Publications 2016

  1. Stadlbauer, P.; Mazzanti, L.; Cragnolini, T.; Wales, D. J.; Derreumaux, P.; Pasquali, S.; Šponer, J. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J Chem Theory Comput 2016, 12 (12), 6077–6097 https://doi.org/10.1021/acs.jctc.6b00667.
  2. Hamdane, D.; Grosjean, H.; Fontecave, M. Flavin-Dependent Methylation of RNAs: Complex Chemistry for a Simple Modification. J. Mol. Biol. 2016, 428 (24 Pt B), 4867–4881 https://doi.org/10.1016/j.jmb.2016.10.031.
  3. Pérez-Pérez, M. E.; Lemaire, S. D.; Crespo, J. L. Control of Autophagy in Chlamydomonas Is Mediated through Redox-Dependent Inactivation of the ATG4 Protease. Plant Physiology 2016, 172 (4), 2219–2234 https://doi.org/10.1104/pp.16.01582.
  4. Nguyen, P. H.; Sterpone, F.; Pouplana, R.; Derreumaux, P.; Campanera, J. M. Dimerization Mechanism of Alzheimer Aβ40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J Phys Chem B 2016, 120 (47), 12111–12126 https://doi.org/10.1021/acs.jpcb.6b10722.
  5. Wollman, F.-A. An Antimicrobial Origin of Transit Peptides Accounts for Early Endosymbiotic Events. Traffic 2016, 17 (12), 1322–1328 https://doi.org/10.1111/tra.12446.
  6. Esther Perez-Perez, M.; Lemaire, S. D.; Crespo, J. L. Control of Autophagy in Chlamydomonas Is Mediated through Redox-Dependent Inactivation of the ATG4 Protease. Plant Physiol. 2016, 172 (4), 2219–2234 https://doi.org/10.1104/pp.16.01582.
  7. Brosse, A.; Korobeinikova, A.; Gottesman, S.; Guillier, M. Unexpected Properties of SRNA Promoters Allow Feedback Control via Regulation of a Two-Component System. Nucleic Acids Res. 2016, 44 (20), 9650–9666 https://doi.org/10.1093/nar/gkw642.
  8. Chiricotto, M.; Sterpone, F.; Derreumaux, P.; Melchionna, S. Multiscale Simulation of Molecular Processes in Cellular Environments. Philos Trans A Math Phys Eng Sci 2016, 374 (2080) https://doi.org/10.1098/rsta.2016.0225.
  9. Fontaine, F.; Gasiorowski, E.; Gracia, C.; Ballouche, M.; Caillet, J.; Marchais, A.; Hajnsdorf, E. The Small RNA SraG Participates in PNPase Homeostasis. RNA 2016, 22 (10), 1560–1573 https://doi.org/10.1261/rna.055236.115.
  10. Huan, T. N.; Simon, P.; Benayad, A.; Guetaz, L.; Artero, V.; Fontecave, M. Cu/Cu2O Electrodes and CO2 Reduction to Formic Acid: Effects of Organic Additives on Surface Morphology and Activity. Chem. Eur. J. 2016, 22 (39), 14029–14035 https://doi.org/10.1002/chem.201602618.
  11. Huan, T. N.; Prakash, P.; Simon, P.; Rousse, G.; Xu, X.; Artero, V.; Gravel, E.; Doris, E.; Fontecave, M. CO2 Reduction to CO in Water: Carbon Nanotube–Gold Nanohybrid as a Selective and Efficient Electrocatalyst. ChemSusChem 2016, 9 (17), 2317–2320 https://doi.org/10.1002/cssc.201600597.
  12. Casiraghi, M.; Damian, M.; Lescop, E.; Point, E.; Moncoq, K.; Morellet, N.; Levy, D.; Marie, J.; Guittet, E.; Banères, J.-L.; Catoire, L. J. Functional Modulation of a G Protein-Coupled Receptor Conformational Landscape in a Lipid Bilayer. J. Am. Chem. Soc. 2016, 138 (35), 11170–11175 https://doi.org/10.1021/jacs.6b04432.
