2014

Publications 2014

  1. Zorin, B., Grundman, O., Khozin-Goldberg, I., Leu, S., Shapira, M., Kaye, Y., Tourasse, N., Vallon, O. and Boussiba, S. (2014) 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, 9, e105223. http://www.ncbi.nlm.nih.gov/pubmed/25133787
  2. Zaffagnini, M., Michelet, L., Sciabolini, C., Di Giacinto, N., Morisse, S., Marchand, C.H., Trost, P., Fermani, S. and Lemaire, S.D. (2014) High-resolution crystal structure and redox properties of chloroplastic triosephosphate isomerase from Chlamydomonas reinhardtii. Mol Plant, 7, 101-120. http://www.ncbi.nlm.nih.gov/pubmed/24157611
  3. Wei, L., Derrien, B., Gautier, A., Houille-Vernes, L., Boulouis, A., Saint-Marcoux, D., Malnoe, A., Rappaport, F., de Vitry, C., Vallon, O. et al. (2014) Nitric oxide-triggered remodeling of chloroplast bioenergetics and thylakoid proteins upon nitrogen starvation in Chlamydomonas reinhardtii. Plant Cell, 26, 353-372. http://www.ncbi.nlm.nih.gov/pubmed/24474630
  4. Wang, M., Baaden, M., Wang, J. and Liang, Z. (2014) A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450. J Chem Inf Model, 54, 1218-1225. http://www.ncbi.nlm.nih.gov/pubmed/24611729
  5. Tehei, M., Perlmutter, J.D., Giusti, F., Sachs, J.N., Zaccai, G. and Popot, J.L. (2014) Thermal fluctuations in amphipol A8-35 particles: a neutron scattering and molecular dynamics study. J Membr Biol, 247, 897-908. http://www.ncbi.nlm.nih.gov/pubmed/25204390
  6. Sverzhinsky, A., Qian, S., Yang, L., Allaire, M., Moraes, I., Ma, D., Chung, J.W., Zoonens, M., Popot, J.L. and Coulton, J.W. (2014) Amphipol-trapped ExbB-ExbD membrane protein complex from Escherichia coli: a biochemical and structural case study. J Membr Biol, 247, 1005-1018. http://www.ncbi.nlm.nih.gov/pubmed/24862870
  7. Sun, J., Jia, L., Emond, M., Li, M.-H., Marie, E., Jullien, L. and Tribet, C. (2014) Photocontrolled Ionization in the Corona of Rodlike Assemblies of Diblock Copolymers. Macromolecules, 47, 1684-1692. https://doi.org/10.1021/ma402591y
  8. Sugiura, M., Ozaki, Y., Nakamura, M., Cox, N., Rappaport, F. and Boussac, A. (2014) 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, 1837, 1922-1931. http://www.ncbi.nlm.nih.gov/pubmed/25193561
  9. Sugiura, M., Azami, C., Koyama, K., Rutherford, A.W., Rappaport, F. and Boussac, A. (2014) Modification of the pheophytin redox potential in Thermosynechococcus elongatus Photosystem II with PsbA3 as D1. Biochim Biophys Acta, 1837, 139-148. http://www.ncbi.nlm.nih.gov/pubmed/24060528
  10. Sterpone, F., Melchionna, S., Tuffery, P., Pasquali, S., Mousseau, N., Cragnolini, T., Chebaro, Y., St-Pierre, J.F., Kalimeri, M., Barducci, A. et al. (2014) The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev, 43, 4871-4893. http://www.ncbi.nlm.nih.gov/pubmed/24759934
  11. Soudet, J., Jolivet, P. and Teixeira, M.T. (2014) Elucidation of the DNA End-Replication Problem in Saccharomyces cerevisiae. Mol Cell, 53, 954-964. http://www.ncbi.nlm.nih.gov/pubmed/24656131
  12. Senissar, M., Le Saux, A., Belgareh-Touze, N., Adam, C., Banroques, J. and Tanner, N.K. (2014) The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus. Nucleic Acids Res, 42, 10005-10022. http://www.ncbi.nlm.nih.gov/pubmed/25013175
  13. Polovinkin, V., Gushchin, I., Sintsov, M., Round, E., Balandin, T., Chervakov, P., Shevchenko, V., Utrobin, P., Popov, A., Borshchevskiy, V. et al. (2014) High-resolution structure of a membrane protein transferred from amphipol to a lipidic mesophase. J Membr Biol, 247, 997-1004. http://www.ncbi.nlm.nih.gov/pubmed/25192977
