Major publications of the Structural Biology and Chemistry Department

2011

 

  • Babault, N., Cordier, F., Lafage, M., Cockburn, J., Haouz, A., Prehaud, C. Rey, F. A., Delepierre, M., Buc, H., Lafon, M. and Wolff, N. (2011) Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death. Structure, 19, 1518-1524.
  • Chiaravalli, J., Fontan, E., Fsihi, H., Coïc, Y.-M., Baleux, F., Véron, M. and Agou, F. (2011) Direct Inhibition of NF-kB activation by peptide targeting the NOA ubiquitin binding domain of NEMO. Biochem. Pharmacol., 82, 1163-1174.
  • Hubeau, M., Ngadjeua, F., Puel, A., Israel, L., Feinberg, J., Chrabieh, M., Belani, K., Bodemer, C., Fabre, I., Plebani, A., Boisson-Dupuis, S., Picard, C., Fischer, A., Israël, A., Abel, L., Véron, M., Casanova, J.-L., Agou, F. and Bustamante, J. (2011) A new mechanism of X-linked anhidrotic ectodermal dysplasia with immunodeficiency: impairment of ubiquitin binding despite normal folding of NEMO protein. Blood, 118, 926-935.
  • Mascarell, L., Saint-Lu, N., Moussu, H., Zimmer, A., Louise, A., Lone, Y., Ladant, D., Leclerc, C., Tourdot, S., Van Overtvelt, L. and Moingeon, P. (2011) Oral macrophage-like cells play a key role in tolerance induction following sublingual immunotherapy of asthmatic mice. Mucosal. Immunol., 4, 638-647.
  • Nickerson, N. N., Tosi, T., Dessen, A., Baron, B., Raynal, B., England, P. and Pugsley, A. P. (2011) Outer membrane targeting of secretin PulD protein relies on disordered domain recognition by a dedicated chaperone. J. Biol. Chem., 286, 38833-38843.
  • Nury, H., Van Renterghem, C., Weng, Y., Tran, A., Baaden, M., Dufresne, V., Changeux, J.-P., Sonner, J. M. and Corringer, P.-J. (2011) X-ray structures of general anaesthetics bound to pentameric ligand-gated ion channel. Nature, 469, 428-431.
  • Paccani, S.R., Finetti, F., Davi, M., Patrussi, L., D'Elios, M. M., Ladant, D. and Baldari, C. T. (2011) The Bordetella pertussis adenylate cyclase toxin binds to T cells via LFA-1 and induces its disengagement from the immune synapse. J. Exp. Med., 208, 1317-1330.
  • Robichon, C., Karimova, G., Beckwith, J. and Ladant, D. (2011) Role of leucine zipper motifs in the association of the Escherichia coli cell division proteins FtsL and FtsB. J. Bact., 193, 4988-4992.
  • Rossi, C., Doumiati, S., Lazzarelli, C., Davi, M., Meddar, F., Ladant, D. and Chopineau, J. (2011) A tethered bilayer assembled on top of immobilized calmodulin to mimic cellular compartmentalization. PLoS One, 6(4), e19101.
  • Shepard, W., Soutourina, O., Courtois, E., England, P., Haouz, A. and Martin-Verstraete, I. (2011) Insights into the Rrf2 repressor family - the structure of CymR, the global cysteine regulator of Bacillus subtilis. FEBS J., 278, 2689-2701.
  • Sotomayor Pérez, A.C., Ladant, D. and Chenal, A. (2011) Calcium-induced folding of intrinsically disordered Repeat-in-Toxin (RTX) motifs via changes of protein charges and oligomerization states. J. Biol. Chem., 286, 16997-17004.

 