  13. Bergdoll, L.; Ten Brink, F.; Nitschke, W.; Picot, D.; Baymann, F. From Low- to High-Potential Bioenergetic Chains: Thermodynamic Constraints of Q-Cycle Function. Biochim. Biophys. Acta 2016, 1857 (9), 1569–1579 https://doi.org/10.1016/j.bbabio.2016.06.006.
  14. Chiricotto, M.; Tran, T. T.; Nguyen, P. H.; Melchionna, S.; Sterpone, F.; Derreumaux, P. Coarse-Grained and All-Atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr. J. Chem. 2016, n/a-n/a https://doi.org/10.1002/ijch.201600048.
  15. Zaffagnini, M.; De Mia, M.; Morisse, S.; Di Giacinto, N.; Marchand, C. H.; Maes, A.; Lemaire, S. D.; Trost, P. Protein S-Nitrosylation in Photosynthetic Organisms: A Comprehensive Overview with Future Perspectives. BBA-Proteins Proteomics 2016, 1864 (8), 952–966 https://doi.org/10.1016/j.bbapap.2016.02.006.
  16. Hamdane, D.; Velours, C.; Cornu, D.; Nicaise, M.; Lombard, M.; Fontecave, M. A Chemical Chaperone Induces Inhomogeneous Conformational Changes in Flexible Proteins. Phys Chem Chem Phys 2016, 18 (30), 20410–20421 https://doi.org/10.1039/c6cp03635j.
  17. Chiricotto, M.; Melchionna, S.; Derreumaux, P.; Sterpone, F. Hydrodynamic Effects on β-Amyloid (16-22) Peptide Aggregation. J Chem Phys 2016, 145 (3), 035102 https://doi.org/10.1063/1.4958323.
  18. Ruiz-Larrabeiti, O.; Plágaro, A. H.; Gracia, C.; Sevillano, E.; Gallego, L.; Hajnsdorf, E.; Kaberdin, V. R. A New Custom Microarray for SRNA Profiling in Escherichia Coli. FEMS Microbiol. Lett. 2016, 363 (13) https://doi.org/10.1093/femsle/fnw131.
  19. Guetle, D. D.; Roret, T.; Mueller, S. J.; Couturier, J.; Lemaire, S. D.; Hecker, A.; Dhalleine, T.; Buchanan, B. B.; Reski, R.; Einsle, O.; Jacquot, J.-P. Chloroplast FBPase and SBPase Are Thioredoxin-Linked Enzymes with Similar Architecture but Different Evolutionary Histories. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (24), 6779–6784 https://doi.org/10.1073/pnas.1606241113.
  20. Brandt, T.; Cavellini, L.; Kuehlbrandt, W.; Cohen, M. M. A Mitofusin-Dependent Docking Ring Complex Triggers Mitochondrial Fusion in Vitro. eLife 2016, 5, e14618 https://doi.org/10.7554/eLife.14618.
  21. Berger, H.; De Mia, M.; Morisse, S.; Marchand, C. H.; Lemaire, S. D.; Wobbe, L.; Kruse, O. A Light Switch Based on Protein S-Nitrosylation Fine-Tunes Photosynthetic Light Harvesting in Chlamydomonas. Plant Physiol. 2016, 171 (2), 821–832 https://doi.org/10.1104/pp.15.01878.
  22. Tran, T. T.; Nguyen, P. H.; Derreumaux, P. Lattice Model for Amyloid Peptides: OPEP Force Field Parametrization and Applications to the Nucleus Size of Alzheimer’s Peptides. J Chem Phys 2016, 144 (20), 205103 https://doi.org/10.1063/1.4951739.
  23. Zambolin, S.; Clantin, B.; Chami, M.; Hoos, S.; Haouz, A.; Villeret, V.; Delepelaire, P. Structural Basis for Haem Piracy from Host Haemopexin by Haemophilus Influenzae. Nat Commun 2016, 7, 11590 https://doi.org/10.1038/ncomms11590.
