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Accueil > Départements > Biochimie, Biophysique et Biologie Structurale > Jean-Baptiste CHARBONNIER, Marie-Hélène LE DU, Sophie ZINN-JUSTIN : Enveloppe Nucléaire, Télomères et Réparation de l’ADN

Publications de l’équipe

2017



  • J. - P. Charbonnier, E. M. van Rikxoort, A. A. A. Setio, C. M. Schaefer-Prokop, B. van Ginneken, et F. Ciompi, « Improving airway segmentation in computed tomography using leak detection with convolutional networks », Medical Image Analysis, vol. 36, p. 52-60, 2017.


  • P. Cuniasse, P. Tavares, E. V. Orlova, et S. Zinn-Justin, « Structures of biomolecular complexes by combination of NMR and cryoEM methods », Current Opinion in Structural Biology, vol. 43, p. 104-113, 2017.


  • Y. Duroc, R. Kumar, L. Ranjha, C. Adam, R. Guérois, K. Md Muntaz, M. - C. Marsolier-Kergoat, F. Dingli, R. Laureau, D. Loew, B. Llorente, J. - B. Charbonnier, P. Cejka, et V. Borde, « Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion », eLife, vol. 6, janv. 2017.
    Mots-clés : AMIG, B3S, biochemistry, Chromosomes, genes, INTGEN, Meiosis, mismatch repair, Recombination, S. cerevisiae.

  • S. Mohr, M. Masella, L. E. Ratcliff, et L. Genovese, « Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis », Journal of Chemical Theory and Computation, 2017.
    Résumé : We present, within Kohn-Sham density functional theory calculations, a quantitative method to identify and assess the partitioning of a large quantum-mechanical system into fragments. We then show how within this framework simple generalizations of other well-known population analyses can be used to extract, from first-principles, reliable electrostatic multipoles for the identified fragments. Our approach reduces arbitrariness in the fragmentation procedure and enables the possibility to assess quantitatively whether the corresponding fragment multipoles can be interpreted as observable quantities associated with a system moiety. By applying our formalism within the code BigDFT, we show that the use of a minimal set of in situ-optimized basis functions allows at the same time a proper fragment definition and an accurate description of the electronic structure.
    Mots-clés : B3S, INTGEN.

  • C. Pattamadilok, V. Chanoine, C. Pallier, J. - L. Anton, B. Nazarian, P. Belin, et J. C. Ziegler, « Automaticity of phonological and semantic processing during visual word recognition », NeuroImage, vol. 149, p. 244-255, 2017.
    Résumé : Reading involves activation of phonological and semantic knowledge. Yet, the automaticity of the activation of these representations remains subject to debate. The present study addressed this issue by examining how different brain areas involved in language processing responded to a manipulation of bottom-up (level of visibility) and top-down information (task demands) applied to written words. The analyses showed that the same brain areas were activated in response to written words whether the task was symbol detection, rime detection, or semantic judgment. This network included posterior, temporal and prefrontal regions, which clearly suggests the involvement of orthographic, semantic and phonological/articulatory processing in all tasks. However, we also found interactions between task and stimulus visibility, which reflected the fact that the strength of the neural responses to written words in several high-level language areas varied across tasks. Together, our findings suggest that the involvement of phonological and semantic processing in reading is supported by two complementary mechanisms. First, an automatic mechanism that results from a task-independent spread of activation throughout a network in which orthography is linked to phonology and semantics. Second, a mechanism that further fine-tunes the sensitivity of high-level language areas to the sensory input in a task-dependent manner.
    Mots-clés : Automatic activation, B3S, Bottom-up process, INTGEN, Stimulus-driven, Task-dependent, Top-down process.


  • C. Samson, F. Celli, K. Hendriks, M. Zinke, N. Essawy, I. Herrada, A. - A. Arteni, F. - X. Theillet, B. Alpha-Bazin, J. Armengaud, C. Coirault, A. Lange, et S. Zinn-Justin, « Emerin self-assembly mechanism: role of the LEM domain », The FEBS Journal, vol. 284, nᵒ 2, p. 338-352, 2017.
    Mots-clés : B3S, CRYOEM, INTGEN, PF.

  • E. Vernhes, M. Renouard, B. Gilquin, P. Cuniasse, D. Durand, P. England, S. Hoos, A. Huet, J. F. Conway, A. Glukhov, V. Ksenzenko, E. Jacquet, N. Nhiri, S. Zinn-Justin, et P. Boulanger, « Erratum: High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid », Scientific Reports, vol. 7, p. 43977, 2017.
    Mots-clés : B3S, FAAM, INTGEN, T5PHAG, VIRO.


