretical Study on the GNNQQNY Peptide.” The Journal of Physical Chemistry B 124 (29): 6266–77. https://doi.org/10.1021/acs.jpcb.0c05385.
Lacoux, Caroline, Ludivine Wacheul, Kritika Saraf, Nicolas Pythoud, Emmeline Huvelle, Sabine Figaro, Marc Graille, Christine Carapito, Denis L. J. Lafontaine, and Valérie Heurgué-Hamard. 2020. “The Catalytic Activity of the Translation Termination Factor Methyltransferase Mtq2-Trm112 Complex Is Required for Large Ribosomal Subunit Biogenesis.” Nucleic Acids Research 48 (21): 12310–25. https://doi.org/10.1093/nar/gkaa972.
Laureanti, Joseph, Juan Brandi, Elvis Offor, David Engel, Robert Rallo, Bojana Ginovska, Xavier Martinez, Marc Baaden, and Nathan A. Baker. 2020. “Visualizing Biomolecular Electrostatics in Virtual Reality with UnityMol-APBS.” Protein Science: A Publication of the Protein Society 29 (1): 237–46. https://doi.org/10.1002/pro.3773.
Lejars, Maxence, and Eliane Hajnsdorf. 2020. “The World of AsRNAs in Gram-Negative and Gram-Positive Bacteria.” Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms 1863 (2): 194489. https://doi.org/10.1016/j.bbagrm.2020.194489.
Lejars, Maxence, and Eliane Hajnsdorf. 2020. “The World of AsRNAs in Gram-Negative and Gram-Positive Bacteria.” Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms 1863 (2): 194489. https://doi.org/10.1016/j.bbagrm.2020.194489.
Marconnet, Anaïs, Baptiste Michon, Christel Le Bon, Fabrice Giusti, Christophe Tribet, and Manuela Zoonens. 2020. “Solubilization and Stabilization of Membrane Proteins by Cycloalkane-Modified Amphiphilic Polymers.” Biomacromolecules, June. https://doi.org/10.1021/acs.biomac.0c00929.
Martinez, Xavier, Matthieu Chavent, and Marc Baaden. 2020. “Visualizing Protein Structures — Tools and Trends.” Biochemical Society Transactions 48 (2): 499–506. https://doi.org/10.1042/BST20190621.
Martinez, Xavier, Arthur Hardiagon, Hubert Santuz, Samuel Murail, Mihail Barboiu, Fabio Sterpone, and Marc Baaden. 2020. “Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels.” In Lecture Notes in Bioengineering / Advances in Bionanomaterials IISelected Papers from the 3rd International Conference on Bio and Nanomaterials, BIONAM 2019, September 29 – October 3, 2019, 78–99. https://doi.org/10.1007/978-3-030-47705-9_8.
Martinez, Xavier, Matthieu Chavent, and Marc Baaden. 2020. “Visualizing Protein Structures — Tools and Trends.” Biochemical Society Transactions 48 (2): 499–506. https://doi.org/10.1042/BST20190621.
Martins, Laura, Johannes Knuesting, Laetitia Bariat, Avilien Dard, Sven A. Freibert, Christophe Marchand, David Young, et al. 2020. “Redox Modification of the Fe-S Glutaredoxin GRXS17 Activates Holdase Activity and Protects Plants from Heat Stress.” Plant Physiology, January. https://doi.org/10.1104/pp.20.00906.
Migliore, Mattia, Andrea Bonvicini, Vincent Tognetti, Laure Guilhaudis, Marc Baaden, Hassan Oulyadi, Laurent Joubert, and Isabelle Ségalas-Milazzo. 2020. “Characterization of β-Turns by Electronic Circular Dichroism Spectroscopy: A Coupled Molecular Dynamics and Time-Dependent Density Functional Theory Computational Study.” Physical Chemistry Chemical Physics 22 (3): 1611–23. https://doi.org/10.1039/C9CP05776E.
Navickas, Albertas, Sébastien Chamois, Rénette Saint-Fort, Julien Henri, Claire Torchet, and Lionel Benard. 2020. “No-Go Decay MRNA Cleavage in the Ribosome Exit Tunnel Produces 5′-OH Ends Phosphorylated by Trl1.” Nature Communications 11 (1): 122. https://doi.org/10.1038/s41467-019-13991-9.
Ngo, Son Tung, Phuong H. Nguyen, and Philippe Derreumaux. 2020. “Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics.” The Journal of Physical Chemistry B 124 (7): 1175–82. https://doi.org/10.1021/acs.jpcb.9b11881.
Nguyen, Phuong H., and Philippe Derreumaux. 2020. “Structures of the Intrinsically Disordered Aβ, Tau and α-Synuclein Proteins in Aqueous Solution from Computer Simulations.” Biophysical Chemistry 264 (September): 106421. https://doi.org/10.1016/j.bpc.2020.106421.
Nguyen, Phuong H., Fabio Sterpone, and Philippe Derreumaux. 2020. “Chapter Nine – Aggregation of Disease-Related Peptides.” In Progress in Molecular Biology and Translational Science, edited by Birgit Strodel and Bogdan Barz, 170:435–60. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly. Academic Press. https://doi.org/10.1016/bs.pmbts.2019.12.002.