  24. Frka-Petesic, B.; Zanchi, D.; Martin, N.; Carayon, S.; Huille, S.; Tribet, C. Aggregation of Antibody Drug Conjugates at Room Temperature: SAXS and Light Scattering Evidence for Colloidal Instability of a Specific Subpopulation. Langmuir 2016, 32 (19), 4848–4861 https://doi.org/10.1021/acs.langmuir.6600653.
  25. Tourasse, N. J.; Barbi, T.; Waterhouse, J. C.; Shtaida, N.; Leu, S.; Boussiba, S.; Purton, S.; Vallon, O. The Complete Sequence of the Chloroplast Genome of the Green Microalga Lobosphaera (Parietochloris) Incisa. Mitochondrial DNA A DNA Mapp Seq Anal 2016, 27 (3), 2073–2075 https://doi.org/10.3109/19401736.2014.982562.
  26. Dalier, F.; Eghiaian, F.; Scheuring, S.; Marie, E.; Tribet, C. Temperature-Switchable Control of Ligand Display on Adlayers of Mixed Poly(Lysine)-g-(PEO) and Poly(Lysine)-g-(Ligand-Modified Poly-N-Isopropylacrylamide). Biomacromolecules 2016, 17 (5), 1727–1736 https://doi.org/10.1021/acs.biomac.6b00136.
  27. DiChiara, J. M.; Liu, B.; Figaro, S.; Condon, C.; Bechhofer, D. H. Mapping of Internal Monophosphate 5’ Ends of Bacillus Subtilis Messenger RNAs and Ribosomal RNAs in Wild-Type and Ribonuclease-Mutant Strains. Nucleic Acids Res. 2016, 44 (7), 3373–3389 https://doi.org/10.1093/nar/gkw073.
  28. Mazur, A. K. Homologous Pairing between Long DNA Double Helices. Phys. Rev. Lett. 2016, 116 (15), 158101 https://doi.org/10.1103/PhysRevLett.116.158101.
  29. Laurent, B.; Murail, S.; Shahsavar, A.; Sauguet, L.; Delarue, M.; Baaden, M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure 2016, 24 (4), 595–605 https://doi.org/10.1016/j.str.2016.02.014.
  30. Takahashi, H.; Schmollinger, S.; Lee, J.-H.; Schroda, M.; Rappaport, F.; Wollman, F.-A.; Vallon, O. PETO Interacts with Other Effectors of Cyclic Electron Flow in Chlamydomonas. Mol Plant 2016, 9 (4), 558–568 https://doi.org/10.1016/j.molp.2015.12.017.
  31. Nawrocki, W. J.; Santabarbara, S.; Mosebach, L.; Wollman, F.-A.; Rappaport, F. State Transitions Redistribute Rather than Dissipate Energy between the Two Photosystems in Chlamydomonas. Nat Plants 2016, 2, 16031 https://doi.org/10.1038/nplants.2016.31.
  32. Porcher, J.-P.; Fogeron, T.; Gomez-Mingot, M.; Chamoreau, L.-M.; Li, Y.; Fontecave, M. Synthesis and Reactivity of a Bio-Inspired Dithiolene Ligand and Its Mo Oxo Complex. Chemistry 2016, 22 (13), 4447–4453 https://doi.org/10.1002/chem.201504373.
  33. Katava, M.; Kalimeri, M.; Stirnemann, G.; Sterpone, F. Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue. J Phys Chem B 2016, 120 (10), 2721–2730 https://doi.org/10.1021/acs.jpcb.6b00306.
  34. Fortunato, A. E.; Jaubert, M.; Enomoto, G.; Bouly, J.-P.; Raniello, R.; Thaler, M.; Malviya, S.; Bernardes, J. S.; Rappaport, F.; Gentili, B.; Huysman, M. J. J.; Carbone, A.; Bowler, C.; d’Alcalà, M. R.; Ikeuchi, M.; Falciatore, A. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean. Plant Cell 2016, 28 (3), 616–628 https://doi.org/10.1105/tpc.15.00928.
