2015

Publications 2015

(1) Adamska-Venkatesh, A.; Roy, S.; Siebel, J. F.; Simmons, T. R.; Fontecave, M.; Artero, V.; Reijerse, E.; Lubitz, W. Spectroscopic Characterization of the Bridging Amine in the Active Site of [FeFe] Hydrogenase Using Isotopologues of the H-Cluster. J. Am. Chem. Soc. 2015, 137 (40), 12744–12747 DOI: 10.1021/jacs.5b06240.

(2) Adamska-Venkatesh, A.; Simmons, T. R.; Siebel, J. F.; Artero, V.; Fontecave, M.; Reijerse, E.; Lubitz, W. Artificially Maturated [FeFe] Hydrogenase from Chlamydomonas Reinhardtii: A HYSCORE and ENDOR Study of a Non-Natural H-Cluster. Phys Chem Chem Phys 2015, 17 (7), 5421–5430 DOI: 10.1039/c4cp05426a.

(3) Artero, V.; Berggren, G.; Atta, M.; Caserta, G.; Roy, S.; Pecqueur, L.; Fontecave, M. From Enzyme Maturation to Synthetic Chemistry: The Case of Hydrogenases. Acc. Chem. Res. 2015, 48 (8), 2380–2387 DOI: 10.1021/acs.accounts.5b00157.

(4) Bailleul, B.; Berne, N.; Murik, O.; Petroutsos, D.; Prihoda, J.; Tanaka, A.; Villanova, V.; Bligny, R.; Flori, S.; Falconet, D.; Krieger-Liszkay, A.; Santabarbara, S.; Rappaport, F.; Joliot, P.; Tirichine, L.; Falkowski, P. G.; Cardol, P.; Bowler, C.; Finazzi, G. Energetic Coupling between Plastids and Mitochondria Drives CO2 Assimilation in Diatoms. Nature 2015, 524 (7565), 366–369 DOI: 10.1038/nature14599.

(5) Banroques, J.; Tanner, N. K. Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-Box RNA Helicases. Methods Mol. Biol. 2015, 1259, 165–181 DOI: 10.1007/978-1-4939-2214-7_11.

(6) Berthoumieu, O.; Nguyen, P. H.; Castillo-Frias, M. P. D.; Ferre, S.; Tarus, B.; Nasica-Labouze, J.; Noël, S.; Saurel, O.; Rampon, C.; Doig, A. J.; Derreumaux, P.; Faller, P. Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry 2015, 21 (36), 12657–12666 DOI: 10.1002/chem.201500888.

(7) Bizebard, T.; Dreyfus, M. A FRET-Based, Continuous Assay for the Helicase Activity of DEAD-Box Proteins. Methods Mol. Biol. 2015, 1259, 199–209 DOI: 10.1007/978-1-4939-2214-7_13.

(8) Blaby, I. K.; Blaby-Haas, C. E.; Perez-Perez, M. E.; Schmollinger, S.; Fitz-Gibbon, S.; Lemaire, S. D.; Merchant, S. S. Genome-Wide Analysis on Chlamydomonas Reinhardtii Reveals the Impact of Hydrogen Peroxide on Protein Stress Responses and Overlap with Other Stress Transcriptomes. Plant J. 2015, 84 (5), 974–988 DOI: 10.1111/tpj.13053.

(9) Boulouis, A.; Drapier, D.; Razafimanantsoa, H.; Wostrikoff, K.; Tourasse, N. J.; Pascal, K.; Girard-Bascou, J.; Vallon, O.; Wollman, F.-A.; Choquet, Y. Spontaneous Dominant Mutations in Chlamydomonas Highlight Ongoing Evolution by Gene Diversification. Plant Cell 2015, 27 (4), 984–1001 DOI: 10.1105/tpc.15.00010.

(10) Bou-Nader, C.; Pecqueur, L.; Bregeon, D.; Kamah, A.; Guérineau, V.; Golinelli-Pimpaneau, B.; Guimarães, B. G.; Fontecave, M.; Hamdane, D. An Extended DsRBD Is Required for Post-Transcriptional Modification in Human TRNAs. Nucleic Acids Res. 2015, 43 (19), 9446–9456 DOI: 10.1093/nar/gkv989.