Oerum, Stephanie, Tom Dendooven, Marjorie Catala, Laetitia Gilet, Clément Dégut, Aude Trinquier, Maxime Bourguet, et al. 2020. “Structures of B. Subtilis Maturation RNases Captured on 50S Ribosome with Pre-RRNAs.” Molecular Cell 80 (2): 227-236.e5. https://doi.org/10.1016/j.molcel.2020.09.008.
Ozawa, Shin-Ichiro, Marina Cavaiuolo, Domitille Jarrige, Richard Kuras, Mark Rutgers, Stephan Eberhard, Dominique Drapier, Francis-André Wollman, and Yves Choquet. 2020. “The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas Reinhardtii.” The Plant Cell 32 (4): 1179–1203. https://doi.org/10.1105/tpc.19.00770.
Peltier, Johann, Audrey Hamiot, Julian R. Garneau, Pierre Boudry, Anna Maikova, Louis-Charles Fortier, Bruno Dupuy, and Olga Soutourina. 2020. “Type I Toxin-Antitoxin Systems Contribute to Mobile Genetic Elements Maintenance in Clostridioides Difficile and Can Be Used as a Counter-Selectable Marker for Chromosomal Manipulation.” https://doi.org/10.1101/2020.03.04.976019.
Robescu, Marina Simona, Rudy Rubini, Elisa Beneventi, Michele Tavanti, Chiara Lonigro, Francesca Zito, Francesco Filippini, Laura Cendron, and Elisabetta Bergantino. 2020. “From the Amelioration of a NADP+-Dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice.” ChemCatChem n/a (n/a). https://doi.org/10.1002/cctc.201902089.

2019

Asadi-Atoi, Paria, Pierre Barraud, Carine Tisne, and Stefanie Kellner. 2019. “Benefits of Stable Isotope Labeling in RNA Analysis.” Biological Chemistry 400 (7): 847–65. https://doi.org/10.1515/hsz-2018-0447.
Baaden, Marc. 2019. “Visualizing Biological Membrane Organization and Dynamics.” Journal of Molecular Biology 431 (10): 1889–1919. https://doi.org/10.1016/j.jmb.2019.02.018.
Barraud, Pierre, and Carine Tisné. 2019. “To Be or Not to Be Modified: Miscellaneous Aspects Influencing Nucleotide Modifications in TRNAs.” IUBMB Life 71 (8): 1126–40. https://doi.org/10.1002/iub.2041.
Barraud, Pierre, Alexandre Gato, Matthias Heiss, Marjorie Catala, Stefanie Kellner, and Carine Tisné. 2019. “Time-Resolved NMR Monitoring of TRNA Maturation.” Nature Communications 10 (1): 3373. https://doi.org/10.1038/s41467-019-11356-w.
Barroso da Silva, Fernando Luís, Fabio Sterpone, and Philippe Derreumaux. 2019. “OPEP6: A New Constant-PH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field.” Journal of Chemical Theory and Computation 15 (6): 3875–88. https://doi.org/10.1021/acs.jctc.9b00202.
Bou-Nader, Charles, Ludovic Pecqueur, Pierre Barraud, Marc Fontecave, Carine Tisné, Sophie Sacquin-Mora, and Djemel Hamdane. 2019. “Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand.” Biochemistry 58 (20): 2463–73. https://doi.org/10.1021/acs.biochem.9b00111.
Bou-Nader, Charles, Pierre Barraud, Ludovic Pecqueur, Javier Pérez, Christophe Velours, William Shepard, Marc Fontecave, Carine Tisné, and Djemel Hamdane. 2019. “Molecular Basis for Transfer RNA Recognition by the Double-Stranded RNA-Binding Domain of Human Dihydrouridine Synthase 2.” Nucleic Acids Research 47 (6): 3117–26. https://doi.org/10.1093/nar/gky1302.
Boyer, Benjamin, Claudia Danilowicz, Mara Prentiss, and Chantal Prévost. 2019. “Weaving DNA Strands: Structural Insight on ATP Hydrolysis in RecA-Induced Homologous Recombination.” Nucleic Acids Research 47 (15): 7798–7808. https://doi.org/10.1093/nar/gkz667.
Brandner, Astrid, Dario De Vecchis, Marc Baaden, Mickael M. Cohen, and Antoine Taly. 2019. “Physics-Based Oligomeric Models of the Yeast Mitofusin Fzo1 at the Molecular Scale in the Context of Membrane Docking.” Mitochondrion 49: 234–44. https://doi.org/10.1016/j.mito.2019.06.010.
Brandner, Astrid, Dario De Vecchis, Marc Baaden, Mickael M. Cohen, and Antoine Taly. 2019. “Structural Dataset from Microsecond-Long Simulations of Yeast Mitofusin Fzo1 in the Context of Membrane Docking.” Data in Brief 26 (October): 104460. https://doi.org/10.1016/j.dib.2019.104460.
Caillet, Joël, Bruno Baron, Irina V. Boni, Célia Caillet-Saguy, and Eliane Hajnsdorf. 2019. “Identification of Protein-Protein and Ribonucleoprotein Complexes Containing Hfq.” Scientific Reports 9 (1): 14054. https://doi.org/10.1038/s41598-019-50562-w.
