2015

Publications 2015

135.     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. http://www.ncbi.nlm.nih.gov/pubmed/25985144

134.     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. http://www.ncbi.nlm.nih.gov/pubmed/25831539

133.     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. http://www.ncbi.nlm.nih.gov/pubmed/26384422

132.     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. http://www.ncbi.nlm.nih.gov/pubmed/25325882

131.     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. http://www.ncbi.nlm.nih.gov/pubmed/26158780

130.     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. http://www.ncbi.nlm.nih.gov/pubmed/26682804

129.     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. http://www.ncbi.nlm.nih.gov/pubmed/25898982

128.     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. http://www.ncbi.nlm.nih.gov/pubmed/26238519

127.     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. http://www.ncbi.nlm.nih.gov/pubmed/26228450

126.     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. http://www.ncbi.nlm.nih.gov/pubmed/25011560

125.     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. http://www.ncbi.nlm.nih.gov/pubmed/26642979

124.     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. http://www.ncbi.nlm.nih.gov/pubmed/26574390

123.     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. http://www.ncbi.nlm.nih.gov/pubmed/26344770

122.     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. http://www.ncbi.nlm.nih.gov/pubmed/25809266

121.     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. http://www.ncbi.nlm.nih.gov/pubmed/25317828

120.     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. http://www.ncbi.nlm.nih.gov/pubmed/26404460

119.     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. http://www.ncbi.nlm.nih.gov/pubmed/26159076

118.     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. http://www.ncbi.nlm.nih.gov/pubmed/25475093

117.     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. http://www.ncbi.nlm.nih.gov/pubmed/26260787

116.     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. http://www.ncbi.nlm.nih.gov/pubmed/25580838

115.     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. http://www.ncbi.nlm.nih.gov/pubmed/25789869

114.     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. http://www.ncbi.nlm.nih.gov/pubmed/25730860

113.     Mazur, A.K. and Shepelyansky, D.L. (2015) Algebraic Statistics of Poincare Recurrences in a DNA Molecule. Phys Rev Lett, 115, 188104. http://www.ncbi.nlm.nih.gov/pubmed/26565502

112.     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. http://www.ncbi.nlm.nih.gov/pubmed/25495869

111.     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. http://www.ncbi.nlm.nih.gov/pubmed/26051794

110.     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. http://www.ncbi.nlm.nih.gov/pubmed/26016807

109.     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. http://www.ncbi.nlm.nih.gov/pubmed/25505095

108.     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. http://www.ncbi.nlm.nih.gov/pubmed/28100926

107.     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. http://www.ncbi.nlm.nih.gov/pubmed/25702521

106.     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. http://www.ncbi.nlm.nih.gov/pubmed/25619162

105.     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. http://dx.doi.org/10.1039/C4TA07022D

104.     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. http://www.ncbi.nlm.nih.gov/pubmed/25724636

103.     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. http://dx.doi.org/10.1038/srep12097

102.     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. http://www.ncbi.nlm.nih.gov/pubmed/26120776

101.     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. http://www.ncbi.nlm.nih.gov/pubmed/26492302

100.     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. http://www.ncbi.nlm.nih.gov/pubmed/25402410

99.       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. http://www.ncbi.nlm.nih.gov/pubmed/25597872

98.       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. http://www.ncbi.nlm.nih.gov/pubmed/28706660

97.       Durand, S., Tomasini, A., Braun, F., Condon, C. and Romby, P. (2015) sRNA and mRNA turnover in Gram-positive bacteria. FEMS Microbiol Rev. http://www.ncbi.nlm.nih.gov/pubmed/25934118

96.       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. http://www.ncbi.nlm.nih.gov/pubmed/25643072

95.       Doig, A.J. and Derreumaux, P. (2015) Inhibition of protein aggregation and amyloid formation by small molecules. Curr Opin Struct Biol, 30, 50-56. http://www.ncbi.nlm.nih.gov/pubmed/25559306

94.       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. http://www.ncbi.nlm.nih.gov/pubmed/26089391

93.       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. http://www.ncbi.nlm.nih.gov/pubmed/25760649

92.       Cubellis, M.V., Baaden, M. and Andreotti, G. (2015) Taming molecular flexibility to tackle rare diseases. Biochimie, 113, 54-58. http://www.ncbi.nlm.nih.gov/pubmed/25841341

91.       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. http://www.ncbi.nlm.nih.gov/pubmed/26575783

90.       Cragnolini, T., Derreumaux, P. and Pasquali, S. (2015) Ab initio RNA folding. J Phys Condens Matter, 27, 233102. http://www.ncbi.nlm.nih.gov/pubmed/25993396

89.       Condon, C. (2015) Airpnp: Auto- and Integrated Regulation of Polynucleotide Phosphorylase. J Bacteriol, 197, 3748-3750. http://www.ncbi.nlm.nih.gov/pubmed/26438817

88.       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. http://www.ncbi.nlm.nih.gov/pubmed/25691575

87.       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. http://www.ncbi.nlm.nih.gov/pubmed/25613479

86.       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. http://www.ncbi.nlm.nih.gov/pubmed/26335353

85.       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. http://www.ncbi.nlm.nih.gov/pubmed/25553541

84.       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. http://www.ncbi.nlm.nih.gov/pubmed/25452338

83.       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. http://www.ncbi.nlm.nih.gov/pubmed/25785454

82.       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. http://www.ncbi.nlm.nih.gov/pubmed/26468778

81.       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. http://www.ncbi.nlm.nih.gov/pubmed/25804537

80.       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. http://www.ncbi.nlm.nih.gov/pubmed/26429968

79.       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. http://www.ncbi.nlm.nih.gov/pubmed/26473430

78.       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. http://www.ncbi.nlm.nih.gov/pubmed/25579588

77.       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. http://www.ncbi.nlm.nih.gov/pubmed/26179053

76.       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. http://www.ncbi.nlm.nih.gov/pubmed/25579586

75.       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. http://www.ncbi.nlm.nih.gov/pubmed/26168400

74.       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. http://www.ncbi.nlm.nih.gov/pubmed/26165393

73.       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. http://www.ncbi.nlm.nih.gov/pubmed/25613229

72.       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. http://www.ncbi.nlm.nih.gov/pubmed/26393426

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