2014

Publications 2014

(1) Aussel, L.; Pierrel, F.; Loiseau, L.; Lombard, M.; Fontecave, M.; Barras, F. Biosynthesis and Physiology of Coenzyme Q in Bacteria. Biochim. Biophys. Acta 2014, 1837 (7), 1004–1011 DOI: 10.1016/j.bbabio.2014.01.015.

(2) Benbahouche, N. E. H.; Iliopoulos, I.; Török, I.; Marhold, J.; Henri, J.; Kajava, A. V.; Farkaš, R.; Kempf, T.; Schnölzer, M.; Meyer, P.; Kiss, I.; Bertrand, E.; Mechler, B. M.; Pradet-Balade, B. Drosophila Spag Is the Homolog of RNA Polymerase II-Associated Protein 3 (RPAP3) and Recruits the Heat Shock Proteins 70 and 90 (Hsp70 and Hsp90) during the Assembly of Cellular Machineries. J. Biol. Chem. 2014, 289 (9), 6236–6247 DOI: 10.1074/jbc.M113.499608.

(3) Boudry, P.; Gracia, C.; Monot, M.; Caillet, J.; Saujet, L.; Hajnsdorf, E.; Dupuy, B.; Martin-Verstraete, I.; Soutourina, O. Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium Difficile. J. Bacteriol. 2014, 196 (18), 3234–3248 DOI: 10.1128/JB.01923-14.

(4) Caillet, J.; Gracia, C.; Fontaine, F.; Hajnsdorf, E. Clostridium Difficile Hfq Can Replace Escherichia Coli Hfq for Most of Its Function. RNA 2014, 20 (10), 1567–1578 DOI: 10.1261/rna.043372.113.

(5) Catoire, L. J.; Warnet, X. L.; Warschawski, D. E. Micelles, Bicelles, Amphipols, Nanodiscs, Liposomes, or Intact Cells: The Hitchhiker’s Guide to the Study of Membrane Proteins by NMR. In Membrane Proteins Production for Structural Analysis; Mus-Veteau, I., Ed.; Springer New York, 2014; pp 315–345.

(6) Delan-Forino, C.; Deforges, J.; Benard, L.; Sargueil, B.; Maurel, M.-C.; Torchet, C. Structural Analyses of Avocado Sunblotch Viroid Reveal Differences in the Folding of Plus and Minus RNA Strands. Viruses-Basel 2014, 6 (2), 489–506 DOI: 10.3390/v6020489.

(7) Della Pia, E. A.; Hansen, R. W.; Zoonens, M.; Martinez, K. L. Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology. J. Membr. Biol. 2014, 247 (9–10), 815–826 DOI: 10.1007/s00232-014-9663-y.

(8) Della Pia, E. A.; Holm, J. V.; Lloret, N.; Le Bon, C.; Popot, J.-L.; Zoonens, M.; Nygård, J.; Martinez, K. L. A Step Closer to Membrane Protein Multiplexed Nanoarrays Using Biotin-Doped Polypyrrole. ACS Nano 2014, 8 (2), 1844–1853 DOI: 10.1021/nn406252h.

(9) Dreher, M.; Prevoteau-Jonquet, J.; Trellet, M.; Piuzzi, M.; Baaden, M.; Raffin, B.; Ferey, N.; Robert, S.; Limet, S. ExaViz: A Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations. Faraday Discuss. 2014, 169, 119–142 DOI: 10.1039/c3fd00142c.

(10) Eric Feinstein, H.; Tifrea, D.; Sun, G.; Popot, J.-L.; de la Maza, L. M.; Cocco, M. J. Long-Term Stability of a Vaccine Formulated with the Amphipol-Trapped Major Outer Membrane Protein from Chlamydia Trachomatis. J. Membr. Biol. 2014, 247 (9–10), 1053–1065 DOI: 10.1007/s00232-014-9693-5.

(11) Fallet, E.; Jolivet, P.; Soudet, J.; Lisby, M.; Gilson, E.; Teixeira, M. T. Length-Dependent Processing of Telomeres in the Absence of Telomerase. Nucleic Acids Res. 2014, 42 (6), 3648–3665 DOI: 10.1093/nar/gkt1328.

(12) Fernandez, A.; Le Bon, C.; Baumlin, N.; Giusti, F.; Crémel, G.; Popot, J.-L.; Bagnard, D. In Vivo Characterization of the Biodistribution Profile of Amphipol A8-35. J. Membr. Biol. 2014, 247 (9–10), 1043–1051 DOI: 10.1007/s00232-014-9682-8.