Casiraghi, Marina, Elodie Point, Alexandre Pozza, Karine Moncoq, Jean-Louis Banères, and Laurent J. Catoire. 2019. “NMR Analysis of GPCR Conformational Landscapes and Dynamics.” Molecular and Cellular Endocrinology 484: 69–77. https://doi.org/10.1016/j.mce.2018.12.019.
Chiricotto, Mara, Simone Melchionna, Philippe Derreumaux, and Fabio Sterpone. 2019. “Multiscale Aggregation of the Amyloid Aβ16-22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils.” The Journal of Physical Chemistry Letters 10 (7): 1594–99. https://doi.org/10.1021/acs.jpclett.9b00423.
Dautant, Alain, Julien Henri, Thomas E. Wales, Philippe Meyer, John R. Engen, and Florian Georgescauld. 2019. “Remodeling of the Binding Site of Nucleoside Diphosphate Kinase Revealed by X-Ray Structure and H/D Exchange.” Biochemistry 58 (10): 1440–49. https://doi.org/10.1021/acs.biochem.8b01308.
Carpentier, Félix de, Stéphane D. Lemaire, and Antoine Danon. 2019. “When Unity Is Strength: The Strategies Used by Chlamydomonas to Survive Environmental Stresses.” Cells 8 (11). https://doi.org/10.3390/cells8111307.
De Mia, Marcello, Stéphane D. Lemaire, Yves Choquet, and Francis-André Wollman. 2019. “Nitric Oxide Remodels the Photosynthetic Apparatus upon S-Starvation in Chlamydomonas Reinhardtii.” Plant Physiology 179 (2): 718–31. https://doi.org/10.1104/pp.18.01164.
De Vecchis, Dario, Astrid Brandner, Marc Baaden, Mickael M. Cohen, and Antoine Taly. 2019. “A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin.” The Journal of Membrane Biology 252 (4–5): 293–306. https://doi.org/10.1007/s00232-019-00089-y.
Dégut, Clément, Martine Roovers, Pierre Barraud, Franck Brachet, André Feller, Valéry Larue, Abdalla Al Refaii, Joël Caillet, Louis Droogmans, and Carine Tisné. 2019. “Structural Characterization of B. Subtilis M1A22 TRNA Methyltransferase TrmK: Insights into TRNA Recognition.” Nucleic Acids Research 47 (9): 4736–50. https://doi.org/10.1093/nar/gkz230.
Delepelaire, Philippe. 2019. “Bacterial ABC Transporters of Iron Containing Compounds.” Research in Microbiology 170 (8): 345–57. https://doi.org/10.1016/j.resmic.2019.10.008.
Durand, Sylvain, Adam Callan-Sidat, Josie McKeown, Stephen Li, Gergana Kostova, Juan R. Hernandez-Fernaud, Mohammad Tauqeer Alam, et al. 2019. “Novel Regulation from Novel Interactions: Identification of an RNA Sponge That Controls the Levels, Processing and Efficacy of the RoxS Riboregulator of Central Metabolism in Bacillus Subtilis.” https://doi.org/10.1101/814905.
Eberhard, Stephan, Sona Valuchova, Julie Ravat, Jaroslav Fulneček, Pascale Jolivet, Sandrine Bujaldon, Stéphane D. Lemaire, et al. 2019. “Molecular Characterization of Chlamydomonas Reinhardtii Telomeres and Telomerase Mutants.” Life Science Alliance 2 (3). https://doi.org/10.26508/lsa.201900315.
Esmenjaud, Jean-Baptiste, David Stroebel, Kelvin Chan, Teddy Grand, Mélissa David, Lonnie P. Wollmuth, Antoine Taly, and Pierre Paoletti. 2019. “An Inter-Dimer Allosteric Switch Controls NMDA Receptor Activity.” The EMBO Journal 38 (2). https://doi.org/10.15252/embj.201899894.
F Brandner, Astrid, Stepan Timr, Simone Melchionna, Philippe Derreumaux, Marc Baaden, and Fabio Sterpone. 2019. “Modelling Lipid Systems in Fluid with Lattice Boltzmann Molecular Dynamics Simulations and Hydrodynamics.” Scientific Reports 9 (1): 16450. https://doi.org/10.1038/s41598-019-52760-y.
Fernandez, Marion, and Jacqueline Plumbridge. 2019. “Complex Synergistic Amino Acid-Nucleotide Interactions Contribute to the Specificity of NagC Operator Recognition and Induction.” Microbiology (Reading, England) 165 (7): 792–803. https://doi.org/10.1099/mic.0.000814.
Findinier, Justin, Cédric Delevoye, and Mickael M. Cohen. 2019. “The Dynamin-like Protein Fzl Promotes Thylakoid Fusion and Resistance to Light Stress in Chlamydomonas Reinhardtii.” PLoS Genetics 15 (3): e1008047. https://doi.org/10.1371/journal.pgen.1008047.
Gervason, Sylvain, Djabir Larkem, Amir Ben Mansour, Thomas Botzanowski, Christina S. Müller, Ludovic Pecqueur, Gwenaelle Le Pavec, et al. 2019. “Physiologically Relevant Reconstitution of Iron-Sulfur Cluster Biosynthesis Uncovers Persulfide-Processing Functions of Ferredoxin-2 and Frataxin.” Nature Communications 10 (1): 3566. https://doi.org/10.1038/s41467-019-11470-9.