(11) Bourgeron, T.; Xu, Z.; Doumic, M.; Teixeira, M. T. The Asymmetry of Telomere Replication Contributes to Replicative Senescence Heterogeneity. Sci Rep 2015, 5, 15326 DOI: 10.1038/srep15326.

(12) Boyer, B.; Ezelin, J.; Poulain, P.; Saladin, A.; Zacharias, M.; Robert, C. H.; Prévost, C. An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA. PLoS ONE 2015, 10 (3), e0116414 DOI: 10.1371/journal.pone.0116414.

(13) Bréchemier-Baey, D.; Domínguez-Ramírez, L.; Oberto, J.; Plumbridge, J. Operator Recognition by the ROK Transcription Factor Family Members, NagC and Mlc. Nucleic Acids Res. 2015, 43 (1), 361–372 DOI: 10.1093/nar/gku1265.

(14) Caserta, G.; Roy, S.; Atta, M.; Artero, V.; Fontecave, M. Artificial Hydrogenases: Biohybrid and Supramolecular Systems for Catalytic Hydrogen Production or Uptake. Curr Opin Chem Biol 2015, 25, 36–47 DOI: 10.1016/j.cbpa.2014.12.018.

(15) Chakraborty, D.; Taly, A.; Sterpone, F. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. J Phys Chem B 2015, 119 (40), 12760–12770 DOI: 10.1021/acs.jpcb.5b05791.

(16) Clowez, S.; Godaux, D.; Cardol, P.; Wollman, F.-A.; Rappaport, F. The Involvement of Hydrogen-Producing and ATP-Dependent NADPH-Consuming Pathways in Setting the Redox Poise in the Chloroplast of Chlamydomonas Reinhardtii in Anoxia. J. Biol. Chem. 2015, 290 (13), 8666–8676 DOI: 10.1074/jbc.M114.632588.

(17) Cragnolini, T.; Derreumaux, P.; Pasquali, S. Ab Initio RNA Folding. J Phys Condens Matter 2015, 27 (23), 233102 DOI: 10.1088/0953-8984/27/23/233102.

(18) Cragnolini, T.; Laurin, Y.; Derreumaux, P.; Pasquali, S. Coarse-Grained HiRE-RNA Model for Ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J Chem Theory Comput 2015, 11 (7), 3510–3522 DOI: 10.1021/acs.jctc.5b00200.

(19) Cubellis, M. V.; Baaden, M.; Andreotti, G. Taming Molecular Flexibility to Tackle Rare Diseases. Biochimie 2015, 113, 54–58 DOI: 10.1016/j.biochi.2015.03.018.

(20) Damodaran, S. P.; Eberhard, S.; Boitard, L.; Rodriguez, J. G.; Wang, Y.; Bremond, N.; Baudry, J.; Bibette, J.; Wollman, F.-A. A Millifluidic Study of Cell-to-Cell Heterogeneity in Growth-Rate and Cell-Division Capability in Populations of Isogenic Cells of Chlamydomonas Reinhardtii. PLoS ONE 2015, 10 (3), e0118987 DOI: 10.1371/journal.pone.0118987.

(21) Danilowicz, C.; Yang, D.; Kelley, C.; Prévost, C.; Prentiss, M. The Poor Homology Stringency in the Heteroduplex Allows Strand Exchange to Incorporate Desirable Mismatches without Sacrificing Recognition in Vivo. Nucleic Acids Res. 2015, 43 (13), 6473–6485 DOI: 10.1093/nar/gkv610.

(22) Doig, A. J.; Derreumaux, P. Inhibition of Protein Aggregation and Amyloid Formation by Small Molecules. Curr. Opin. Struct. Biol. 2015, 30, 50–56 DOI: 10.1016/j.sbi.2014.12.004.

