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2016 publications

An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb.
Kobbi L, Demey-Thomas E, Braye F, Proux F, Kolesnikova O, Vinh J, Poterszman A, Bensaude O
Proc Natl Acad Sci U S A 2016 Oct 25;:

Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins.
Berardozzi R, Adam V, Martins A, Bourgeois D
J Am Chem Soc 2016 Jan 20;138:558-65

ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy.
Andronov L, Orlov I, Lutz Y, Vonesch JL, Klaholz BP
Sci Rep 2016 Apr 12;6:24084

Gbp2 interacts with THO/TREX through a novel type of RRM domain.
Martínez-Lumbreras S, Taverniti V, Zorrilla S, Séraphin B, Pérez-Cañadillas JM
Nucleic Acids Res 2016 Jan 8;44:437-48

Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1.
Latrick CM, Marek M, Ouararhni K, Papin C, Stoll I, Ignatyeva M, Obri A, Ennifar E, Dimitrov S, Romier C, Hamiche A
Nat Struct Mol Biol 2016 Apr;23:309-16

Monitoring of the retinoic acid receptor-retinoid X receptor dimerization upon DNA binding by native mass spectrometry.
Nguyen-Huynh NT, Osz J, Peluso-Iltis C, Rochel N, Potier N, Leize-Wagner E
Biophys Chem 2016 Mar;210:2-8

Production of unstable proteins through the formation of stable core complexes.
Levy N, Eiler S, Pradeau-Aubreton K, Maillot B, Stricher F, Ruff M
Nat Commun 2016 Mar 17;7:10932

Structural Studies of Vitamin D Nuclear Receptor Ligand-Binding Properties.
Belorusova AY, Rochel N
Vitam Horm 2016 ;100:83-116

2015 publications

A flexible extension of the Drosophila ultrabithorax homeodomain defines a novel Hox/PBC interaction mode.
Foos N, Maurel-Zaffran C, Maté MJ, Vincentelli R, Hainaut M, Berenger H, Pradel J, Saurin AJ, Ortiz-Lombardía M, Graba Y
Structure 2015 Feb 3;23:270-9

Analytical ultracentrifugation and preliminary X-ray studies of the chloroplast envelope quinone oxidoreductase homologue from Arabidopsis thaliana.
Mas y mas S, Giustini C, Ferrer JL, Rolland N, Curien G, Cobessi D
Acta Crystallogr F Struct Biol Commun 2015 Apr;71:455-8

An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin.
Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V
PLoS One 2015 ;10:e0128390

A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation.
Deniaud A, Karuppasamy M, Bock T, Masiulis S, Huard K, Garzoni F, Kerschgens K, Hentze MW, Kulozik AE, Beck M, Neu-Yilik G, Schaffitzel C
Nucleic Acids Res 2015 Sep 3;43:7600-11

Asymmetric ring structure of Vps4 required for ESCRT-III disassembly.
Caillat C, Macheboeuf P, Wu Y, McCarthy AA, Boeri-Erba E, Effantin G, Göttlinger HG, Weissenhorn W, Renesto P
Nat Commun 2015 Dec 3;6:8781

A vitamin D receptor selectively activated by gemini analogs reveals ligand dependent and independent effects.
Huet T, Laverny G, Ciesielski F, Molnár F, Ramamoorthy TG, Belorusova AY, Antony P, Potier N, Metzger D, Moras D, Rochel N
Cell Rep 2015 Feb 3;10:516-26

Biogenesis and structure of a type VI secretion membrane core complex.
Durand E, Nguyen VS, Zoued A, Logger L, Péhau-Arnaudet G, Aschtgen MS, Spinelli S, Desmyter A, Bardiaux B, Dujeancourt A, Roussel A, Cambillau C, Cascales E, Fronzes R
Nature 2015 Jul 30;523:555-60

Characterization and production of protein complexes by co-expression in Escherichia coli.
Haffke M, Marek M, Pelosse M, Diebold ML, Schlattner U, Berger I, Romier C
Methods Mol Biol 2015 ;1261:63-89

Conformational switching in a light-harvesting protein as followed by single-molecule spectroscopy.
Gall A, Ilioaia C, Krüger TP, Novoderezhkin VI, Robert B, van Grondelle R
Biophys J 2015 Jun 2;108:2713-20

Conformation transitions of eukaryotic polyribosomes during multi-round translation.
Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS
Nucleic Acids Res 2015 Jan;43:618-28