Gnutt, David, Stepan Timr, Jonas Ahlers, Benedikt König, Emily Manderfeld, Matthias Heyden, Fabio Sterpone, and Simon Ebbinghaus. 2019. “Stability Effect of Quinary Interactions Reversed by Single Point Mutations.” Journal of the American Chemical Society 141 (11): 4660–69. https://doi.org/10.1021/jacs.8b13025.
Gurrieri, Libero, Alessandra Del Giudice, Nicola Demitri, Giuseppe Falini, Nicolae Viorel Pavel, Mirko Zaffagnini, Maurizio Polentarutti, et al. 2019. “Arabidopsis and Chlamydomonas Phosphoribulokinase Crystal Structures Complete the Redox Structural Proteome of the Calvin-Benson Cycle.” Proceedings of the National Academy of Sciences of the United States of America 116 (16): 8048–53. https://doi.org/10.1073/pnas.1820639116.
Hajj Chehade, Mahmoud, Ludovic Pelosi, Cameron David Fyfe, Laurent Loiseau, Bérengère Rascalou, Sabine Brugière, Katayoun Kazemzadeh, et al. 2019. “A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone.” Cell Chemical Biology 26 (4): 482-492.e7. https://doi.org/10.1016/j.chembiol.2018.12.001.
Jolivet, Pascale, Kamar Serhal, Marco Graf, Stephan Eberhard, Zhou Xu, Brian Luke, and Maria Teresa Teixeira. 2019. “A Subtelomeric Region Affects Telomerase-Negative Replicative Senescence in Saccharomyces Cerevisiae.” Scientific Reports 9 (1): 1845. https://doi.org/10.1038/s41598-018-38000-9.
Kanonenberg, Kerstin, Jorge Royes, Alexej Kedrov, Gereon Poschmann, Federica Angius, Audrey Solgadi, Olivia Spitz, et al. 2019. “Shaping the Lipid Composition of Bacterial Membranes for Membrane Protein Production.” Microbial Cell Factories 18 (1): 131. https://doi.org/10.1186/s12934-019-1182-1.
Laage, Damien, and Guillaume Stirnemann. 2019. “Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions.” The Journal of Physical Chemistry. B 123 (15): 3312–24. https://doi.org/10.1021/acs.jpcb.9b01053.
Lamrabet, Otmane, Jacqueline Plumbridge, Mikaël Martin, Richard E. Lenski, Dominique Schneider, and Thomas Hindré. 2019. “Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene.” Molecular Biology and Evolution 36 (6): 1121–33. https://doi.org/10.1093/molbev/msz042.
Law-Hine, Didier, Sergii Rudiuk, Audrey Bonestebe, Romain Ienco, Sylvain Huille, and Christophe Tribet. 2019. “Distinctive Low-Resolution Structural Features of Dimers of Antibody-Drug Conjugates and Parent Antibody Determined by Small-Angle X-Ray Scattering.” Molecular Pharmaceutics, October. https://doi.org/10.1021/acs.molpharmaceut.9b00792.
Lejars, Maxence, Asaki Kobayashi, and Eliane Hajnsdorf. 2019. “Physiological Roles of Antisense RNAs in Prokaryotes.” Biochimie 164 (September): 3–16. https://doi.org/10.1016/j.biochi.2019.04.015.
Li, Chastity, Claudia Danilowicz, Tommy F. Tashjian, Veronica G. Godoy, Chantal Prévost, and Mara Prentiss. 2019. “The Positioning of Chi Sites Allows the RecBCD Pathway to Suppress Some Genomic Rearrangements.” Nucleic Acids Research 47 (4): 1836–46. https://doi.org/10.1093/nar/gky1252.
Lipońska, Anna, Farès Ousalem, Daniel P. Aalberts, John F. Hunt, and Grégory Boël. 2019. “The New Strategies to Overcome Challenges in Protein Production in Bacteria.” Microbial Biotechnology 12 (1): 44–47. https://doi.org/10.1111/1751-7915.13338.
Lu, Yan, Xiao-Feng Shi, Phuong H. Nguyen, Fabio Sterpone, Freddie R. Salsbury, and Philippe Derreumaux. 2019. “Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids.” The Journal of Physical Chemistry. B 123 (12): 2687–96. https://doi.org/10.1021/acs.jpcb.9b00431.
Lu, Daniel, Claudia Danilowicz, Tommy F. Tashjian, Chantal Prévost, Veronica G. Godoy, and Mara Prentiss. 2019. “Slow Extension of the Invading DNA Strand in a D-Loop Formed by RecA-Mediated Homologous Recombination May Enhance Recognition of DNA Homology.” The Journal of Biological Chemistry 294 (21): 8606–16. https://doi.org/10.1074/jbc.RA119.007554.
Ma, Wei, Christophe Tribet, Sylvain Guyot, and Dražen Zanchi. 2019. “Tannin-Controlled Micelles and Fibrils of κ-Casein.” The Journal of Chemical Physics 151 (24): 245103. https://doi.org/10.1063/1.5128057.
Majeran, Wojciech, Katia Wostrikoff, Francis-André Wollman, and Olivier Vallon. 2019. “Role of ClpP in the Biogenesis and Degradation of RuBisCO and ATP Synthase in Chlamydomonas Reinhardtii.” Plants (Basel, Switzerland) 8 (7). https://doi.org/10.3390/plants8070191.
