2015

Publications 2015

  1. Zhang, T., Nguyen, P.H., Nasica-Labouze, J., Mu, Y. and Derreumaux, P. (2015) Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B, 119, 6941-6951.
  2. Yoo, B.K., Lamarre, I., Martin, J.L., Rappaport, F. and Negrerie, M. (2015) Motion of proximal histidine and structural allosteric transition in soluble guanylate cyclase. Proc Natl Acad Sci U S A, 112, E1697-1704.
  3. Yang, D., Boyer, B., Prevost, C., Danilowicz, C. and Prentiss, M. (2015) Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res, 43, 10251-10263.
  4. Yadav, D., Lacombat, F., Dozova, N., Rappaport, F., Plaza, P. and Espagne, A. (2015) Real-time monitoring of chromophore isomerization and deprotonation during the photoactivation of the fluorescent protein Dronpa. J Phys Chem B, 119, 2404-2414.
  5. Xu, Z., Fallet, E., Paoletti, C., Fehrmann, S., Charvin, G. and Teixeira, M.T. (2015) Two routes to senescence revealed by real-time analysis of telomerase-negative single lineages. Nat Commun, 6, 7680.
  6. Warnet, X.L., Arnold, A.A., Marcotte, I. and Warschawski, D.E. (2015) In-Cell Solid-State NMR: An Emerging Technique for the Study of Biological Membranes. Biophys J, 109, 2461-2466.
  7. Wang, F., Johnson, X., Cavaiuolo, M., Bohne, A.V., Nickelsen, J. and Vallon, O. (2015) Two Chlamydomonas OPR proteins stabilize chloroplast mRNAs encoding small subunits of photosystem II and cytochrome b6 f. Plant J, 82, 861-873.
  8. Tourasse, N.J., Shtaida, N., Khozin-Goldberg, I., Boussiba, S. and Vallon, O. (2015) The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. BMC Genomics, 16, 580.
  9. Tarus, B., Tran, T.T., Nasica-Labouze, J., Sterpone, F., Nguyen, P.H. and Derreumaux, P. (2015) Structures of the Alzheimer's Wild-Type Abeta1-40 Dimer from Atomistic Simulations. J Phys Chem B, 119, 10478-10487.
  10. Tarus, B., Nguyen, P.H., Berthoumieu, O., Faller, P., Doig, A.J. and Derreumaux, P. (2015) Molecular structure of the NQTrp inhibitor with the Alzheimer Abeta1-28 monomer. Eur J Med Chem, 91, 43-50.
  11. Stirnemann, G. and Sterpone, F. (2015) Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent. J Chem Theory Comput, 11, 5573-5577.
  12. Sterpone, F., Derreumaux, P. and Melchionna, S. (2015) Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J Chem Theory Comput, 11, 1843-1853.
  13. Sinturel, F., Navickas, A., Wery, M., Descrimes, M., Morillon, A., Torchet, C. and Benard, L. (2015) Cytoplasmic Control of Sense-Antisense mRNA Pairs. Cell Rep, 12, 1853-1864.
  14. Santabarbara, S., Bullock, B., Rappaport, F. and Redding, K.E. (2015) Controlling electron transfer between the two cofactor chains of photosystem I by the redox state of one of their components. Biophys J, 108, 1537-1547.
  15. Rahaman, O., Kalimeri, M., Melchionna, S., Henin, J. and Sterpone, F. (2015) Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. J Phys Chem B, 119, 8939-8949.
  16. Porcher, J.P., Fogeron, T., Gomez-Mingot, M., Derat, E., Chamoreau, L.M., Li, Y. and Fontecave, M. (2015) A Bioinspired Molybdenum Complex as a Catalyst for the Photo- and Electroreduction of Protons. Angew Chem Int Ed Engl, 54, 14090-14093.
  17. Plumbridge, J. (2015) Regulation of the Utilization of Amino Sugars by Escherichia coli and Bacillus subtilis: Same Genes, Different Control. J Mol Microbiol Biotechnol, 25, 154-167.