(13) Ferrandez, Y.; Dezi, M.; Bosco, M.; Urvoas, A.; Valerio-Lepiniec, M.; Le Bon, C.; Giusti, F.; Broutin, I.; Durand, G.; Polidori, A.; Popot, J.-L.; Picard, M.; Minard, P. Amphipol-Mediated Screening of Molecular Orthoses Specific for Membrane Protein Targets. J. Membr. Biol. 2014, 247 (9–10), 925–940 DOI: 10.1007/s00232-014-9707-3.

(14) Gaugué, I.; Oberto, J.; Plumbridge, J. Regulation of Amino Sugar Utilization in Bacillus Subtilis by the GntR Family Regulators, NagR and GamR. Mol. Microbiol. 2014, 92 (1), 100–115 DOI: 10.1111/mmi.12544.

(15) Giusti, F.; Rieger, J.; Catoire, L. J.; Qian, S.; Calabrese, A. N.; Watkinson, T. G.; Casiraghi, M.; Radford, S. E.; Ashcroft, A. E.; Popot, J.-L. Synthesis, Characterization and Applications of a Perdeuterated Amphipol. J. Membr. Biol. 2014, 247 (9–10), 909–924 DOI: 10.1007/s00232-014-9656-x.

(16) Hamdane, D.; Guelorget, A.; Guérineau, V.; Golinelli-Pimpaneau, B. Dynamics of RNA Modification by a Multi-Site-Specific TRNA Methyltransferase. Nucleic Acids Res. 2014, 42 (18), 11697–11706 DOI: 10.1093/nar/gku820.

(17) Hattab, G.; Suisse, A. Y. T.; Ilioaia, O.; Casiraghi, M.; Dezi, M.; Warnet, X. L.; Warschawski, D. E.; Moncoq, K.; Zoonens, M.; Miroux, B. Membrane Protein Production in Escherichia Coli: Overview and Protocols. In Membrane Proteins Production for Structural Analysis; Mus-Veteau, I., Ed.; Springer New York, 2014; pp 87–106.

(18) Hirst, J. D.; Glowacki, D. R.; Baaden, M. Molecular Simulations and Visualization: Introduction and Overview. Faraday Discuss. 2014, 169, 9–22 DOI: 10.1039/c4fd90024c.

(19) Jamalli, A.; Hébert, A.; Zig, L.; Putzer, H. Control of Expression of the RNases J1 and J2 in Bacillus Subtilis. J. Bacteriol. 2014, 196 (2), 318–324 DOI: 10.1128/JB.01053-13.

(20) Johnson, X.; Steinbeck, J.; Dent, R. M.; Takahashi, H.; Richaud, P.; Ozawa, S.-I.; Houille-Vernes, L.; Petroutsos, D.; Rappaport, F.; Grossman, A. R.; Niyogi, K. K.; Hippler, M.; Alric, J. Proton Gradient Regulation 5-Mediated Cyclic Electron Flow under ATP- or Redox-Limited Conditions: A Study of ΔATpase Pgr5 and ΔrbcL Pgr5 Mutants in the Green Alga Chlamydomonas Reinhardtii. Plant Physiol. 2014, 165 (1), 438–452 DOI: 10.1104/pp.113.233593.

(21) Kalimeri, M.; Girard, E.; Madern, D.; Sterpone, F. Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase. PLoS ONE 2014, 9 (12), e113895 DOI: 10.1371/journal.pone.0113895.

(22) Laalami, S.; Zig, L.; Putzer, H. Initiation of MRNA Decay in Bacteria. Cell. Mol. Life Sci. 2014, 71 (10), 1799–1828 DOI: 10.1007/s00018-013-1472-4.

(23) Le Bon, C.; Della Pia, E. A.; Giusti, F.; Lloret, N.; Zoonens, M.; Martinez, K. L.; Popot, J.-L. Synthesis of an Oligonucleotide-Derivatized Amphipol and Its Use to Trap and Immobilize Membrane Proteins. Nucleic Acids Res. 2014, 42 (10), e83 DOI: 10.1093/nar/gku250.

(24) Le Bon, C.; Popot, J.-L.; Giusti, F. Labeling and Functionalizing Amphipols for Biological Applications. J. Membr. Biol. 2014, 247 (9–10), 797–814 DOI: 10.1007/s00232-014-9655-y.

(25) Létoquart, J.; Huvelle, E.; Wacheul, L.; Bourgeois, G.; Zorbas, C.; Graille, M.; Heurgué-Hamard, V.; Lafontaine, D. L. J. Structural and Functional Studies of Bud23-Trm112 Reveal 18S RRNA N7-G1575 Methylation Occurs on Late 40S Precursor Ribosomes. Proc. Natl. Acad. Sci. U.S.A. 2014, 111 (51), E5518-5526 DOI: 10.1073/pnas.1413089111.