Man, Viet Hoang, Mai Suan Li, Junmei Wang, Philippe Derreumaux, and Phuong H. Nguyen. 2019. “Interaction Mechanism between the Focused Ultrasound and Lipid Membrane at the Molecular Level.” The Journal of Chemical Physics 150 (21): 215101. https://doi.org/10.1063/1.5099008.
Man, Viet Hoang, Xibing He, Philippe Derreumaux, Beihong Ji, Xiang-Qun Xie, Phuong H. Nguyen, and Junmei Wang. 2019. “Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer.” Journal of Chemical Theory and Computation 15 (2): 1440–52. https://doi.org/10.1021/acs.jctc.8b01107.
Man, Viet Hoang, Mai Suan Li, Junmei Wang, Philippe Derreumaux, and Phuong H. Nguyen. 2019. “Nonequilibrium Atomistic Molecular Dynamics Simulation of Tubular Nanomotor Propelled by Bubble Propulsion.” The Journal of Chemical Physics 151 (2): 024103. https://doi.org/10.1063/1.5109101.
Marchand, Christophe H., Simona Fermani, Jacopo Rossi, Libero Gurrieri, Daniele Tedesco, Julien Henri, Francesca Sparla, Paolo Trost, Stéphane D. Lemaire, and Mirko Zaffagnini. 2019. “Structural and Biochemical Insights into the Reactivity of Thioredoxin H1 from Chlamydomonas Reinhardtii.” Antioxidants (Basel, Switzerland) 8 (1). https://doi.org/10.3390/antiox8010010.
Martinez, Xavier, Michael Krone, Naif Alharbi, Alexander S. Rose, Robert S. Laramee, Sean O’Donoghue, Marc Baaden, and Matthieu Chavent. 2019. “Molecular Graphics: Bridging Structural Biologists and Computer Scientists.” Structure (London, England: 1993) 27 (11): 1617–23. https://doi.org/10.1016/j.str.2019.09.001.
Mason, Philip E., Pavel Jungwirth, and Elise Duboué-Dijon. 2019. “Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics.” The Journal of Physical Chemistry Letters 10 (12): 3254–59. https://doi.org/10.1021/acs.jpclett.9b01309.
Nawrocki, W. J., B. Bailleul, P. Cardol, F. Rappaport, F.-A. Wollman, and P. Joliot. 2019. “Maximal Cyclic Electron Flow Rate Is Independent of PGRL1 in Chlamydomonas.” Biochimica Et Biophysica Acta. Bioenergetics 1860 (5): 425–32. https://doi.org/10.1016/j.bbabio.2019.01.004.
Nawrocki, W. J., B. Bailleul, D. Picot, P. Cardol, F. Rappaport, F.-A. Wollman, and P. Joliot. 2019. “The Mechanism of Cyclic Electron Flow.” Biochimica Et Biophysica Acta. Bioenergetics 1860 (5): 433–38. https://doi.org/10.1016/j.bbabio.2018.12.005.
Ngo, Son Tung, Philippe Derreumaux, and Van V. Vu. 2019. “Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions.” The Journal of Physical Chemistry. B 123 (12): 2645–53. https://doi.org/10.1021/acs.jpcb.8b10792.

2018

Abdelkrim, Yosser Zina, Emna Harigua-Souiai, Mourad Barhoumi, Josette Banroques, Arnaud Blondel, Ikram Guizani, and N. Kyle Tanner. 2018. “The Steroid Derivative 6-Aminocholestanol Inhibits the DEAD-Box Helicase EIF4A (LieIF4A) from the Trypanosomatid Parasite Leishmania by Perturbing the RNA and ATP Binding Sites.” Molecular and Biochemical Parasitology 226: 9–19. https://doi.org/10.1016/j.molbiopara.2018.10.001.
Angius, Federica, Oana Ilioaia, Amira Amrani, Annabelle Suisse, Lindsay Rosset, Amélie Legrand, Abbas Abou-Hamdan, Marc Uzan, Francesca Zito, and Bruno Miroux. 2018. “A Novel Regulation Mechanism of the T7 RNA Polymerase Based Expression System Improves Overproduction and Folding of Membrane Proteins.” Scientific Reports 8 (1): 8572. https://doi.org/10.1038/s41598-018-26668-y.
Aymé, Laure, Simon Arragain, Michel Canonge, Sébastien Baud, Nadia Touati, Ornella Bimai, Franjo Jagic, et al. 2018. “Arabidopsis Thaliana DGAT3 Is a [2Fe-2S] Protein Involved in TAG Biosynthesis.” Scientific Reports 8 (1): 17254. https://doi.org/10.1038/s41598-018-35545-7.
Baaden, Marc, Olivier Delalande, Nicolas Ferey, Samuela Pasquali, Jérôme Waldispühl, and Antoine Taly. 2018. “Ten Simple Rules to Create a Serious Game, Illustrated with Examples from Structural Biology.” PLOS Computational Biology 14 (3): e1005955. https://doi.org/10.1371/journal.pcbi.1005955.
Barroso da Silva, Fernando Luís, Philippe Derreumaux, and Samuela Pasquali. 2018. “Protein-RNA Complexation Driven by the Charge Regulation Mechanism.” Biochemical and Biophysical Research Communications, Multiscale Modeling, 498 (2): 264–73. https://doi.org/10.1016/j.bbrc.2017.07.027.