  • E. Vernhes, M. Renouard, B. Gilquin, P. Cuniasse, D. Durand, P. England, S. Hoos, A. Huet, J. F. Conway, A. Glukhov, V. Ksenzenko, E. Jacquet, N. Nhiri, S. Zinn-Justin, et P. Boulanger, « High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid », Scientific Reports, vol. 7, p. 41662, févr. 2017.
    Mots-clés : B3S, FAAM, INTGEN, T5PHAG, VIRO.

  • M. Zinke, P. Fricke, C. Samson, S. Hwang, J. Wall, S. Lange, S. Zinn-Justin, et A. Lange, « Bacteriophage Tail Tube Assembly Studied by Proton-Detected 4D Solid-State NMR », Angewandte Chemie (International Ed. in English), 2017.
    Résumé : Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2%). As a proof-of-principle we acquired 4D (H)COCANH, (H)CACONH and (H)CBCANH spectra of the 20 kDa bacteriophage tail tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
    Mots-clés : B3S, gp17.1, INTGEN, non-uniform sampling, Proteins, solid-state NMR, SPP1.

2016



  • A. Araye, A. Goudet, J. Barbier, S. Pichard, B. Baron, P. England, J. Pérez, S. Zinn-Justin, A. Chenal, et D. Gillet, « Correction: The Translocation Domain of Botulinum Neurotoxin A Moderates the Propensity of the Catalytic Domain to Interact with Membranes at Acidic pH », PLOS ONE, vol. 11, nᵒ 8, p. e0161743, août 2016.


  • A. Araye, A. Goudet, J. Barbier, S. Pichard, B. Baron, P. England, J. Pérez, S. Zinn-Justin, A. Chenal, et D. Gillet, « The Translocation Domain of Botulinum Neurotoxin A Moderates the Propensity of the Catalytic Domain to Interact with Membranes at Acidic pH », PLOS ONE, vol. 11, nᵒ 4, p. e0153401, avr. 2016.


  • D. Benarroch-Popivker, S. Pisano, A. Mendez-Bermudez, L. Lototska, P. Kaur, S. Bauwens, N. Djerbi, C.  M. Latrick, V. Fraisier, B. Pei, A. Gay, E. Jaune, K. Foucher, J. Cherfils-Vicini, E. Aeby, S. Miron, A. Londoño-Vallejo, J. Ye, M. - H. Le Du, H. Wang, E. Gilson, et M. - J. Giraud-Panis, « TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection », Molecular Cell, vol. 61, nᵒ 2, p. 274-286, 2016.


  • J. P. Coles, C. Houriez, M. Meot-Ner (Mautner), et M. Masella, « Extrapolating Single Organic Ion Solvation Thermochemistry from Simulated Water Nanodroplets », The Journal of Physical Chemistry B, vol. 120, nᵒ 35, p. 9402-9409, sept. 2016.


  • G. Gaullier, S. Miron, S. Pisano, R. Buisson, Y. - V. Le Bihan, C. Tellier-Lebègue, W. Messaoud, P. Roblin, B. G. Guimarães, R. Thai, M. - J. Giraud-Panis, E. Gilson, et M. - H. Le Du, « A higher-order entity formed by the flexible assembly of RAP1 with TRF2 », Nucleic Acids Research, vol. 44, nᵒ 4, p. 1962-1976, févr. 2016.
    Mots-clés : B3S, DNA Damage, DNA-Binding Proteins, Genomic Instability, Humans, INTGEN, Multiprotein Complexes, Protein Binding, Telomere, Telomere-Binding Proteins, Telomeric Repeat Binding Protein 2.


  • I. Herrada, B. Bourgeois, C. Samson, B. Buendia, H. J. Worman, et S. Zinn-Justin, « Purification and Structural Analysis of LEM-Domain Proteins », in Methods in Enzymology, vol. 569, Elsevier, 2016, p. 43-61.

