2015

Publications 2015

  1. 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.
  2. Condon, C. Airpnp: Auto- and Integrated Regulation of Polynucleotide Phosphorylase. J. Bacteriol. 2015, 197 (24), 3748–3750 .
  3. 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.
  4. 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.
  5. 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.
  6. Mazur, A. K.; Shepelyansky, D. L. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule. Phys. Rev. Lett. 2015, 115 (18), 188104.
  7. 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.
  8. 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 .
  9. Bourgeron, T.; Xu, Z.; Doumic, M.; Teixeira, M. T. The Asymmetry of Telomere Replication Contributes to Replicative Senescence Heterogeneity. Sci Rep 2015, 5, 15326.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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), 10478–1048.
  18. 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 .
  19. 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.
  20. 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.
  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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. Cragnolini, T.; Derreumaux, P.; Pasquali, S. Ab Initio RNA Folding. J Phys Condens Matter 2015, 27 (23), 233102.
  28. 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 .
  29. 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.
  30. 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 .
  31. Cubellis, M. V.; Baaden, M.; Andreotti, G. Taming Molecular Flexibility to Tackle Rare Diseases. Biochimie 2015, 113, 54–58 .
  32. 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.
  33. 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.
  34. 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 .
  35. 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 .
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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 .
  45. 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 .
  46. 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.
  47. 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.
  48. 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), 2404–2414f.
  49. Huan, T. N.; Andreiadis, E. S.; Heidkamp, J.; Simon, P.; Derat, E.; Cobo, S.; Royal, G.; Bergmann, A.; Strasser, P.; Dau, H.; Artero, V.; Fontecave, M. From Molecular Copper Complexes to Composite Electrocatalytic Materials for Selective Reduction of CO2 to Formic Acid. J. Mater. Chem. A 2015, 3 (7), 3901–3907.
  50. Chambers, M. B.; Wang, X.; Elgrishi, N.; Hendon, C. H.; Walsh, A.; Bonnefoy, J.; Canivet, J.; Quadrelli, E. A.; Farrusseng, D.; Mellot‐Draznieks, C.; Fontecave, M. Photocatalytic Carbon Dioxide Reduction with Rhodium‐based Catalysts in Solution and Heterogenized within Metal–Organic Frameworks. ChemSusChem 2015, 8 (4), 603–608 .
  51. Chambers, M. B.; Wang, X.; Elgrishi, N.; Hendon, C. H.; Walsh, A.; Bonnefoy, J.; Canivet, J.; Quadrelli, E. A.; Farrusseng, D.; Mellot‐Draznieks, C.; Fontecave, M. Photocatalytic Carbon Dioxide Reduction with Rhodium‐based Catalysts in Solution and Heterogenized within Metal–Organic Frameworks. ChemSusChem 2015, 8 (4), 603–608.
  52. 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.
  53. Doig, A. J.; Derreumaux, P. Inhibition of Protein Aggregation and Amyloid Formation by Small Molecules. Curr. Opin. Struct. Biol. 2015, 30, 50–56.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. Elgrishi, N.; B. Chambers, M.; Fontecave, M. Turning It off! Disfavouring Hydrogen Evolution to Enhance Selectivity for CO Production during Homogeneous CO 2 Reduction by Cobalt–terpyridine Complexes. Chemical Science 2015, 6 (4), 2522–2531 
  61. 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.
  62. 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 .
  63. Bizebard, T.; Dreyfus, M. A FRET-Based, Continuous Assay for the Helicase Activity of DEAD-Box Proteins. Methods Mol. Biol. 2015, 1259, 199–209.
  64. 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.
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