Baumgardt, Kathrin, Laetitia Gilet, Sabine Figaro, and Ciarán Condon. 2018. “The Essential Nature of YqfG, a YbeY Homologue Required for 3′ Maturation of Bacillus Subtilis 16S Ribosomal RNA Is Suppressed by Deletion of RNase R.” Nucleic Acids Research. https://doi.org/10.1093/nar/gky488.
Beedle, Amy E. M., Marc Mora, Colin T. Davis, Ambrosius P. Snijders, Guillaume Stirnemann, and Sergi Garcia-Manyes. 2018. “Forcing the Reversibility of a Mechanochemical Reaction.” Nature Communications 9 (1): 3155. https://doi.org/10.1038/s41467-018-05115-6.
Berkovich, Ronen, Vicente I. Fernandez, Guillaume Stirnemann, Jessica Valle-Orero, and Julio M. Fernández. 2018. “Segmentation and the Entropic Elasticity of Modular Proteins.” The Journal of Physical Chemistry Letters 9 (16): 4707–13. https://doi.org/10.1021/acs.jpclett.8b01925.
Bernaschi, Massimo, Simone Melchionna, Philippe Derreumaux, Fabio Sterpone, and Sauro Succi. 2018. “Multilevel Lattice Boltzmann-Particle Dynamics Simulations at the Physics-Biology Interface.” Journal of Physics: Conference Series 1136 (December): 012013. https://doi.org/10.1088/1742-6596/1136/1/012013.
Boniello, Giuseppe, Christophe Tribet, Emmanuelle Marie, Vincent Croquette, and Dražen Zanchi. 2018. “Rolling and Aging in Temperature-Ramp Soft Adhesion.” Physical Review E 97 (1): 012609. https://doi.org/10.1103/PhysRevE.97.012609.
Bou-Nader, Charles, Damien Brégeon, Ludovic Pecqueur, Marc Fontecave, and Djemel Hamdane. 2018. “Electrostatic Potential in the TRNA Binding Evolution of Dihydrouridine Synthases.” Biochemistry, August. https://doi.org/10.1021/acs.biochem.8b00584.
Brosse, Anaïs, and Maude Guillier. 2018. “Bacterial Small RNAs in Mixed Regulatory Networks.” Microbiology Spectrum 6 (3). https://doi.org/10.1128/microbiolspec.RWR-0014-2017.
Caserta, Giorgio, Cecilia Papini, Agnieszka Adamska-Venkatesh, Ludovic Pecqueur, Constanze Sommer, Edward Reijerse, Wolfgang Lubitz, et al. 2018. “Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O2 Resistance and Catalytic Bias?” Journal of the American Chemical Society 140 (16): 5516–26. https://doi.org/10.1021/jacs.8b01689.
Casiraghi, Marina, Marjorie Damian, Ewen Lescop, Jean-Louis Baneres, and Laurent J Catoire. 2018. “Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia Coli as an Expression Host.” Biochemistry 57 (16): 2297–2307. https://doi.org/10.1021/acs.biochem.8b00035.
Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. 2018. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” Chemical Reviews 118 (7): 3559–3607. https://doi.org/10.1021/acs.chemrev.7b00570.
Cohen, Mickael M, and David Tareste. 2018. “Recent Insights into the Structure and Function of Mitofusins in Mitochondrial Fusion.” F1000Research 7 (December). https://doi.org/10.12688/f1000research.16629.1.
Condon, Ciarán, Jéremie Piton, and Frédérique Braun. 2018. “Distribution of the Ribosome Associated Endonuclease Rae1 and the Potential Role of Conserved Amino Acids in Codon Recognition.” RNA Biology 0 (0): 1–6. https://doi.org/10.1080/15476286.2018.1454250.
Corey, Robin A., Euan Pyle, William J. Allen, Daniel W. Watkins, Marina Casiraghi, Bruno Miroux, Ignacio Arechaga, Argyris Politis, and Ian Collinson. 2018. “Specific Cardiolipin-SecY Interactions Are Required for Proton-Motive Force Stimulation of Protein Secretion.” Proceedings of the National Academy of Sciences of the United States of America 115 (31): 7967–72. https://doi.org/10.1073/pnas.1721536115.
Coutelier, Héloïse, Zhou Xu, Mony Chenda Morisse, Maoussi Lhuillier-Akakpo, Serge Pelet, Gilles Charvin, Karine Dubrana, and Maria Teresa Teixeira. 2018. “Adaptation to DNA Damage Checkpoint in Senescent Telomerase-Negative Cells Promotes Genome Instability.” Genes & Development 32 (23–24): 1499–1513. https://doi.org/10.1101/gad.318485.118.
Crozet, Pierre, Francisco J Navarro, Felix Willmund, Payam Mehrshahi, Kamil Bakowski, Kyle Jonathan Lauersen, Maria-Esther Pérez-Pérez, et al. 2018. “Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas Reinhardtii.” ACS Synthetic Biology, August. https://doi.org/10.1021/acssynbio.8b00251.
Dalier, F., G. V. Dubacheva, M. Coniel, D. Zanchi, A. Galtayries, M. Piel, E. Marie, and C. Tribet. 2018. “Mixed Copolymer Adlayers Allowing Reversible Thermal Control of Single Cell Aspect Ratio.” ACS Applied Materials & Interfaces, January. https://doi.org/10.1021/acsami.7b18513.