Crystallization of mutants of Turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition.
Ayach M, Bressanelli S
Acta Crystallogr F Struct Biol Commun 2015 Apr;71:405-8

Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules.
Trowitzsch S, Viola C, Scheer E, Conic S, Chavant V, Fournier M, Papai G, Ebong IO, Schaffitzel C, Zou J, Haffke M, Rappsilber J, Robinson CV, Schultz P, Tora L, Berger I
Nat Commun 2015 Jan 14;6:6011

Drugging the schistosome zinc-dependent HDACs: current progress and future perspectives.
Marek M, Oliveira G, Pierce RJ, Jung M, Sippl W, Romier C
Future Med Chem 2015 ;7:783-800

Electron transfer pathways from the S2-states to the S3-states either after a Ca2+/Sr2+ or a Cl-/I- exchange in Photosystem II from Thermosynechococcus elongatus.
Boussac A, Rutherford AW, Sugiura M
Biochim Biophys Acta 2015 Jun-Jul;1847:576-86

FEM: feature-enhanced map.
Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD
Acta Crystallogr D Biol Crystallogr 2015 Mar;71:646-66

From deep TLS validation to ensembles of atomic models built from elemental motions.
Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD
Acta Crystallogr D Biol Crystallogr 2015 Aug;71:1668-83

Functional insights from high resolution structures of mouse protein arginine methyltransferase 6.
Bonnefond L, Stojko J, Mailliot J, Troffer-Charlier N, Cura V, Wurtz JM, Cianférani S, Cavarelli J
J Struct Biol 2015 Aug;191:175-83

HDAC8: a multifaceted target for therapeutic interventions.
Chakrabarti A, Oehme I, Witt O, Oliveira G, Sippl W, Romier C, Pierce RJ, Jung M
Trends Pharmacol Sci 2015 Jul;36:481-92

Hydration water mobility is enhanced around tau amyloid fibers.
Fichou Y, Schirò G, Gallat FX, Laguri C, Moulin M, Combet J, Zamponi M, Härtlein M, Picart C, Mossou E, Lortat-Jacob H, Colletier JP, Tobias DJ, Weik M
Proc Natl Acad Sci U S A 2015 May 19;112:6365-70

IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes.
Beinsteiner B, Michalon J, Klaholz BP
Bioinformatics 2015 Oct 15;31:3339-44

Insights from a decade of biophysical studies on MutL: Roles in strand discrimination and mismatch removal.
Guarné A, Charbonnier JB
Prog Biophys Mol Biol 2015 Mar;117:149-56

Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α.
Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Jensen MR, Hart DJ, Blackledge M
J Am Chem Soc 2015 Dec 9;137:15122-34

Live cell immunogold labelling of RNA polymerase II.
Orlov I, Schertel A, Zuber G, Klaholz B, Drillien R, Weiss E, Schultz P, Spehner D
Sci Rep 2015 Feb 9;5:8324

Metazoan Maelstrom is an RNA-binding protein that has evolved from an ancient nuclease active in protists.
Chen KM, Campbell E, Pandey RR, Yang Z, McCarthy AA, Pillai RS
RNA 2015 May;21:833-9

Micellar and biochemical properties of a propyl-ended fluorinated surfactant designed for membrane-protein study.
Abla M, Unger S, Keller S, Bonneté F, Ebel C, Pucci B, Breyton C, Durand G
J Colloid Interface Sci 2015 May 1;445:127-36

Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2.
Gaubitz C, Oliveira TM, Prouteau M, Leitner A, Karuppasamy M, Konstantinidou G, Rispal D, Eltschinger S, Robinson GC, Thore S, Aebersold R, Schaffitzel C, Loewith R
Mol Cell 2015 Jun 18;58:977-88

Nanometric distance measurements between Mn(ii)DOTA centers.
Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S
Phys Chem Chem Phys 2015 Sep 28;17:23368-77

OrthoInspector 2.0: Software and database updates.
Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O
Bioinformatics 2015 Feb 1;31:447-8

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.
Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS
Acta Crystallogr D Biol Crystallogr 2015 Aug;71:1657-67

Programming new geometry restraints: parallelity of atomic groups.
Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A
J Appl Crystallogr 2015 Aug 1;48:1130-1141

Pulse Electron Double Resonance Detected Multinuclear NMR Spectra of Distant and Low Sensitivity Nuclei and Its Application to the Structure of Mn(II) Centers in Organisms.
Bruch EM, Warner MT, Thomine S, Tabares LC, Un S
J Phys Chem B 2015 Oct 29;119:13515-23