2010

  • Corringer, P. J., Baaden, M., Bocquet, N., Delarue, M., Dufresne, V., Nury, H., Prevost, M. and Van Renterghem, C. (2010). Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J Physiol., 588, 565-572.
  • Grubisha, O., Kaminska, M., Duquerroy, S., Fontan, E., Cordier, F., Haouz, A., Raynal, B., Chiravalli, J., Delepierre, M., Israël, A., Véron, M. and Agou, F. (2010) DARPin-assisted crystallography of the CC2-LZ domain of NEMO reveals a coupling between dimerization and ubiquitin-binding. J. Mol. Biol., 395, 89-104.
  • Koehl, P. and Delarue, M. (2010). AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. J Chem Phys., 132, 064101.
  • Laplantine, E., Fontan, E., Chiaravalli, J., Lopez, T., Lakisic, G., Véron, M., Agou, F. and Israël, A. (2009) NEMO specifically recognizes K63-linked poly-ubiquitin chains through a new bipartite ubiquitin-binding domain. EMBO J., 28, 2885-2895.
  • Nury, H., Bocquet, N., Le Poupon, C., Raynal, B., Haouz, A., Corringer, P. J. and Delarue, M. (2010). Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel. J Mol Biol., 395, 1114-27.
  • Nury, H., Poitevin, F., Van Renterghem, C., Changeux, J. P., Corringer, P. J., Delarue, M. and Baaden, M. (2010). One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc Natl Acad Sci U S A, 107, 6275-80.
  • Piton, J., Petrella, S., Delarue, M., Andre-Leroux, G., Jarlier, V., Aubry, A. and Mayer, C. (2010). Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase. PLoS One, 5, e12245.
  • Prehaud, C., Wolff, N., Terrien, E., Lafage, M., Megret, F., Babault, F., Cordier, F., Tan, G.S., Maitrepierre, E., Menager, P., Chopy, D., Hoos, S., England, P., Delepierre, M., Schnell, M.J., Buc, H. and Lafon, M. (2010) Attenuation of rabies virulence: take-over by the cytoplasmic domain of the envelope protein. Science Signaling, 3 (105), ra5.
  • Srivastava, A., Gangnard, S., Round, A., Dechavanne, S., Juillerat, A., Raynal, B., Faure, G., Baron, B., Ramboarina, S., Singh, S.K., Belrhali, H., England, P., Lewit-Bentley, A., Scherf, A., Bentley, G.A. and Gamain, B. (2010) Full-length extracellular region of the var2CSA variant of PfEMP1 is required for specific, high-affinity binding to CSA. Proc Natl Acad Sci U S A., 107, 4884-4889.