  14. Polovinkin, V., Balandin, T., Volkov, O., Round, E., Borshchevskiy, V., Utrobin, P., von Stetten, D., Royant, A., Willbold, D., Arzumanyan, G. et al. (2014) Nanoparticle surface-enhanced Raman scattering of bacteriorhodopsin stabilized by amphipol A8-35. J Membr Biol, 247, 971-980. http://www.ncbi.nlm.nih.gov/pubmed/25192978
  15. Plumbridge, J., Bossi, L., Oberto, J., Wade, J.T. and Figueroa-Bossi, N. (2014) Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella. Mol Microbiol, 92, 648-658. http://www.ncbi.nlm.nih.gov/pubmed/24593230
  16. Planchard, N., Point, E., Dahmane, T., Giusti, F., Renault, M., Le Bon, C., Durand, G., Milon, A., Guittet, E., Zoonens, M. et al. (2014) The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media. J Membr Biol, 247, 827-842. http://www.ncbi.nlm.nih.gov/pubmed/24676477
  17. Pérez-Pérez, M.E., Zaffagnini, M., Marchand, C.H., Crespo, J.L. and Lemaire, S.D. (2014) The yeast autophagy protease Atg4 is regulated by thioredoxin. Autophagy, 10, 1953-1964. http://www.ncbi.nlm.nih.gov/pubmed/25483965
  18. Pérez-Martin, M., Pérez-Pérez, M.E., Lemaire, S.D. and Crespo, J.L. (2014) Oxidative stress contributes to autophagy induction in response to endoplasmic reticulum stress in Chlamydomonas reinhardtii. Plant Physiol, 166, 997-1008. http://www.ncbi.nlm.nih.gov/pubmed/25143584
  19. Oteri, F., Ciaccafava, A., de Poulpiquet, A., Baaden, M., Lojou, E. and Sacquin-Mora, S. (2014) The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys Chem Chem Phys, 16, 11318-11322. http://www.ncbi.nlm.nih.gov/pubmed/24789038
  20. Oteri, F., Baaden, M., Lojou, E. and Sacquin-Mora, S. (2014) Multiscale simulations give insight into the hydrogen in and out pathways of [NiFe]-hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J Phys Chem B, 118, 13800-13811. http://www.ncbi.nlm.nih.gov/pubmed/25399809
  21. Opacic, M., Giusti, F., Popot, J.L. and Broos, J. (2014) Isolation of Escherichia coli mannitol permease, EIImtl, trapped in amphipol A8-35 and fluorescein-labeled A8-35. J Membr Biol, 247, 1019-1030. http://www.ncbi.nlm.nih.gov/pubmed/24952466
  22. Opacic, M., Durand, G., Bosco, M., Polidori, A. and Popot, J.L. (2014) Amphipols and photosynthetic light-harvesting pigment-protein complexes. J Membr Biol, 247, 1031-1041. http://www.ncbi.nlm.nih.gov/pubmed/25107304
  23. Nilsson, H., Rappaport, F., Boussac, A. and Messinger, J. (2014) Substrate-water exchange in photosystem II is arrested before dioxygen formation. Nat Commun, 5, 4305. http://www.ncbi.nlm.nih.gov/pubmed/24993602
  24. Nguyen, P.H., Tarus, B. and Derreumaux, P. (2014) Familial Alzheimer A2 V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Abeta1-28 monomer. J Phys Chem B, 118, 501-510. http://www.ncbi.nlm.nih.gov/pubmed/24372615
  25. Nguyen, P.H., Li, M.S. and Derreumaux, P. (2014) Amyloid oligomer structure characterization from simulations: a general method. J Chem Phys, 140, 094105. http://www.ncbi.nlm.nih.gov/pubmed/24606351
  26. Morisse, S., Zaffagnini, M., Gao, X.H., Lemaire, S.D. and Marchand, C.H. (2014) Insight into protein S-nitrosylation in Chlamydomonas reinhardtii. Antioxid Redox Signal, 21, 1271-1284. http://www.ncbi.nlm.nih.gov/pubmed/24328795
  27. Morisse, S., Michelet, L., Bedhomme, M., Marchand, C.H., Calvaresi, M., Trost, P., Fermani, S., Zaffagnini, M. and Lemaire, S.D. (2014) Thioredoxin-dependent redox regulation of chloroplastic phosphoglycerate kinase from Chlamydomonas reinhardtii. J Biol Chem, 289, 30012-30024. http://www.ncbi.nlm.nih.gov/pubmed/25202015