Schistosome sirtuins as drug targets.
Lancelot J, Cabezas-Cruz A, Caby S, Marek M, Schultz J, Romier C, Sippl W, Jung M, Pierce RJ
Future Med Chem 2015 ;7:765-82

Self protein-protein interactions are involved in TPPP/p25 mediated microtubule bundling.
DeBonis S, Neumann E, Skoufias DA
Sci Rep 2015 Aug 20;5:13242

Structural analysis of sulindac as an inhibitor of aldose reductase and AKR1B10.
Cousido-Siah A, Ruiz FX, Crespo I, Porté S, Mitschler A, Parés X, Podjarny A, Farrés J
Chem Biol Interact 2015 Jun 5;234:290-6

Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi.
Borshchevskiy V, Round E, Bertsova Y, Polovinkin V, Gushchin I, Ishchenko A, Kovalev K, Mishin A, Kachalova G, Popov A, Bogachev A, Gordeliy V
PLoS One 2015 ;10:e0118548

Structural basis of natural promoter recognition by the retinoid X nuclear receptor.
Osz J, McEwen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N
Sci Rep 2015 Feb 3;5:8216

Structural characterization of metal binding to a cold-adapted frataxin.
Noguera ME, Roman EA, Rigal JB, Cousido-Siah A, Mitschler A, Podjarny A, Santos J
J Biol Inorg Chem 2015 Jun;20:653-64

Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7.
Uchikawa E, Natchiar KS, Han X, Proux F, Roblin P, Zhang E, Durand A, Klaholz BP, Dock-Bregeon AC
Nucleic Acids Res 2015 Mar 31;43:3373-88

Structural Insights into Bunyavirus Replication and Its Regulation by the vRNA Promoter.
Gerlach P, Malet H, Cusack S, Reguera J
Cell 2015 Jun 4;161:1267-79

Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi.
de Guillen K, Ortiz-Vallejo D, Gracy J, Fournier E, Kroj T, Padilla A
PLoS Pathog 2015 Oct;11:e1005228

Structure and Conformation of the Carotenoids in Human Retinal Macular Pigment.
Arteni AA, Fradot M, Galzerano D, Mendes-Pinto MM, Sahel JA, Picaud S, Robert B, Pascal AA
PLoS One 2015 ;10:e0135779

Structure and function insights into the NuRD chromatin remodeling complex.
Torchy MP, Hamiche A, Klaholz BP
Cell Mol Life Sci 2015 Jul;72:2491-507

Structure and primase-mediated activation of a bacterial dodecameric replicative helicase.
Bazin A, Cherrier MV, Gutsche I, Timmins J, Terradot L
Nucleic Acids Res 2015 Sep 30;43:8564-76

Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRNA modification.
Kolaj-Robin O, McEwen AG, Cavarelli J, Séraphin B
FEBS J 2015 Mar;282:819-33

Structure of the human 80S ribosome.
Khatter H, Myasnikov AG, Natchiar SK, Klaholz BP
Nature 2015 Apr 30;520:640-5

Structure of the low pH conformation of Chandipura virus G reveals important features in the evolution of the vesiculovirus glycoprotein.
Baquero E, Albertini AA, Raux H, Buonocore L, Rose JK, Bressanelli S, Gaudin Y
PLoS Pathog 2015 Mar;11:e1004756

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition.
Fanfrlík J, Ruiz FX, Kadlčíková A, Řezáč J, Cousido-Siah A, Mitschler A, Haldar S, Lepšík M, Kolář MH, Majer P, Podjarny AD, Hobza P
ACS Chem Biol 2015 Jul 17;10:1637-42

The production of multiprotein complexes in insect cells using the baculovirus expression system.
Abdulrahman W, Radu L, Garzoni F, Kolesnikova O, Gupta K, Osz-Papai J, Berger I, Poterszman A
Methods Mol Biol 2015 ;1261:91-114

Toxoplasma gondii: biochemical and biophysical characterization of recombinant soluble dense granule proteins GRA2 and GRA6.
Bittame A, Effantin G, Pètre G, Ruffiot P, Travier L, Schoehn G, Weissenhorn W, Cesbron-Delauw MF, Gagnon J, Mercier C
Biochem Biophys Res Commun 2015 Mar 27;459:107-12

Variations in Mn(II) speciation among organisms: what makes D. radiodurans different.
Bruch EM, Thomine S, Tabares LC, Un S
Metallomics 2015 Jan;7:136-44