(23) Durand, S.; Braun, F.; Lioliou, E.; Romilly, C.; Helfer, A.-C.; Kuhn, L.; Quittot, N.; Nicolas, P.; Romby, P.; Condon, C. A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus Subtilis. PLoS Genet. 2015, 11 (2), e1004957 DOI: 10.1371/journal.pgen.1004957.

(24) Durand, S.; Tomasini, A.; Braun, F.; Condon, C.; Romby, P. SRNA and MRNA Turnover in Gram-Positive Bacteria. FEMS Microbiol. Rev. 2015, 39 (3), 316–330 DOI: 10.1093/femsre/fuv007.

(25) Gilet, L.; DiChiara, J. M.; Figaro, S.; Bechhofer, D. H.; Condon, C. Small Stable RNA Maturation and Turnover in Bacillus Subtilis. Mol. Microbiol. 2015, 95 (2), 270–282 DOI: 10.1111/mmi.12863.

(26) Giusti, F.; Kessler, P.; Westh Hansen, R.; Della Pia, E. A.; Le Bon, C.; Mourier, G.; Popot, J.-L.; Martinez, K. L.; Zoonens, M. Synthesis of a Polyhistidine-Bearing Amphipol and Its Use for Immobilizing Membrane Proteins. Biomacromolecules 2015 DOI: 10.1021/acs.biomac.5b01010.

(27) Hamdane, D.; Bou-Nader, C.; Cornu, D.; Hui-Bon-Hoa, G.; Fontecave, M. Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry 2015, 54 (28), 4354–4364 DOI: 10.1021/acs.biochem.5b00501.

(28) Hattab, G.; Warschawski, D. E.; Moncoq, K.; Miroux, B. Escherichia Coli as Host for Membrane Protein Structure Determination: A Global Analysis. Sci Rep 2015, 5, 12097 DOI: 10.1038/srep12097.

(29) Hotto, A. M.; Castandet, B.; Gilet, L.; Higdon, A.; Condon, C.; Stern, D. B. Arabidopsis Chloroplast Mini-Ribonuclease III Participates in RRNA Maturation and Intron Recycling. Plant Cell 2015, 27 (3), 724–740 DOI: 10.1105/tpc.114.134452.

(30) Indrisiunaite, G.; Pavlov, M. Y.; Heurgué-Hamard, V.; Ehrenberg, M. On the PH Dependence of Class-1 RF-Dependent Termination of MRNA Translation. J. Mol. Biol. 2015, 427 (9), 1848–1860 DOI: 10.1016/j.jmb.2015.01.007.

(31) Jalal, A.; Schwarz, C.; Schmitz-Linneweber, C.; Vallon, O.; Nickelsen, J.; Bohne, A.-V. A Small Multifunctional Pentatricopeptide Repeat Protein in the Chloroplast of Chlamydomonas Reinhardtii. Mol Plant 2015, 8 (3), 412–426 DOI: 10.1016/j.molp.2014.11.019.

(32) Kalimeri, M.; Derreumaux, P.; Sterpone, F. Are Coarse-Grained Models Apt to Detect Protein Thermal Stability? The Case of OPEP Force Field. J Non Cryst Solids 2015, 407, 494–501 DOI: 10.1016/j.jnoncrysol.2014.07.005.

(33) Laurent, B.; Chavent, M.; Cragnolini, T.; Dahl, A. C. E.; Pasquali, S.; Derreumaux, P.; Sansom, M. S. P.; Baaden, M. Epock: Rapid Analysis of Protein Pocket Dynamics. Bioinformatics 2015, 31 (9), 1478–1480 DOI: 10.1093/bioinformatics/btu822.

(34) Laurin, Y.; Savarin, P.; Robert, C. H.; Takahashi, M.; Eyer, J.; Prevost, C.; Sacquin-Mora, S. Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry 2015, 54 (23), 3660–3669 DOI: 10.1021/acs.biochem.5b00146.

(35) Longatte, G.; Fu, H.-Y.; Buriez, O.; Labbé, E.; Wollman, F.-A.; Amatore, C.; Rappaport, F.; Guille-Collignon, M.; Lemaître, F. Evaluation of Photosynthetic Electrons Derivation by Exogenous Redox Mediators. Biophys. Chem. 2015, 205, 1–8 DOI: 10.1016/j.bpc.2015.05.003.