  28. Molza, A.E., Ferey, N., Czjzek, M., Le Rumeur, E., Hubert, J.F., Tek, A., Laurent, B., Baaden, M. and Delalande, O. (2014) Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discuss, 169, 45-62. http://www.ncbi.nlm.nih.gov/pubmed/25340652
  29. Martin, N., Ma, D., Herbet, A., Boquet, D., Winnik, F.M. and Tribet, C. (2014) Prevention of thermally induced aggregation of IgG antibodies by noncovalent interaction with poly(acrylate) derivatives. Biomacromolecules, 15, 2952-2962. http://www.ncbi.nlm.nih.gov/pubmed/25019321
  30. Marie, E., Sagan, S., Cribier, S. and Tribet, C. (2014) Amphiphilic macromolecules on cell membranes: from protective layers to controlled permeabilization. J Membr Biol, 247, 861-881. http://www.ncbi.nlm.nih.gov/pubmed/24903487
  31. Malnoe, A., Wang, F., Girard-Bascou, J., Wollman, F.A. and de Vitry, C. (2014) Thylakoid FtsH protease contributes to photosystem II and cytochrome b6f remodeling in Chlamydomonas reinhardtii under stress conditions. Plant Cell, 26, 373-390. http://www.ncbi.nlm.nih.gov/pubmed/24449688
  32. Ma, D., Martin, N., Tribet, C. and Winnik, F.M. (2014) Quantitative characterization by asymmetrical flow field-flow fractionation of IgG thermal aggregation with and without polymer protective agents. Anal Bioanal Chem, 406, 7539-7547. http://www.ncbi.nlm.nih.gov/pubmed/25323742
  33. Letoquart, J., Huvelle, E., Wacheul, L., Bourgeois, G., Zorbas, C., Graille, M., Heurgue-Hamard, V. and Lafontaine, D.L. (2014) 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, 111, E5518-5526. http://www.ncbi.nlm.nih.gov/pubmed/25489090
  34. Le Bon, C., Popot, J.L. and Giusti, F. (2014) Labeling and functionalizing amphipols for biological applications. J Membr Biol, 247, 797-814. http://www.ncbi.nlm.nih.gov/pubmed/24696186
  35. Le Bon, C., Della Pia, E.A., Giusti, F., Lloret, N., Zoonens, M., Martinez, K.L. and Popot, J.L. (2014) Synthesis of an oligonucleotide-derivatized amphipol and its use to trap and immobilize membrane proteins. Nucleic Acids Res, 42, e83. http://www.ncbi.nlm.nih.gov/pubmed/24744236
  36. Laalami, S., Zig, L. and Putzer, H. (2014) Initiation of mRNA decay in bacteria. Cell Mol Life Sci, 71, 1799-1828. http://www.ncbi.nlm.nih.gov/pubmed/24064983
  37. Kalimeri, M., Girard, E., Madern, D. and Sterpone, F. (2014) Interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase. PLoS One, 9, e113895. http://www.ncbi.nlm.nih.gov/pubmed/25437494
  38. Johnson, X., Steinbeck, J., Dent, R.M., Takahashi, H., Richaud, P., Ozawa, S., Houille-Vernes, L., Petroutsos, D., Rappaport, F., Grossman, A.R. et al. (2014) Proton gradient regulation 5-mediated cyclic electron flow under ATP- or redox-limited conditions: a study of DeltaATpase pgr5 and DeltarbcL pgr5 mutants in the green alga Chlamydomonas reinhardtii. Plant Physiol, 165, 438-452. http://www.ncbi.nlm.nih.gov/pubmed/24623849
  39. Jamalli, A., Hebert, A., Zig, L. and Putzer, H. (2014) Control of expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol, 196, 318-324. http://www.ncbi.nlm.nih.gov/pubmed/24187087
  40. Hirst, J.D., Glowacki, D.R. and Baaden, M. (2014) Molecular simulations and visualization: introduction and overview. Faraday Discuss, 169, 9-22. http://www.ncbi.nlm.nih.gov/pubmed/25285906
  41. Hattab, G., Suisse, A.Y.T., Ilioaia, O., Casiraghi, M., Dezi, M., Warnet, X.L., Warschawski, D.E., Moncoq, K., Zoonens, M. and Miroux, B. (2014) In Mus-Veteau, I. (ed.), Membrane Proteins Production for Structural Analysis. Springer, New York, pp. 87-106.