Dilworth, Marvin V., Mathilde S. Piel, Kim E. Bettaney, Pikyee Ma, Ji Luo, David Sharples, David R. Poyner, et al. 2018. “Microbial Expression Systems for Membrane Proteins.” Methods (San Diego, Calif.) 147 (April): 3–39. https://doi.org/10.1016/j.ymeth.2018.04.009.
Dumas, Louis, Francesca Zito, Pascaline Auroy, Xenie Johnson, Gilles Peltier, and Jean Alric. 2018. “Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR.” Plant Physiology 177 (2): 465–75. https://doi.org/10.1104/pp.17.01618.
El Meshri, Salah Edin, Emmanuel Boutant, Assia Mouhand, Audrey Thomas, Valéry Larue, Ludovic Richert, Valérie Vivet-Boudou, et al. 2018. “The NC Domain of HIV-1 Gag Contributes to the Interaction of Gag with TSG101.” Biochimica et Biophysica Acta (BBA) – General Subjects 1862 (6): 1421–31. https://doi.org/10.1016/j.bbagen.2018.03.020.
Elbahnsi, Ahmad, Romain Retureau, Marc Baaden, Brigitte Hartmann, and Christophe Oguey. 2018. “Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution.” Journal of Chemical Theory and Computation 14 (2): 1045–58. https://doi.org/10.1021/acs.jctc.7b00936.
Esque, Jérémy, Mark S. P. Sansom, Marc Baaden, and Christophe Oguey. 2018. “Analyzing Protein Topology Based on Laguerre Tessellation of a Pore-Traversing Water Network.” Scientific Reports 8 (1): 13540. https://doi.org/10.1038/s41598-018-31422-5.
Fogeron, Thibault, Pascal Retailleau, Maria Gomez-Mingot, Yun Li, and Marc Fontecave. 2018. “Nickel Complexes Based on Molybdopterin-like Dithiolenes: Catalysts for CO2 Electroreduction.” Organometallics, November. https://doi.org/10.1021/acs.organomet.8b00655.
Fogeron, Thibault, Pascal Retailleau, Lise-Marie Chamoreau, Yun Li, and Marc Fontecave. 2018. “Pyranopterin Related Dithiolene Molybdenum Complexes as Homogeneous Catalysts for CO2 Photoreduction.” Angewandte Chemie 130 (52): 17279–83. https://doi.org/10.1002/ange.201809084.
Fogeron, Thibault, Tanya K. Todorova, jean philippe Porcher, Maria Gomez-Mingot, Lise-Marie Chamoreau, Caroline Mellot-Draznieks, Yun Li, and Marc Fontecave. 2018. “A Bioinspired Nickel(Bis-Dithiolene) Complex as a Homogeneous Catalyst for Carbon Dioxide Electroreduction.” ACS Catalysis, January. https://doi.org/10.1021/acscatal.7b03383.
Guerin, Marcelo E., Guillaume Stirnemann, and David Giganti. 2018. “Conformational Entropy of a Single Peptide Controlled under Force Governs Protease Recognition and Catalysis.” Proceedings of the National Academy of Sciences 115 (45): 11525–30. https://doi.org/10.1073/pnas.1803872115.
Hajnsdorf Eliane, and Kaberdin Vladimir R. 2018. “RNA Polyadenylation and Its Consequences in Prokaryotes.” Philosophical Transactions of the Royal Society B: Biological Sciences 373 (1762): 20180166. https://doi.org/10.1098/rstb.2018.0166.
Hardouin, Pierre, Christophe Velours, Charles Bou-Nader, Nadine Assrir, Soumaya Laalami, Harald Putzer, Dominique Durand, and Béatrice Golinelli-Pimpaneau. 2018. “Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding.” Biophysical Journal 115 (11): 2102–13. https://doi.org/10.1016/j.bpj.2018.10.016.
Harigua-Souiai, Emna, Yosser Zina Abdelkrim, Imen Bassoumi-Jamoussi, Ons Zakraoui, Guillaume Bouvier, Khadija Essafi-Benkhadir, Josette Banroques, et al. 2018. “Identification of Novel Leishmanicidal Molecules by Virtual and Biochemical Screenings Targeting Leishmania Eukaryotic Translation Initiation Factor 4A.” PLOS Neglected Tropical Diseases 12 (1): e0006160. https://doi.org/10.1371/journal.pntd.0006160.
Henri, Julien, Marie-Eve Chagot, Maxime Bourguet, Yoann Abel, Guillaume Terral, Chloé Maurizy, Christelle Aigueperse, et al. 2018. “Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-Chaperone R2TP Complex.” Structure 26 (9): 1196-1209.e8. https://doi.org/10.1016/j.str.2018.06.002.
Hitaishi, Vivek, Romain Clement, Nicolas Bourassin, Marc Baaden, Anne de Poulpiquet, Sophie Sacquin-Mora, Alexandre Ciaccafava, et al. 2018. “Controlling Redox Enzyme Orientation at Planar Electrodes.” Catalysts 8 (5): 192. https://doi.org/10.3390/catal8050192.
Joseph, Thomas T., and Jérôme Hénin. 2018. “Molecular Mechanics Parameterization of Anesthetic Molecules.” In , edited by BT  – Methods in Enzymology. Academic Press. https://doi.org/10.1016/bs.mie.2018.01.003.