  • S. McGovern, S. Baconnais, P. Roblin, P. Nicolas, P. Drevet, H. Simonson, O. Piétrement, J. - B. Charbonnier, E. Le Cam, P. Noirot, et F. Lecointe, « C-terminal region of bacterial Ku controls DNA bridging, DNA threading and recruitment of DNA ligase D for double strand breaks repair », Nucleic Acids Research, 2016.
    Résumé : Non-homologous end joining is a ligation process repairing DNA double strand breaks in eukaryotes and many prokaryotes. The ring structured eukaryotic Ku binds DNA ends and recruits other factors which can access DNA ends through the threading of Ku inward the DNA, making this protein a key ingredient for the scaffolding of the NHEJ machinery. However, this threading ability seems unevenly conserved among bacterial Ku. As bacterial Ku differ mainly by their C-terminus, we evaluate the role of this region in the loading and the threading abilities of Bacillus subtilis Ku and the stimulation of the DNA ligase LigD. We identify two distinct sub-regions: a ubiquitous minimal C-terminal region and a frequent basic C-terminal extension. We show that truncation of one or both of these sub-regions in Bacillus subtilis Ku impairs the stimulation of the LigD end joining activity in vitro. We further demonstrate that the minimal C-terminus is required for the Ku-LigD interaction, whereas the basic extension controls the threading and DNA bridging abilities of Ku. We propose that the Ku basic C-terminal extension increases the concentration of Ku near DNA ends, favoring the recruitment of LigD at the break, thanks to the minimal C-terminal sub-region.
    Mots-clés : B3S, INTGEN.


  • E. Pompe, E. M. van Rikxoort, O. M. Mets, J. - P. Charbonnier, J. - M. Kuhnigk, H. J. de Koning, M. Oudkerk, R. Vliegenthart, P. Zanen, J. - W. J. Lammers, B. van Ginneken, P. A. de Jong, et F. A. A. Mohamed Hoesein, « Follow-up of CT-derived airway wall thickness: Correcting for changes in inspiration level improves reliability », European Journal of Radiology, vol. 85, nᵒ 11, p. 2008-2013, 2016.


  • F. Réal, A. Severo Pereira Gomes, Y. O. Guerrero Martínez, T. Ayed, N. Galland, M. Masella, et V. Vallet, « Structural, dynamical, and transport properties of the hydrated halides: How do At− bulk properties compare with those of the other halides, from F− to I−? », The Journal of Chemical Physics, vol. 144, nᵒ 12, p. 124513, mars 2016.
    Mots-clés : astatine,bromine,chlorine,fluorine,free energy,halides,hydrogen bonds,iodine,molecular force constants,perturbation theory,polarisability,solvation,spin-orbit interactions, B3S, INTGEN.

  • C. Samson, I. Herrada, F. Celli, F. - X. Theillet, et S. Zinn-Justin, « 1H, 13C and 15N backbone resonance assignment of the intrinsically disordered region of the nuclear envelope protein emerin », Biomolecular NMR assignments, vol. 10, nᵒ 1, p. 179-182, 2016.
    Résumé : Human emerin is an inner nuclear membrane protein involved in the response of the nucleus to mechanical stress. It contributes to the physical connection between the cytoskeleton and the nucleoskeleton. It is also involved in chromatin organization. Its N-terminal region is nucleoplasmic and comprises a globular LEM domain from residue 1 to residue 43. The three-dimensional structure of this LEM domain in complex with the chromatin BAF protein was solved from NMR data. Apart from the LEM domain, the nucleoplasmic region of emerin, from residue 44 to residue 221, is predicted to be intrinsically disordered. Mutations in this region impair binding to several emerin partners as lamin A, actin or HDAC3. However the molecular details of these recognition defects are unknown. Here we report (1)H, (15)N, (13)CO, (13)Cα and (13)Cβ NMR chemical shift assignments of the emerin fragment from residue 67 to residue 170, which is sufficient for nuclear localization and involved in lamin A binding. Chemical shift analysis confirms that this fragment is intrinsically disordered in 0 and 8 M urea.
    Mots-clés : B3S, Dose-Response Relationship, Drug, Emerin, Humans, INTGEN, intrinsically disordered protein, Lamin Type A, Membrane Proteins, Muscular dystrophy, NMR spectroscopy, Nuclear Envelope, Nuclear Magnetic Resonance, Biomolecular, Nuclear Proteins, Urea.


  • S.  K. Tadi, C. Tellier-Lebègue, C. Nemoz, P. Drevet, S. Audebert, S. Roy, K. Meek, J. - B. Charbonnier, et M. Modesti, « PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF », Cell Reports, vol. 17, nᵒ 2, p. 541-555, 2016.

2015



  • Y. Chaban, R. Lurz, S. Brasilès, C. Cornilleau, M. Karreman, S. Zinn-Justin, P. Tavares, et E. V. Orlova, « Structural rearrangements in the phage head-to-tail interface during assembly and infection », Proceedings of the National Academy of Sciences, vol. 112, nᵒ 22, p. 7009-7014, juin 2015.
    Mots-clés : allosteric mechanism, B3S, Bacteriophage, Bacteriophages, Cryoelectron Microscopy, DNA gatekeeper, Genome, Viral, hybrid methods, INTGEN, Models, Molecular, PHAG+, Protein Conformation, viral infection, Viral Proteins, Viral Tail Proteins, VIRO, Virus Assembly, Virus Internalization.