  42. Hamdane, D., Guelorget, A., Guerineau, V. and Golinelli-Pimpaneau, B. (2014) Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase. Nucleic Acids Res, 42, 11697-11706. http://www.ncbi.nlm.nih.gov/pubmed/25217588
  43. Giusti, F., Rieger, J., Catoire, L.J., Qian, S., Calabrese, A.N., Watkinson, T.G., Casiraghi, M., Radford, S.E., Ashcroft, A.E. and Popot, J.L. (2014) Synthesis, characterization and applications of a perdeuterated amphipol. J Membr Biol, 247, 909-924. http://www.ncbi.nlm.nih.gov/pubmed/24652511
  44. Gaugue, I., Oberto, J. and Plumbridge, J. (2014) Regulation of amino sugar utilization in Bacillus subtilis by the GntR family regulators, NagR and GamR. Mol Microbiol, 92, 100-115. http://www.ncbi.nlm.nih.gov/pubmed/24673833
  45. Ferrandez, Y., Dezi, M., Bosco, M., Urvoas, A., Valerio-Lepiniec, M., Le Bon, C., Giusti, F., Broutin, I., Durand, G., Polidori, A. et al. (2014) Amphipol-mediated screening of molecular orthoses specific for membrane protein targets. J Membr Biol, 247, 925-940. http://www.ncbi.nlm.nih.gov/pubmed/25086771
  46. Fernandez, A., Le Bon, C., Baumlin, N., Giusti, F., Cremel, G., Popot, J.L. and Bagnard, D. (2014) In vivo characterization of the biodistribution profile of amphipol A8-35. J Membr Biol, 247, 1043-1051. http://www.ncbi.nlm.nih.gov/pubmed/24898094
  47. Feinstein, H.E., Tifrea, D., Sun, G., Popot, J.L., de la Maza, L.M. and Cocco, M.J. (2014) Long-term stability of a vaccine formulated with the amphipol-trapped major outer membrane protein from Chlamydia trachomatis. J Membr Biol, 247, 1053-1065. http://www.ncbi.nlm.nih.gov/pubmed/24942817
  48. Fallet, E., Jolivet, P., Soudet, J., Lisby, M., Gilson, E. and Teixeira, M.T. (2014) Length-dependent processing of telomeres in the absence of telomerase. Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/24393774
  49. Elgrishi, N., Chambers, M.B., Artero, V. and Fontecave, M. (2014) Terpyridine complexes of first row transition metals and electrochemical reduction of CO(2) to CO. Phys Chem Chem Phys, 16, 13635-13644. http://www.ncbi.nlm.nih.gov/pubmed/24651983
  50. Dreher, M., Prevoteau-Jonquet, J., Trellet, M., Piuzzi, M., Baaden, M., Raffin, B., Ferey, N., Robert, S. and Limet, S. (2014) ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations. Faraday Discuss, 169, 119-142. http://www.ncbi.nlm.nih.gov/pubmed/25340956
  51. Della Pia, E.A., Holm, J.V., Lloret, N., Le Bon, C., Popot, J.L., Zoonens, M., Nygard, J. and Martinez, K.L. (2014) A step closer to membrane protein multiplexed nanoarrays using biotin-doped polypyrrole. ACS Nano, 8, 1844-1853. http://www.ncbi.nlm.nih.gov/pubmed/24476392
  52. Della Pia, E.A., Hansen, R.W., Zoonens, M. and Martinez, K.L. (2014) Functionalized amphipols: a versatile toolbox suitable for applications of membrane proteins in synthetic biology. J Membr Biol, 247, 815-826. http://www.ncbi.nlm.nih.gov/pubmed/24728227
  53. Delan-Forino, C., Deforges, J., Benard, L., Sargueil, B., Maurel, M.C. and Torchet, C. (2014) Structural analyses of Avocado sunblotch viroid reveal differences in the folding of plus and minus RNA strands. Viruses, 6, 489-506. http://www.ncbi.nlm.nih.gov/pubmed/24481250
  54. Catoire, L.J., Warnet, X.L. and Warschawski, D.E. (2014) In Mus-Veteau, I. (ed.), Membrane Proteins Production for Structural Analysis. Springer New York, pp. 315-345.
  55. Caillet, J., Gracia, C., Fontaine, F. and Hajnsdorf, E. (2014) Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function. RNA, 20, 1567-1578. http://www.ncbi.nlm.nih.gov/pubmed/25147238
  56. Boudry, P., Gracia, C., Monot, M., Caillet, J., Saujet, L., Hajnsdorf, E., Dupuy, B., Martin-Verstraete, I. and Soutourina, O. (2014) Pleiotropic role of the RNA chaperone protein Hfq in the human pathogen Clostridium difficile. J Bacteriol, 196, 3234-3248. http://www.ncbi.nlm.nih.gov/pubmed/24982306
  57. Benbahouche, N.H., Iliopoulos, I., Torok, I., Marhold, J., Henri, J., Kajava, A.V., Farkas, R., Kempf, T., Schnolzer, M., Meyer, P. et al. (2014) 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, 289, 6236-6247. http://www.ncbi.nlm.nih.gov/pubmed/24394412
  58. Aussel, L., Pierrel, F., Loiseau, L., Lombard, M., Fontecave, M. and Barras, F. (2014) Biosynthesis and physiology of coenzyme Q in bacteria. Biochim Biophys Acta, 1837, 1004-1011. http://www.ncbi.nlm.nih.gov/pubmed/24480387
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