Kim, Raeyeong, Shuji Kanamaru, Tsutomu Mikawa, Chantal Prévost, Kentaro Ishii, Kentaro Ito, Susumu Uchiyama, et al. 2018. “RecA Requires Two Molecules of Mg2+ Ions for Its Optimal Strand Exchange Activity in Vitro.” Nucleic Acids Research, January. https://doi.org/10.1093/nar/gky048.
Kocsis, Istvan, Mirco Sorci, Heather Vanselous, Samuel Murail, Stephanie E. Sanders, Erol Licsandru, Yves-Marie Legrand, et al. 2018. “Oriented Chiral Water Wires in Artificial Transmembrane Channels.” Science Advances 4 (3): eaao5603. https://doi.org/10.1126/sciadv.aao5603.
Lagarde, Nathalie, Alessandra Carbone, and Sophie Sacquin‐Mora. 2018. “Hidden Partners: Using Cross‐docking Calculations to Predict Binding Sites for Proteins with Multiple Interactions.” Proteins: Structure, Function, and Bioinformatics 86 (7): 723–37. https://doi.org/10.1002/prot.25506.
Languin-Cattoën, Olivier, Simone Melchionna, Philippe Derreumaux, Guillaume Stirnemann, and Fabio Sterpone. 2018. “Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses.” The Journal of Physical Chemistry B 122 (50): 11922–30. https://doi.org/10.1021/acs.jpcb.8b08711.
Le Bon, Christel, Anaïs Marconnet, Sandrine Masscheleyn, Jean-Luc Popot, and Manuela Zoonens. 2018. “Folding and Stabilizing Membrane Proteins in Amphipol A8-35.” Methods (San Diego, Calif.) 147 (April): 95–105. https://doi.org/10.1016/j.ymeth.2018.04.012.
Lemaire, Stéphane D., Daniele Tedesco, Pierre Crozet, Laure Michelet, Simona Fermani, Mirko Zaffagnini, and Julien Henri. 2018. “Crystal Structure of Chloroplastic Thioredoxin F2 from Chlamydomonas Reinhardtii Reveals Distinct Surface Properties.” Antioxidants 7 (12): 171. https://doi.org/10.3390/antiox7120171.
Liponska, Anna, Ailar Jamalli, Richard Kuras, Loreto Suay, Enrico Garbe, Francis-André Wollman, Soumaya Laalami, and Harald Putzer. 2018. “Tracking the Elusive 5’ Exonuclease Activity of Chlamydomonas Reinhardtii RNase J.” Plant Molecular Biology, March. https://doi.org/10.1007/s11103-018-0720-2.
Longatte, Guillaume, Adnan Sayegh, Jérôme Delacotte, Fabrice Rappaport, Francis-André Wollman, Manon Guille Collignon, and Frédéric Lemaître. 2018. “Investigation of Photocurrents Resulting from Living Unicellular Algae Suspension with Quinones over Time.” Chemical Science, August. https://doi.org/10.1039/C8SC03058H.
Maes, Alexandre, Xavier Martinez, Karen Druart, Benoist Laurent, Sean Guégan, Christophe H. Marchand, Stéphane D. Lemaire, and Marc Baaden. 2018. “MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.” Journal of Integrative Bioinformatics 15 (2). https://doi.org/10.1515/jib-2018-0006.
Maikova, Anna, Johann Peltier, Pierre Boudry, Eliane Hajnsdorf, Nicolas Kint, Marc Monot, Isabelle Poquet, Isabelle Martin-Verstraete, Bruno Dupuy, and Olga Soutourina. 2018. “Discovery of New Type I Toxin–Antitoxin Systems Adjacent to CRISPR Arrays in Clostridium Difficile.” Nucleic Acids Research. https://doi.org/10.1093/nar/gky124.
Mazur, Alexey K., and Eugene Gladyshev. 2018. “Structural Aspects of Homologous DNA-DNA Interactions Revealed by Partitioning of RIP Mutations.” BioRxiv, June, 344036. https://doi.org/10.1101/344036.
Mora, Liliana, Saravuth Ngo, Soumaya Laalami, and Harald Putzer. 2018. “Chapter Fourteen – In Vitro Study of the Major Bacillus Subtilis Ribonucleases Y and J.” In Methods in Enzymology, edited by Agamemnon J. Carpousis, 612:343–59. High-Density Sequencing Applications in Microbial Molecular Genetics. Academic Press. https://doi.org/10.1016/bs.mie.2018.08.004.
Mouhand, Assia, Anissa Belfetmi, Marjorie Catala, Valéry Larue, Loussiné Zargarian, Franck Brachet, Robert J. Gorelick, et al. 2018. “Modulation of the HIV Nucleocapsid Dynamics Finely Tunes Its RNA-Binding Properties during Virion Genesis.” Nucleic Acids Research. https://doi.org/10.1093/nar/gky612.
Murail, Samuel, Tudor Vasiliu, Andrei Neamtu, Mihail Barboiu, Fabio Sterpone, and Marc Baaden. 2018. “Water Permeation across Artificial I-Quartet Membrane Channels: From Structure to Disorder.” Faraday Discussions, May. https://doi.org/10.1039/C8FD00046H.

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