(26) Ma, D.; Martin, N.; Tribet, C.; Winnik, F. M. Quantitative Characterization by Asymmetrical Flow Field-Flow Fractionation of IgG Thermal Aggregation with and without Polymer Protective Agents. Anal. Bioanal. Chem. 2014, 406 (29), 7539–7547 DOI: 10.1007/s00216-014-8200-2.

(27) Malnoë, A.; Wang, F.; Girard-Bascou, J.; Wollman, F.-A.; de Vitry, C. Thylakoid FtsH Protease Contributes to Photosystem II and Cytochrome B6f Remodeling in Chlamydomonas Reinhardtii under Stress Conditions. Plant Cell 2014, 26 (1), 373–390 DOI: 10.1105/tpc.113.120113.

(28) Marie, E.; Sagan, S.; Cribier, S.; Tribet, C. Amphiphilic Macromolecules on Cell Membranes: From Protective Layers to Controlled Permeabilization. J. Membr. Biol. 2014, 247 (9–10), 861–881 DOI: 10.1007/s00232-014-9679-3.

(29) Martin, N.; Ma, D.; Herbet, A.; Boquet, D.; Winnik, F. M.; Tribet, C. Prevention of Thermally Induced Aggregation of IgG Antibodies by Noncovalent Interaction with Poly(Acrylate) Derivatives. Biomacromolecules 2014, 15 (8), 2952–2962 DOI: 10.1021/bm5005756.

(30) Molza, A.-E.; Férey, N.; Czjzek, M.; Le Rumeur, E.; Hubert, J.-F.; Tek, A.; Laurent, B.; Baaden, M.; Delalande, O. Innovative Interactive Flexible Docking Method for Multi-Scale Reconstruction Elucidates Dystrophin Molecular Assembly. Faraday Discuss. 2014, 169, 45–62 DOI: 10.1039/c3fd00134b.

(31) Morisse, S.; Michelet, L.; Bedhomme, M.; Marchand, C. H.; Calvaresi, M.; Trost, P.; Fermani, S.; Zaffagnini, M.; Lemaire, S. D. Thioredoxin- Dependent Redox Regulation of Chloroplastic Phosphoglycerate Kinase from Chlamydomonas Reinhardtii. J. Biol. Chem. 2014, 289 (43), 30012–30024 DOI: 10.1074/jbc.M114.597997.

(32) Morisse, S.; Zaffagnini, M.; Gao, X.-H.; Lemaire, S. D.; Marchand, C. H. Insight into Protein S-Nitrosylation in Chlamydomonas Reinhardtii. Antioxid. Redox Signal. 2014, 21 (9), 1271–1284 DOI: 10.1089/ars.2013.5632.

(33) Nguyen, P. H.; Li, M. S.; Derreumaux, P. Amyloid Oligomer Structure Characterization from Simulations: A General Method. J Chem Phys 2014, 140 (9), 094105 DOI: 10.1063/1.4866902.

(34) Nguyen, P. H.; Tarus, B.; Derreumaux, P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1-28 Monomer. J Phys Chem B 2014, 118 (2), 501–510 DOI: 10.1021/jp4115404.

(35) Nguyen, P. H.; Tarus, B.; Derreumaux, P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1-28 Monomer. J Phys Chem B 2014, 118 (2), 501–510 DOI: 10.1021/jp4115404.

(36) Nilsson, H.; Rappaport, F.; Boussac, A.; Messinger, J. Substrate-Water Exchange in Photosystem II Is Arrested before Dioxygen Formation. Nat Commun 2014, 5, 4305 DOI: 10.1038/ncomms5305.

(37) Opačić, M.; Durand, G.; Bosco, M.; Polidori, A.; Popot, J.-L. Amphipols and Photosynthetic Light-Harvesting Pigment-Protein Complexes. J. Membr. Biol. 2014, 247 (9–10), 1031–1041 DOI: 10.1007/s00232-014-9712-6.

(38) Opačić, M.; Giusti, F.; Popot, J.-L.; Broos, J. Isolation of Escherichia Coli Mannitol Permease, EII(Mtl), Trapped in Amphipol A8-35 and Fluorescein-Labeled A8-35. J. Membr. Biol. 2014, 247 (9–10), 1019–1030 DOI: 10.1007/s00232-014-9691-7.