  • J. P. Coles et M. Masella, « The fast multipole method and point dipole moment polarizable force fields », The Journal of Chemical Physics, vol. 142, nᵒ 2, p. 024109, janv. 2015.


  • A. Guarné et J. - B. Charbonnier, « Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal », Progress in Biophysics and Molecular Biology, vol. 117, nᵒ 2-3, p. 149-156, 2015.

  • I. Herrada, C. Samson, C. Velours, L. Renault, C. Östlund, P. Chervy, D. Puchkov, H. J. Worman, B. Buendia, et S. Zinn-Justin, « Muscular Dystrophy Mutations Impair the Nuclear Envelope Emerin Self-assembly Properties », ACS chemical biology, vol. 10, nᵒ 12, p. 2733-2742, 2015.
    Résumé : More than 100 genetic mutations causing X-linked Emery-Dreifuss muscular dystrophy have been identified in the gene encoding the integral inner nuclear membrane protein emerin. Most mutations are nonsense or frameshift mutations that lead to the absence of emerin in cells. Only very few cases are due to missense or short in-frame deletions. Molecular mechanisms explaining the corresponding emerin variants' loss of function are particularly difficult to identify because of the mostly intrinsically disordered state of the emerin nucleoplasmic region. We now demonstrate that this EmN region can be produced as a disordered monomer, as revealed by nuclear magnetic resonance, but rapidly self-assembles in vitro. Increases in concentration and temperature favor the formation of long curvilinear filaments with diameters of approximately 10 nm, as observed by electron microscopy. Assembly of these filaments can be followed by fluorescence through Thioflavin-T binding and by Fourier-transform Infrared spectrometry through formation of β-structures. Analysis of the assembly properties of five EmN variants reveals that del95-99 and Q133H impact filament assembly capacities. In cells, these variants are located at the nuclear envelope, but the corresponding quantities of emerin-emerin and emerin-lamin proximities are decreased compared to wild-type protein. Furthermore, variant P183H favors EmN aggregation in vitro, and variant P183T provokes emerin accumulation in cytoplasmic foci in cells. Substitution of residue Pro183 might systematically favor oligomerization, leading to emerin aggregation and mislocalization in cells. Our results suggest that emerin self-assembly is necessary for its proper function and that a loss of either the protein itself or its ability to self-assemble causes muscular dystrophy.
    Mots-clés : ACTIN, B3S, Genetic Variation, HeLa Cells, Humans, Hydrophobic and Hydrophilic Interactions, INTGEN, Magnetic Resonance Spectroscopy, Membrane Proteins, Muscular Dystrophies, Nuclear Envelope, Nuclear Proteins, PF, PIM, Proteostasis Deficiencies, Spectroscopy, Fourier Transform Infrared.


  • C. Houriez, M. Meot-Ner (Mautner), et M. Masella, « Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties », The Journal of Physical Chemistry B, vol. 119, nᵒ 36, p. 12094-12107, sept. 2015.


  • C. Langlois, S. Ramboarina, A. Cukkemane, I. Auzat, B. Chagot, B. Gilquin, A. Ignatiou, I. Petitpas, E. Kasotakis, M. Paternostre, H. E. White, E. V. Orlova, M. Baldus, P. Tavares, et S. Zinn-Justin, « Bacteriophage SPP1 Tail Tube Protein Self-assembles into β-Structure-rich Tubes », Journal of Biological Chemistry, vol. 290, nᵒ 6, p. 3836-3849, févr. 2015.
    Mots-clés : Amino Acid Sequence, B3S, Bacteriophage, Bacteriophages, Electron Microscopy, Fourier Transform IR (FTIR), IMAPP, INTGEN, Molecular Sequence Data, PHAG+, Protein Folding, Protein Structure, Tertiary, Solid State NMR, Tail Tube, Tertiary Structure, Viral Proteins, Virion, VIRO, Virus Assembly.


  • Y. Udi, M. Grossman, I. Solomonov, O. Dym, H. Rozenberg, V. Moreno, P. Cuniasse, V. Dive, A.  G. Arroyo, et I. Sagi, « Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational Antibody », Structure, vol. 23, nᵒ 1, p. 104-115, 2015.