  18. Perez, S., Tubiana, T., Imberty, A. and Baaden, M. (2015) Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software. Glycobiology, 25, 483-491.
  19. Ozeir, M., Pelosi, L., Ismail, A., Mellot-Draznieks, C., Fontecave, M. and Pierrel, F. (2015) Coq6 is responsible for the C4-deamination reaction in coenzyme Q biosynthesis in Saccharomyces cerevisiae. J Biol Chem, 290, 24140-24151.
  20. Nawrocki, W.J., Tourasse, N.J., Taly, A., Rappaport, F. and Wollman, F.A. (2015) The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. Annu Rev Plant Biol, 66, 49-74.
  21. Nasica-Labouze, J., Nguyen, P.H., Sterpone, F., Berthoumieu, O., Buchete, N.V., Cote, S., De Simone, A., Doig, A.J., Faller, P., Garcia, A. et al. (2015) Amyloid beta Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev, 115, 3518-3563.
  22. Moraga-Cid, G., Sauguet, L., Huon, C., Malherbe, L., Girard-Blanc, C., Petres, S., Murail, S., Taly, A., Baaden, M., Delarue, M. et al. (2015) Allosteric and hyperekplexic mutant phenotypes investigated on an alpha1 glycine receptor transmembrane structure. Proc Natl Acad Sci U S A, 112, 2865-2870.
  23. Mazur, A.K. and Shepelyansky, D.L. (2015) Algebraic Statistics of Poincare Recurrences in a DNA Molecule. Phys Rev Lett, 115, 188104.
  24. Martin, N., Ruchmann, J. and Tribet, C. (2015) Prevention of aggregation and renaturation of carbonic anhydrase via weak association with octadecyl- or azobenzene-modified poly(acrylate) derivatives. Langmuir, 31, 338-349.
  25. Longatte, G., Fu, H.Y., Buriez, O., Labbe, E., Wollman, F.A., Amatore, C., Rappaport, F., Guille-Collignon, M. and Lemaitre, F. (2015) Evaluation of photosynthetic electrons derivation by exogenous redox mediators. Biophys Chem, 205, 1-8.
  26. Laurin, Y., Savarin, P., Robert, C.H., Takahashi, M., Eyer, J., Prevost, C. and Sacquin-Mora, S. (2015) Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry, 54, 3660-3669.
  27. Laurent, B., Chavent, M., Cragnolini, T., Dahl, A.C., Pasquali, S., Derreumaux, P., Sansom, M.S. and Baaden, M. (2015) Epock: rapid analysis of protein pocket dynamics. Bioinformatics, 31, 1478-1480.
  28. Kalimeri, M., Derreumaux, P. and Sterpone, F. (2015) Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field. J Non Cryst Solids, 407, 494-501.
  29. Jalal, A., Schwarz, C., Schmitz-Linneweber, C., Vallon, O., Nickelsen, J. and Bohne, A.V. (2015) A small multifunctional pentatricopeptide repeat protein in the chloroplast of Chlamydomonas reinhardtii. Mol Plant, 8, 412-426.
  30. Indrisiunaite, G., Pavlov, M.Y., Heurgue-Hamard, V. and Ehrenberg, M. (2015) On the pH dependence of class-1 RF-dependent termination of mRNA translation. J Mol Biol, 427, 1848-1860.
  31. Huan, T.N., Andreiadis, E.S., Heidkamp, J., Simon, P., Derat, E., Cobo, S., Royal, G., Bergmann, A., Strasser, P., Dau, H. et al. (2015) From molecular copper complexes to composite electrocatalytic materials for selective reduction of CO2 to formic acid. Journal of Materials Chemistry A, 3, 3901-3907.
  32. Hotto, A.M., Castandet, B., Gilet, L., Higdon, A., Condon, C. and Stern, D.B. (2015) Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling. Plant Cell, 27, 724-740.