(39) Oteri, F.; Baaden, M.; Lojou, E.; Sacquin-Mora, S. Multiscale Simulations Give Insight into the Hydrogen in and out Pathways of [NiFe]-Hydrogenases from Aquifex Aeolicus and Desulfovibrio Fructosovorans. J Phys Chem B 2014, 118 (48), 13800–13811 DOI: 10.1021/jp5089965.

(40) Oteri, F.; Ciaccafava, A.; de Poulpiquet, A.; Baaden, M.; Lojou, E.; Sacquin-Mora, S. The Weak, Fluctuating, Dipole Moment of Membrane-Bound Hydrogenase from Aquifex Aeolicus Accounts for Its Adaptability to Charged Electrodes. Phys Chem Chem Phys 2014, 16 (23), 11318–11322 DOI: 10.1039/c4cp00510d.

(41) Perez-Martin, M.; Perez-Perez, M. E.; Lemaire, S. D.; Crespo, J. L. Oxidative Stress Contributes to Autophagy Induction in Response to Endoplasmic Reticulum Stress in Chlamydomonas Reinhardtii. Plant Physiol. 2014, 166 (2), 997-U829 DOI: 10.1104/pp.114.243659.

(42) Perez-Perez, M. E.; Zaffagnini, M.; Marchand, C. H.; Crespo, J. L.; Lemaire, S. D. The Yeast Autophagy Protease Atg4 Is Regulated by Thioredoxin. Autophagy 2014, 10 (11), 1953–1964 DOI: 10.4161/auto.34396.

(43) Planchard, N.; Point, E.; Dahmane, T.; Giusti, F.; Renault, M.; Le Bon, C.; Durand, G.; Milon, A.; Guittet, E.; Zoonens, M.; Popot, J.-L.; Catoire, L. J. The Use of Amphipols for Solution NMR Studies of Membrane Proteins: Advantages and Constraints as Compared to Other Solubilizing Media. J. Membr. Biol. 2014, 247 (9–10), 827–842 DOI: 10.1007/s00232-014-9654-z.

(44) Plumbridge, J.; Bossi, L.; Oberto, J.; Wade, J. T.; Figueroa-Bossi, N. Interplay of Transcriptional and Small RNA-Dependent Control Mechanisms Regulates Chitosugar Uptake in Escherichia Coli and Salmonella. Mol. Microbiol. 2014, 92 (4), 648–658 DOI: 10.1111/mmi.12573.

(45) Polovinkin, V.; Balandin, T.; Volkov, O.; Round, E.; Borshchevskiy, V.; Utrobin, P.; von Stetten, D.; Royant, A.; Willbold, D.; Arzumanyan, G.; Chupin, V.; Popot, J.-L.; Gordeliy, V. Nanoparticle Surface-Enhanced Raman Scattering of Bacteriorhodopsin Stabilized by Amphipol A8-35. J. Membr. Biol. 2014, 247 (9–10), 971–980 DOI: 10.1007/s00232-014-9701-9.

(46) Polovinkin, V.; Gushchin, I.; Sintsov, M.; Round, E.; Balandin, T.; Chervakov, P.; Schevchenko, V.; Utrobin, P.; Popov, A.; Borshchevskiy, V.; Mishin, A.; Kuklin, A.; Willbold, D.; Chupin, V.; Popot, J.-L.; Gordeliy, V. High-Resolution Structure of a Membrane Protein Transferred from Amphipol to a Lipidic Mesophase. J. Membr. Biol. 2014, 247 (9–10), 997–1004 DOI: 10.1007/s00232-014-9700-x.

(47) Senissar, M.; Le Saux, A.; Belgareh-Touzé, N.; Adam, C.; Banroques, J.; Tanner, N. K. The DEAD-Box Helicase Ded1 from Yeast Is an MRNP Cap-Associated Protein That Shuttles between the Cytoplasm and Nucleus. Nucleic Acids Res. 2014, 42 (15), 10005–10022 DOI: 10.1093/nar/gku584.

(48) Senissar, M.; Le Saux, A.; Belgareh-Touzé, N.; Adam, C.; Banroques, J.; Tanner, N. K. The DEAD-Box Helicase Ded1 from Yeast Is an MRNP Cap-Associated Protein That Shuttles between the Cytoplasm and Nucleus. Nucleic Acids Res. 2014, 42 (15), 10005–10022 DOI: 10.1093/nar/gku584.

(49) Soudet, J.; Jolivet, P.; Teixeira, M. T. Elucidation of the DNA End-Replication Problem in Saccharomyces Cerevisiae. Mol. Cell 2014, 53 (6), 954–964 DOI: 10.1016/j.molcel.2014.02.030.