2009

  • Bocquet, N., Nury, H., Baaden, M., Le Poupon, C., Changeux, J. P., Delarue, M. and Corringer, P. J. (2009). X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature, 457, 111-114.
  • Albanesi, D., Martin, M., Trajtenberg, F., Mansilla, M.C., Haouz, A., Alzari, P.M., de Mendoza, D. and Buschiazzo, A. (2009) Structural insights into the signal transduction mechanism of the thermosensor histidine-kinase DesK. Proc Natl Acad Sci USA, 106, 16185-16190.
  • Baleux, F., Loureiro-Morais, L., Hersant, Y., Clayette, P., Arenzana-Seisdedos, F., Bonnaffé, D. and Lortat-Jacob, H. (2009) A synthetic CD4-heparan sulfate glycoconjugate inhibits CCR5 and CXCR4 HIV-1 attachment and entry. Nat Chem Biol., 5, 743-748.
  • Bay, S., Fort, S., Birikaki, L., Ganneau, C., Samain, E., Coïc, Y-M., Bonhomme, F., Dériaud, E., Leclerc, C. and Lo-Man, R. (2009) Induction of a melanoma-specific antibody response by a monovalent, but not a divalent, synthetic GM2 neoglycopeptide. Chem. Med. Chem., 4, 582-587.
  • Caillet-Saguy, C., Piccioli, M., Turano, P., Izadi-Pruneyre, N., Delepierre, M., Bertini, Y. and Lecroisey, A. (2009) Mapping the Interaction betweeen the hemophore HasA and its 98kDa outer membrane receptor HasR in DPC micelles using CRINEPT-TROSY NMR. J. Am. Chem. Soc., 131 (5), 1736-1744.
  • Chandran, V., Fronzes, R., Duquerroy, S., Cronin, N., Navaza, J. and Waksman, G. (2009) Crystal structure of the outer membrane complex of a type IV secretion system. Nature, 462 (7276), 1011-1015.
  • Chenal, A., Guijarro, J.I., Raynal, B., Delepierre, M. and Ladant, D. (2009) RTX calcium-binding motifs are intrinsically disordered in the absence of calcium: Implication for protein secretion. J. Biol. Chem., 284, 1781-1789.
  • Delfosse, V., Girard, E., Birck, C., Delmarcelle, M., Delarue, M., Poch, O., Schultz, P. and Mayer, C. (2009). Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS One, 4, e4712.
  • Duclert-Savatier, N., Poggi, L., Miclet, E., Lopes, P., Ouazzani, J., Chevalier, N., Nilges, M., Delarue, M. and Stoven, V. (2009). Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation. J Mol Biol., 388, 1009-1021.
  • Fronzes, R., Christie, P.J. and Waksman, G. (2009) The structural biology of type IV secretion systems. Nat. Rev. Microbiol., 7 (10), 703-714.
  • Fronzes, R., Schäfer, E., Wang, L., Saibil, H., Orlova, E. and Waksman G. (2009) Structure of a type IV secretion system core complex. Science, 323 (5911), 266 268.
  • Guilliere, F, Peixeiro, N., Kessler, A., Rayal, B., Desnoues, N., Keller, J., Delipierre, M., Pranguishvili, D., Sezonov, G. and Guijarro, J.I. (2009) Structure, function and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1. J. Biol. Chem., 284 (33), 22222-22237.
  • Hindie, V., Stroba, A., Zhang, H., Lopez-Garcia, L.A., Idrissova, L., Zeuzem, S., Hirschberg, D., Schaeffer, F., Jorgensen, T.J., Engel, M., Alzari, P.M. and Biondi, R.M. (2009) High resolution complex structure and allosteric effects of low molecular weight activators on the protein kinase PDK1. Nature Chem. Biol., 5, 758-764.
  • Karimova, G., Robichon, C. and Ladant, D. (2009) Characterisation of YmgF, a 72 residue-long inner membrane protein that associates to the Escherichia coli cell division machinery. J Bacteriol.,191, 333-346
  • Karst, J.C., Sotomayor Pérez, A.C., Guijarro, J.I., Raynal, B., Chenal, A. and Ladant, D. (2010) Calmodulin-Induced conformational and hydrodynamic changes in the catalytic domain of Bordetella pertussis adenylate cyclase toxin. Biochemistry, 49, 318-328.
  • Koehl, P., Orland, H. and Delarue, M. (2009). Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions. Phys Rev. Lett., 102, 087801.
  •  Koehl, P., Orland, H. and Delarue, M. (2009). Computing ion solvation free energies using the dipolar Poisson model. J Phys Chem B., 113, 5694-5697.
  • Laine, E., Blondel, A. and Malliavin, T.E. (2009) Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex. Biophysical J., 96, 1249-1263.
  • Laplantine, E., Fontan, E., Chiaravalli, J., Lopez, T., Lakisic, G., Véron, M., Agou, F. and Israël, A. (2009) NEMO specifically recognizes K63-linked poly-ubiquitin chains through a new bipartite ubiquitin-binding domain. EMBO J., 28, 2885-2895.
  • Laowanapiban, P., Kapustina, M., Vonrhein, C., Delarue, M., Koehl, P. and Carter, C. W., Jr. (2009). Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc Natl Acad Sci U S A, 106, 1790-1795.
  • Phalipon, A., Tanguy, M., Grandjean, C., Guerreiro, C., Bélot, F., Cohen D., Sansonetti, P.J. and Mulard, L. A. (2009) A synthetic carbohydrate-protein conjugate vaccine candidate against Shigella flexneri 2a infection. J. Immunol., 82, 2241-2247.
  • Piton, J., Matrat, S., Petrella, S., Jarlier, V., Aubry, A. and Mayer, C. (2009). Purification, crystallization and preliminary X-ray diffraction experiments on the breakage-reunion domain of the DNA gyrase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1182-1186.
  • Romain, F., Barbosa, I., Gouge, J., Rougeon, F. and Delarue, M. (2009) Conferring a template-dependant polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region. Nucleic Acids Res., 37, 4642-4656.