(36) Martin, N.; Ruchmann, J.; Tribet, C. Prevention of Aggregation and Renaturation of Carbonic Anhydrase via Weak Association with Octadecyl- or Azobenzene-Modified Poly(Acrylate) Derivatives. Langmuir 2015, 31 (1), 338–349 DOI: 10.1021/la503643q.

(37) Mazur, A. K.; Shepelyansky, D. L. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule. Phys. Rev. Lett. 2015, 115 (18), 188104 DOI: 10.1103/PhysRevLett.115.188104.

(38) Moraga-Cid, G.; Sauguet, L.; Huon, C.; Malherbe, L.; Girard-Blanc, C.; Petres, S.; Murail, S.; Taly, A.; Baaden, M.; Delarue, M.; Corringer, P.-J. Allosteric and Hyperekplexic Mutant Phenotypes Investigated on an Α1 Glycine Receptor Transmembrane Structure. Proc. Natl. Acad. Sci. U.S.A. 2015, 112 (9), 2865–2870 DOI: 10.1073/pnas.1417864112.

(39) Nasica-Labouze, J.; Nguyen, P. H.; Sterpone, F.; Berthoumieu, O.; Buchete, N.-V.; Coté, S.; De Simone, A.; Doig, A. J.; Faller, P.; Garcia, A.; Laio, A.; Li, M. S.; Melchionna, S.; Mousseau, N.; Mu, Y.; Paravastu, A.; Pasquali, S.; Rosenman, D. J.; Strodel, B.; Tarus, B.; Viles, J. H.; Zhang, T.; Wang, C.; Derreumaux, P. Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev. 2015, 115 (9), 3518–3563 DOI: 10.1021/cr500638n.

(40) Nawrocki, W. J.; Tourasse, N. J.; Taly, A.; Rappaport, F.; Wollman, F.-A. The Plastid Terminal Oxidase: Its Elusive Function Points to Multiple Contributions to Plastid Physiology. Annu Rev Plant Biol 2015, 66, 49–74 DOI: 10.1146/annurev-arplant-043014-114744.

(41) Ozeir, M.; Pelosi, L.; Ismail, A.; Mellot-Draznieks, C.; Fontecave, M.; Pierrel, F. Coq6 Is Responsible for the C4-Deamination Reaction in Coenzyme Q Biosynthesis in Saccharomyces Cerevisiae. J. Biol. Chem. 2015, 290 (40), 24140–24151 DOI: 10.1074/jbc.M115.675744.

(42) Pérez, S.; Tubiana, T.; Imberty, A.; Baaden, M. Three-Dimensional Representations of Complex Carbohydrates and Polysaccharides--SweetUnityMol: A Video Game-Based Computer Graphic Software. Glycobiology 2015, 25 (5), 483–491 DOI: 10.1093/glycob/cwu133.

(43) Plumbridge, J. Regulation of the Utilization of Amino Sugars by Escherichia Coli and Bacillus Subtilis: Same Genes, Different Control. J. Mol. Microbiol. Biotechnol. 2015, 25 (2–3), 154–167 DOI: 10.1159/000369583.

(44) Rahaman, O.; Kalimeri, M.; Melchionna, S.; Hénin, J.; Sterpone, F. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. J Phys Chem B 2015, 119 (29), 8939–8949 DOI: 10.1021/jp507571u.

(45) Santabarbara, S.; Bullock, B.; Rappaport, F.; Redding, K. E. Controlling Electron Transfer between the Two Cofactor Chains of Photosystem I by the Redox State of One of Their Components. Biophys. J. 2015, 108 (6), 1537–1547 DOI: 10.1016/j.bpj.2015.01.009.

(46) Sinturel, F.; Navickas, A.; Wery, M.; Descrimes, M.; Morillon, A.; Torchet, C.; Benard, L. Cytoplasmic Control of Sense-Antisense MRNA Pairs. Cell Reports 2015, 12 (11), 1853–1864 DOI: 10.1016/j.celrep.2015.08.016.