  35. Malinge, J.; Mousseau, F.; Zanchi, D.; Brun, G.; Tribet, C.; Marie, E. Tailored Stimuli-Responsive Interaction between Particles Adjusted by Straightforward Adsorption of Mixed Layers of Poly(Lysine)-g-PEG and Poly(Lysine)-g-PNIPAM on Anionic Beads. J. Colloid Interface Sci. 2016, 461, 50–55 https://doi.org/10.1016/j.jcis.2015.09.016.
  36. Warnet, X. L.; Laadhari, M.; Arnold, A. A.; Marcotte, I.; Warschawski, D. E. A (2)H Magic-Angle Spinning Solid-State NMR Characterisation of Lipid Membranes in Intact Bacteria. Biochim. Biophys. Acta 2016, 1858 (1), 146–152 https://doi.org/10.1016/j.bbamem.2015.10.020.
  37. Verméglio, A.; Lavergne, J.; Rappaport, F. Connectivity of the Intracytoplasmic Membrane of Rhodobacter Sphaeroides: A Functional Approach. Photosyn. Res. 2016, 127 (1), 13–24 https://doi.org/10.1007/s11120-014-0068-7.
  38. Nilsson, H.; Cournac, L.; Rappaport, F.; Messinger, J.; Lavergne, J. Estimation of the Driving Force for Dioxygen Formation in Photosynthesis. Biochim. Biophys. Acta 2016, 1857 (1), 23–33 https://doi.org/10.1016/j.bbabio.2015.09.011.
  39. Ismail, A.; Leroux, V.; Smadja, M.; Gonzalez, L.; Lombard, M.; Pierrel, F.; Mellot-Draznieks, C.; Fontecave, M. Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6. PLoS Comput. Biol. 2016, 12 (1), e1004690 https://doi.org/10.1371/journal.pcbi.1004690.
  40. Caserta, G.; Adamska-Venkatesh, A.; Pecqueur, L.; Atta, M.; Artero, V.; Roy, S.; Reijerse, E.; Lubitz, W.; Fontecave, M. Chemical Assembly of Multiple Metal Cofactors: The Heterologously Expressed Multidomain [FeFe]-Hydrogenase from Megasphaera Elsdenii. Biochim. Biophys. Acta 2016, 1857 (11), 1734–1740 https://doi.org/10.1016/j.bbabio.2016.07.002.
  41. Longatte, G.; Rappaport, F.; Wollman, F.-A.; Guille-Collignon, M.; Lemaître, F. Mechanism and Analyses for Extracting Photosynthetic Electrons Using Exogenous Quinones - What Makes a Good Extraction Pathway? Photochem. Photobiol. Sci. 2016, 15 (8), 969–979 https://doi.org/10.1039/c6pp00076b.
  42. Nguyen, P. H.; Sterpone, F.; Campanera, J. M.; Nasica-Labouze, J.; Derreumaux, P. Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations. ACS Chem Neurosci 2016, 7 (6), 823–832 https://doi.org/10.1021/acschemneuro.6b00053.
  43. Zito, F.; Alric, J. Heme Ci or Cn of the Cytochrome B6f Complex, A Short Retrospective. In Cytochrome Complexes: Evolution, Structures, Energy Transduction, and Signaling; Advances in Photosynthesis and Respiration; Springer, Dordrecht, 2016; pp 295–306.
  44. Jagodnik, J.; Thieffry, D.; Guillier, M. Bacterial Small RNAs in Mixed Regulatory Circuits. In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria; Bruijn, F. J. de, Ed.; John Wiley & Sons, Inc., 2016; pp 369–382.
  45. Angius, F.; Ilioaia, O.; Uzan, M.; Miroux, B. Membrane Protein Production in Escherichia Coli: Protocols and Rules. In Heterologous Expression of Membrane Proteins; Mus-Veteau, I., Ed.; Springer New York: New York, NY, 2016; Vol. 1432, pp 37–52.
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