2008

  • Azuara, C., Orland, H., Bon, M., Koehl, P. and Delarue, M. (2008). Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys J., 95, 5587-5605.
  • Delarue, M. (2008). Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. Acta Crystallogr D Biol Crystallogr., 64, 40-48.
  • Gasse, C., Douguet, D., Huteau, V., Marchal, G., Munier-Lehmann, H. and Pochet, S. (2008) Substituted benzyl-pyrimidines targeting thymidine monophosphate kinase of Mycobacterium tuberculosis: Synthesis and in vitro anti-mycobacterial activity. Bioorg. Med. Chem., 16, 6075-6085.
  • Lebreton, A., Rousselle, J.C., Lenormand, P., Namane, A., Jacquier, A., Fromont-Racine, M. and Saveanu, C. (2008) 60S ribosomal subunit assembly dynamics defined by semiquantitative mass spectrometry of purified complexes. Nucleic Acid Res., 36 (15), 4988-4999.
  • Morales, M.A., Watanabe, R., Laurent, C., Lenormand, P., Rousselle, J.C., Namane, A. and Späth, G.F. (2008) Phosphoproteomic analysis of Leishmania donovani pro- and amastigote stages. Proteomics, 8 (2), 350-363
  • O’Hare, H.M., Duran ; R., Cerveñansky, C., Bellinzoni, M., Wehenkel, A., Pritsch, O., Obai, G., Baumgartner, J., Vialaret, J., Johnsson, K. and Alzari, P.M. (2008) Regulation of glutamate metabolism by protein kinases in mycobacteria. Mol. Microbiol., 70, 1408-1423.
  • Tafelmeyer, P., Laurent, C., Lenormand, P., Rousselle, J.C., Marsollier, L., Reysset, G., Zhang, R., Sickmann, A., Stinear, T.P., Namane, A and Cole, S.T. (2008) Comprehensive proteome analysis of Mycobacterium ulcerans and quantitative comparison of mycolactone biosynthesis. Proteomics, 8 (15), 3124-3138
  • Vulliez-Le Normand, B., Saul, F.A., Phalipon, A., Bélot, F., Guerreiro, C., Mulard, L.A. and Bentley, G.A. (2008) Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody. Proc Natl Acad Sci U S A.


2007

  • Chau, P.L., Hoang, P.N.M., Picaud, S. and Jedlovszky, P. (2007). A possible mechanism for pressure reversal phenomenon of general anaesthetics from molecular simulations. Chem. Phys. Lett., 438, 294-297.
  • Delarue, M. (2007). An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. Rna. Rna, 13, 161-169.
  • Delarue, M., Duclert-Savatier, N., Miclet, E., Haouz, A., Giganti, D., Ouazzani, J., Lopez, P., Nilges, M. and Stoven, V. (2007). Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei. J. Mol. Biol., 366, 868-881.
  • Franklin, J., Koehl, P., Doniach, S. and Delarue, M. (2007). MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res., 35, W477-482.
  • Ghiorghi, Y.K., Zeller, K.I., Dang, C.V. and Kaminski, P.A. (2007) The C-MYC target gene Rcl (C6orf108) encodes a novel enzyme : Deoxynucleoside 5’-monophosphate N-glycosidase. J. Biol. Chem., 282, 8150-8156.
  • Yeramian, E. and Debonneuil, E. (2007) Probabilistic sequence alignments: realistic models with efficient algorithms. Phys. Rev. Lett., 98, 078101-078104.


2006

  • Azuara, C., Lindahl, E., Koehl, P., Orland, H. and Delarue, M. (2006). PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res., 34, W38-42.
  • Grünberg, R., Nilges, M. and Leckner, J. (2006) Flexibility and conformational entropy in protein-protein binding. Structure, 14, 683–693.
  • Hible, G., Christova, P., Renault, L., Seclaman, E., Thompson, A., Girard, E., Munier-Lehmann, H. and Cherfils, J. (2006) Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase. Proteins, 62, 489-500.
  • Lindahl, E., Azuara, C., Koehl, P. and Delarue, M. (2006) NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., 34, W52-56.
  • Loth, K., Abergel, D., Pelupessy, P., Delarue, M., Lopes, P., Ouazzani, J., Duclert-Savatier, N., Nilges, M., Bodenhausen, G. and Stoven, V. (2006). Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts. Proteins, 64, 931-939
  • MacDonald, D., Demarre, G., Bouvier, M., Mazel, D. and Gopaul, D.N. (2006) Structural basis for broad DNA-specificity in integron recombination. Nature, 440, 1157-1162.
  • Wisner, A., Dufour, E., Messaoudi, M., Nejdi, A., Marcel, A., Ungeheuer, M. N. and Rougeot, C. (2006). Human Opiorphin, a natural antinociceptive modulator of opioid-dependent pathways. Proc. Natl. Acad. Sci. U S A, 103, 17979-17984.


 

 

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