(47) Sterpone, F.; Derreumaux, P.; Melchionna, S. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J Chem Theory Comput 2015, 11 (4), 1843–1853 DOI: 10.1021/ct501015h.

(48) Stirnemann, G.; Sterpone, F. Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent. J Chem Theory Comput 2015, 11 (12), 5573–5577 DOI: 10.1021/acs.jctc.5b00954.

(49) Tarus, B.; Nguyen, P. H.; Berthoumieu, O.; Faller, P.; Doig, A. J.; Derreumaux, P. Molecular Structure of the NQTrp Inhibitor with the Alzheimer Aβ1-28 Monomer. Eur J Med Chem 2015, 91, 43–50 DOI: 10.1016/j.ejmech.2014.07.002.

(50) Tarus, B.; Tran, T. T.; Nasica-Labouze, J.; Sterpone, F.; Nguyen, P. H.; Derreumaux, P. Structures of the Alzheimer’s Wild-Type Aβ1-40 Dimer from Atomistic Simulations. J Phys Chem B 2015, 119 (33), 10478–10487 DOI: 10.1021/acs.jpcb.5b05593.

(51) Tourasse, N. J.; Shtaida, N.; Khozin-Goldberg, I.; Boussiba, S.; Vallon, O. The Complete Mitochondrial Genome Sequence of the Green Microalga Lobosphaera (Parietochloris) Incisa Reveals a New Type of Palindromic Repetitive Repeat. BMC Genomics 2015, 16, 580 DOI: 10.1186/s12864-015-1792-x.

(52) Wang, F.; Johnson, X.; Cavaiuolo, M.; Bohne, A.-V.; Nickelsen, J.; Vallon, O. Two Chlamydomonas OPR Proteins Stabilize Chloroplast MRNAs Encoding Small Subunits of Photosystem II and Cytochrome B6 F. Plant J. 2015, 82 (5), 861–873 DOI: 10.1111/tpj.12858.

(53) Warnet, X. L.; Arnold, A. A.; Marcotte, I.; Warschawski, D. E. In-Cell Solid-State NMR: An Emerging Technique for the Study of Biological Membranes. Biophysical Journal 2015, 109 (12), 2461–2466 DOI: 10.1016/j.bpj.2015.10.041.

(54) Xu, Z.; Fallet, E.; Paoletti, C.; Fehrmann, S.; Charvin, G.; Teixeira, M. T. Two Routes to Senescence Revealed by Real-Time Analysis of Telomerase-Negative Single Lineages. Nat. Commun. 2015, 6, 7680 DOI: 10.1038/ncomms8680.

(55) Yadav, D.; Lacombat, F.; Dozova, N.; Rappaport, F.; Plaza, P.; Espagne, A. Real-Time Monitoring of Chromophore Isomerization and Deprotonation during the Photoactivation of the Fluorescent Protein Dronpa. J Phys Chem B 2015, 119 (6), 2404–2414 DOI: 10.1021/jp507094f.

(56) Yang, D.; Boyer, B.; Prévost, C.; Danilowicz, C.; Prentiss, M. Integrating Multi-Scale Data on Homologous Recombination into a New Recognition Mechanism Based on Simulations of the RecA-SsDNA/DsDNA Structure. Nucleic Acids Res. 2015, 43 (21), 10251–10263 DOI: 10.1093/nar/gkv883.

(57) Yoo, B.-K.; Lamarre, I.; Martin, J.-L.; Rappaport, F.; Negrerie, M. Motion of Proximal Histidine and Structural Allosteric Transition in Soluble Guanylate Cyclase. Proc. Natl. Acad. Sci. U.S.A. 2015, 112 (14), E1697-1704 DOI: 10.1073/pnas.1423098112.

(58) Zhang, T.; Nguyen, P. H.; Nasica-Labouze, J.; Mu, Y.; Derreumaux, P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B 2015, 119 (23), 6941–6951 DOI: 10.1021/acs.jpcb.5b03381.

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