  33. Hattab, G., Warschawski, D.E., Moncoq, K. and Miroux, B. (2015) Escherichia coli as host for membrane protein structure determination: a global analysis. Scientific Reports, 5, 12097.
  34. Hamdane, D., Bou-Nader, C., Cornu, D., Hui-Bon-Hoa, G. and Fontecave, M. (2015) Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry, 54, 4354-4364.
  35. Giusti, F., Kessler, P., Hansen, R.W., Della Pia, E.A., Le Bon, C., Mourier, G., Popot, J.L., Martinez, K.L. and Zoonens, M. (2015) Synthesis of a Polyhistidine-bearing Amphipol and its Use for Immobilizing Membrane Proteins. Biomacromolecules, 16, 3751-3761.
  36. Gilet, L., DiChiara, J.M., Figaro, S., Bechhofer, D.H. and Condon, C. (2015) Small stable RNA maturation and turnover in Bacillus subtilis. Mol Microbiol, 95, 270-282.
  37. Elgrishi, N., Griveau, S., Chambers, M.B., Bedioui, F. and Fontecave, M. (2015) Versatile functionalization of carbon electrodes with a polypyridine ligand: metallation and electrocatalytic H(+) and CO2 reduction. Chem Commun (Camb), 51, 2995-2998.
  38. Elgrishi, N., Chambers, M.B. and Fontecave, M. (2015) Turning it off! Disfavouring hydrogen evolution to enhance selectivity for CO production during homogeneous CO2 reduction by cobalt-terpyridine complexes. Chem Sci, 6, 2522-2531.
  39. Durand, S., Tomasini, A., Braun, F., Condon, C. and Romby, P. (2015) sRNA and mRNA turnover in Gram-positive bacteria. FEMS Microbiol Rev.
  40. Durand, S., Braun, F., Lioliou, E., Romilly, C., Helfer, A.C., Kuhn, L., Quittot, N., Nicolas, P., Romby, P. and Condon, C. (2015) A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis. PLoS Genet, 11, e1004957.
  41. Doig, A.J. and Derreumaux, P. (2015) Inhibition of protein aggregation and amyloid formation by small molecules. Curr Opin Struct Biol, 30, 50-56.
  42. Danilowicz, C., Yang, D., Kelley, C., Prevost, C. and Prentiss, M. (2015) The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res, 43, 6473-6485.
  43. Damodaran, S.P., Eberhard, S., Boitard, L., Rodriguez, J.G., Wang, Y., Bremond, N., Baudry, J., Bibette, J. and Wollman, F.A. (2015) 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, 10, e0118987.
  44. Cubellis, M.V., Baaden, M. and Andreotti, G. (2015) Taming molecular flexibility to tackle rare diseases. Biochimie, 113, 54-58.
  45. Cragnolini, T., Laurin, Y., Derreumaux, P. and Pasquali, S. (2015) Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J Chem Theory Comput, 11, 3510-3522.
  46. Cragnolini, T., Derreumaux, P. and Pasquali, S. (2015) Ab initio RNA folding. J Phys Condens Matter, 27, 233102.
  47. Condon, C. (2015) Airpnp: Auto- and Integrated Regulation of Polynucleotide Phosphorylase. J Bacteriol, 197, 3748-3750.
  48. Clowez, S., Godaux, D., Cardol, P., Wollman, F.A. and Rappaport, F. (2015) 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, 290, 8666-8676.
  49. Chambers, M.B., Wang, X., Elgrishi, N., Hendon, C.H., Walsh, A., Bonnefoy, J., Canivet, J., Quadrelli, E.A., Farrusseng, D., Mellot-Draznieks, C. et al. (2015) Photocatalytic carbon dioxide reduction with rhodium-based catalysts in solution and heterogenized within metal-organic frameworks. ChemSusChem, 8, 603-608.
  50. Chakraborty, D., Taly, A. and Sterpone, F. (2015) Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. J Phys Chem B, 119, 12760-12770.