(50) Sterpone, F.; Melchionna, S.; Tuffery, P.; Pasquali, S.; Mousseau, N.; Cragnolini, T.; Chebaro, Y.; St-Pierre, J.-F.; Kalimeri, M.; Barducci, A.; Laurin, Y.; Tek, A.; Baaden, M.; Nguyen, P. H.; Derreumaux, P. The OPEP Protein Model: From Single Molecules, Amyloid Formation, Crowding and Hydrodynamics to DNA/RNA Systems. Chem Soc Rev 2014, 43 (13), 4871–4893 DOI: 10.1039/c4cs00048j.

(51) Sugiura, M.; Azami, C.; Koyama, K.; Rutherford, A. W.; Rappaport, F.; Boussac, A. Modification of the Pheophytin Redox Potential in Thermosynechococcus Elongatus Photosystem II with PsbA3 as D1. Biochim. Biophys. Acta 2014, 1837 (1), 139–148 DOI: 10.1016/j.bbabio.2013.09.009.

(52) Sugiura, M.; Ozaki, Y.; Nakamura, M.; Cox, N.; Rappaport, F.; Boussac, A. The D1-173 Amino Acid Is a Structural Determinant of the Critical Interaction between D1-Tyr161 (TyrZ) and D1-His190 in Photosystem II. Biochim. Biophys. Acta 2014, 1837 (12), 1922–1931 DOI: 10.1016/j.bbabio.2014.08.008.

(53) Sun, J.; Jia, L.; Emond, M.; Li, M.-H.; Marie, E.; Jullien, L.; Tribet, C. Photocontrolled Ionization in the Corona of Rodlike Assemblies of Diblock Copolymers. Macromolecules 2014, 47 (5), 1684–1692 DOI: 10.1021/ma402591y.

(54) Sverzhinsky, A.; Qian, S.; Yang, L.; Allaire, M.; Moraes, I.; Ma, D.; Chung, J. W.; Zoonens, M.; Popot, J.-L.; Coulton, J. W. Amphipol-Trapped ExbB-ExbD Membrane Protein Complex from Escherichia Coli: A Biochemical and Structural Case Study. J. Membr. Biol. 2014, 247 (9–10), 1005–1018 DOI: 10.1007/s00232-014-9678-4.

(55) Tehei, M.; Perlmutter, J. D.; Giusti, F.; Sachs, J. N.; Zaccai, G.; Popot, J.-L. Thermal Fluctuations in Amphipol A8-35 Particles: A Neutron Scattering and Molecular Dynamics Study. J. Membr. Biol. 2014, 247 (9–10), 897–908 DOI: 10.1007/s00232-014-9725-1.

(56) Wang, M.; Baaden, M.; Wang, J.; Liang, Z. A Cooperative Mechanism of Clotrimazoles in P450 Revealed by the Dissociation Picture of Clotrimazole from P450. J Chem Inf Model 2014, 54 (4), 1218–1225 DOI: 10.1021/ci400660e.

(57) Wei, L.; Derrien, B.; Gautier, A.; Houille-Vernes, L.; Boulouis, A.; Saint-Marcoux, D.; Malnoë, A.; Rappaport, F.; de Vitry, C.; Vallon, O.; Choquet, Y.; Wollman, F.-A. Nitric Oxide-Triggered Remodeling of Chloroplast Bioenergetics and Thylakoid Proteins upon Nitrogen Starvation in Chlamydomonas Reinhardtii. Plant Cell 2014, 26 (1), 353–372 DOI: 10.1105/tpc.113.120121.

(58) Zaffagninia, M.; Michelet, L.; Sciabolini, C.; Di Giacinto, N.; Morisse, S.; Marchand, C. H.; Trost, P.; Fermani, S.; Lemaire, S. D. High-Resolution Crystal Structure and Redox Properties of Chloroplastic Triosephosphate Isomerase from Chlamydomonas Reinhardtii. Mol. Plant. 2014, 7 (1), 101–120 DOI: 10.1093/mp/sst139.

(59) Zorin, B.; Grundman, O.; Khozin-Goldberg, I.; Leu, S.; Shapira, M.; Kaye, Y.; Tourasse, N.; Vallon, O.; Boussiba, S. Development of a Nuclear Transformation System for Oleaginous Green Alga Lobosphaera (Parietochloris) Incisa and Genetic Complementation of a Mutant Strain, Deficient in Arachidonic Acid Biosynthesis. PLoS ONE 2014, 9 (8), e105223 DOI: 10.1371/journal.pone.0105223.

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