  • C. Valéry, S. Deville-Foillard, C. Lefebvre, N. Taberner, P. Legrand, F. Meneau, C. Meriadec, C. Delvaux, T. Bizien, E. Kasotakis, C. Lopez-Iglesias, A. Gall, S. Bressanelli, M. - H. Le Du, M. Paternostre, et F. Artzner, « Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins », Nature Communications, vol. 6, p. 7771, juill. 2015.
    Mots-clés : B3S, Crystallography, X-Ray, Histidine, Hydrogen-Ion Concentration, IMAPP, INTGEN, LBMS, Models, Molecular, Nanotubes, Peptide, Optical Imaging, Protein Conformation, Protein Structure, Secondary, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman, Triptorelin Pamoate.
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Publications avant 2015


2014

- Hug1 is an intrinsically disordered protein that inhibits ribonucleotide reductase activity by directly binding Rnr2 subunit.
Meurisse J, Bacquin A, Richet N, Charbonnier JB, Ochsenbein F, Peyroche A. (2014) Nucleic Acids Res., 42 : 13174-13185.

- Automated classification of tailed bacteriophages according to their neck organization.
Lopes A, Tavares P, Petit MA, Guérois R, Zinn-Justin S. (2014) BMC Genomics, 15 : 1027.

- Regulation of the catalytic activity of the human phosphatase PTPN4 by its PDZ domain.
Maisonneuve P, Caillet-Saguy C, Raynal B, Gilquin B, Chaffotte A, Pérez J, Zinn-Justin S, Delepierre M, Buc H, Cordier F, Wolff N. (2014) FEBS J., 281 : 4852-4865.

- Simulated solvation of organic ions : protonated methylamines in water nanodroplets. Convergence toward bulk properties and the absolute proton solvation enthalpy.
Houriez C, Meot-Ner Mautner M, Masella M. (2014) J. Phys. Chem. B, 118 : 6222-6233.


2013

- Grafting of functional motifs onto protein scaffolds identified by PDB screening—an efficient route to design optimizable protein binders.
Tlatli R, Nozach H, Collet G, Beau F, Vera L, Stura E, Dive V, Cuniasse P (2013) FEBS J. 280 : 139-159.

- The helicase FBH1 is tightly regulated by PCNA via CRL4(Cdt2)-mediated proteolysis in human cells.
Bacquin A, Pouvelle C, Siaud N, Perderiset M, Salomé-Desnoulez S, Tellier-Lebegue C, Lopez B, Charbonnier JB, Kannouche PL. (2013) Nucleic Acids Res., 41 : 6501-6513.

- Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site.
Gueneau E, Dherin C, Legrand P, Tellier-Lebegue C, Gilquin B, Bonnesoeur P, Londino F, Quemener C, Le Du MH, Marquez JE, Moutiez M, Gondry M, Boiteux S, Charbonnier, JB. (2013) Nat. Struct. Mol. Biol., 20 : 461-468.

- Substrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121 : insights from biochemical studies and crystal structures.
Fonvielle M, Le Du MH, Lequin O, Lecoq A, Jacquet M, Thai R, Dubois S, Grach G, Gondry M, Belin P. (2013) J. Biol. Chem., 288 : 17347-17359.

- Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.
Le Bihan YV, Matot B, Pietrement O, Giraud-Panis MJ, Gasparini S, Le Cam E, Gilson E, Sclavi B, Miron S, Le Du MH. (2013) Acta Crystallogr. D Biol. Crystallogr., 69(Pt 3) : 409-419.

- One identity or more for telomeres ?
Giraud-Panis MJ, Pisano S, Benarroch-Popivker D, Pei B, Le Du MH, Gilson E. (2013) Front Oncol., 3 : 48.

- Revisiting a many-body model for water based on a single polarizable site : from gas phase clusters to liquid and air/liquid water systems.
Réal F, Vallet V, Flament JP, Masella M. (2013) J. Chem. Phys., 139 : 114502.

- A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics.
Masella M, Borgis D, Cuniasse P. (2013) J. Comput. Chem., 34:1112-1124.

- Further insights in the ability of classical nonadditive potentials to model actinide ion-water interactions.
Réal F, Trumm M, Schimmelpfennig B, Masella M, Vallet V. (2013) J. Comput. Chem., 34 : 707-719.

- Inhibitory signalling to the Arp2/3 complex steers cell migration.
Dang I, Gorelik R, ..., Herrada I, ..., Zinn-Justin S, Cherfils J, Bièche I, Alexandrova AY, David NB, Small JV, Faix J, Blanchoin L, Gautreau A. (2013) Nature, 503 : 281-284.

- Inhibition of TGF-β signaling at the nuclear envelope : characterization of interactions between MAN1, Smad2 and Smad3, and PPM1A.
Bourgeois B, Gilquin B, Tellier-Lebègue C, Östlund C, Wu W, Pérez J, El Hage P, Lallemand F, Worman HJ, Zinn-Justin S. (2013) Sci. Signal., 6 : ra49.

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