  51. Caserta, G., Roy, S., Atta, M., Artero, V. and Fontecave, M. (2015) Artificial hydrogenases: biohybrid and supramolecular systems for catalytic hydrogen production or uptake. Curr Opin Chem Biol, 25, 36-47.
  52. Brechemier-Baey, D., Dominguez-Ramirez, L., Oberto, J. and Plumbridge, J. (2015) Operator recognition by the ROK transcription factor family members, NagC and Mlc. Nucleic Acids Res, 43, 361-372.
  53. Boyer, B., Ezelin, J., Poulain, P., Saladin, A., Zacharias, M., Robert, C.H. and Prevost, C. (2015) An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One, 10, e0116414.
  54. Bourgeron, T., Xu, Z., Doumic, M. and Teixeira, M.T. (2015) The asymmetry of telomere replication contributes to replicative senescence heterogeneity. Sci Rep, 5, 15326.
  55. Boulouis, A., Drapier, D., Razafimanantsoa, H., Wostrikoff, K., Tourasse, N.J., Pascal, K., Girard-Bascou, J., Vallon, O., Wollman, F.A. and Choquet, Y. (2015) Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification. Plant Cell, 27, 984-1001.
  56. Bou-Nader, C., Pecqueur, L., Bregeon, D., Kamah, A., Guerineau, V., Golinelli-Pimpaneau, B., Guimaraes, B.G., Fontecave, M. and Hamdane, D. (2015) An extended dsRBD is required for post-transcriptional modification in human tRNAs. Nucleic Acids Res, 43, 9446-9456.
  57. Blaby, I.K., Blaby-Haas, C.E., Perez-Perez, M.E., Schmollinger, S., Fitz-Gibbon, S., Lemaire, S.D. and Merchant, S.S. (2015) Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. Plant J, 84, 974-988.
  58. Bizebard, T. and Dreyfus, M. (2015) A FRET-based, continuous assay for the helicase activity of DEAD-box proteins. Methods Mol Biol, 1259, 199-209.
  59. Berthoumieu, O., Nguyen, P.H., Castillo-Frias, M.P., Ferre, S., Tarus, B., Nasica-Labouze, J., Noel, S., Saurel, O., Rampon, C., Doig, A.J. et al. (2015) Combined experimental and simulation studies suggest a revised mode of action of the anti-Alzheimer disease drug NQ-Trp. Chemistry, 21, 12657-12666.
  60. Banroques, J. and Tanner, N.K. (2015) Bioinformatics and biochemical methods to study the structural and functional elements of DEAD-box RNA helicases. Methods Mol Biol, 1259, 165-181.
  61. Bailleul, B., Berne, N., Murik, O., Petroutsos, D., Prihoda, J., Tanaka, A., Villanova, V., Bligny, R., Flori, S., Falconet, D. et al. (2015) Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms. Nature, 524, 366-369.
  62. Artero, V., Berggren, G., Atta, M., Caserta, G., Roy, S., Pecqueur, L. and Fontecave, M. (2015) From enzyme maturation to synthetic chemistry: the case of hydrogenases. Acc Chem Res, 48, 2380-2387.
  63. Adamska-Venkatesh, A., Simmons, T.R., Siebel, J.F., Artero, V., Fontecave, M., Reijerse, E. and Lubitz, W. (2015) Artificially maturated [FeFe] hydrogenase from Chlamydomonas reinhardtii: a HYSCORE and ENDOR study of a non-natural H-cluster. Phys Chem Chem Phys, 17, 5421-5430.
  64. Adamska-Venkatesh, A., Roy, S., Siebel, J.F., Simmons, T.R., Fontecave, M., Artero, V., Reijerse, E. and Lubitz, W. (2015) Spectroscopic Characterization of the Bridging Amine in the Active Site of [FeFe] Hydrogenase Using Isotopologues of the H-Cluster. J Am Chem Soc, 137, 12744-12747.
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