Vpu Exploits the Cross-Talk between BST2 and the ILT7 Receptor to Suppress Anti-HIV-1 Responses by Plasmacytoid Dendritic Cells.
Bego MG, Côté É, Aschman N, Mercier J, Weissenhorn W, Cohen ÉA
PLoS Pathog 2015 Jul;11:e1005024

X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form.
Leone P, Bebeacua C, Opota O, Kellenberger C, Klaholz B, Orlov I, Cambillau C, Lemaitre B, Roussel A
J Biol Chem 2015 May 22;290:13191-201

2014 publications

A fully enzymatic method for site-directed spin labeling of long RNA.
Lebars I, Vileno B, Bourbigot S, Turek P, Wolff P, Kieffer B
Nucleic Acids Res 2014 Sep;42:e117

ANP32E is a histone chaperone that removes H2A.Z from chromatin.
Obri A, Ouararhni K, Papin C, Diebold ML, Padmanabhan K, Marek M, Stoll I, Roy L, Reilly PT, Mak TW, Dimitrov S, Romier C, Hamiche A
Nature 2014 Jan 30;505:648-53

Cloning, expression, purification and preliminary X-ray crystallographic analysis of mouse protein arginine methyltransferase 7.
Cura V, Troffer-Charlier N, Lambert MA, Bonnefond L, Cavarelli J
Acta Crystallogr F Struct Biol Commun 2014 Jan;70:80-6

Cryo-electron microscopy structure of lactococcal siphophage 1358 virion.
Spinelli S, Bebeacua C, Orlov I, Tremblay D, Klaholz BP, Moineau S, Cambillau C
J Virol 2014 Aug;88:8900-10

Discovery of inhibitors of Schistosoma mansoni HDAC8 by combining homology modeling, virtual screening, and in vitro validation.
Kannan S, Melesina J, Hauser AT, Chakrabarti A, Heimburg T, Schmidtkunz K, Walter A, Marek M, Pierce RJ, Romier C, Jung M, Sippl W
J Chem Inf Model 2014 Oct 27;54:3005-19

DNA binding by Sgf11 protein affects histone H2B deubiquitination by Spt-Ada-Gcn5-acetyltransferase (SAGA).
Koehler C, Bonnet J, Stierle M, Romier C, Devys D, Kieffer B
J Biol Chem 2014 Mar 28;289:8989-99

Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study.
Afonina ZA, Myasnikov AG, Shirokov VA, Klaholz BP, Spirin AS
Nucleic Acids Res 2014 Aug;42:9461-9

Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design.
Cousido-Siah A, Ruiz FX, Mitschler A, Porté S, de Lera ÁR, Martín MJ, Manzanaro S, de la Fuente JA, Terwesten F, Betz M, Klebe G, Farrés J, Parés X, Podjarny A
Acta Crystallogr D Biol Crystallogr 2014 Mar;70:889-903

Mapping the deubiquitination module within the SAGA complex.
Durand A, Bonnet J, Fournier M, Chavant V, Schultz P
Structure 2014 Nov 4;22:1553-9

Modulators of vitamin D nuclear receptor: recent advances from structural studies.
Belorusova AY, Rochel N
Curr Top Med Chem 2014 ;14:2368-77

Molecular basis for the antiparasitic activity of a mercaptoacetamide derivative that inhibits histone deacetylase 8 (HDAC8) from the human pathogen schistosoma mansoni.
Stolfa DA, Marek M, Lancelot J, Hauser AT, Walter A, Leproult E, Melesina J, Rumpf T, Wurtz JM, Cavarelli J, Sippl W, Pierce RJ, Romier C, Jung M
J Mol Biol 2014 Oct 9;426:3442-53

Nuclear position dictates DNA repair pathway choice.
Lemaître C, Grabarz A, Tsouroula K, Andronov L, Furst A, Pankotai T, Heyer V, Rogier M, Attwood KM, Kessler P, Dellaire G, Klaholz B, Reina-San-Martin B, Soutoglou E
Genes Dev 2014 Nov 15;28:2450-63

Production and characterization of a retinoic acid receptor RARγ construction encompassing the DNA binding domain and the disordered N-terminal proline rich domain.
Martinez-Zapien D, Delsuc MA, Travé G, Lutzing R, Rochette-Egly C, Kieffer B
Protein Expr Purif 2014 Mar;95:113-20

Purification, characterization and crystallization of the human 80S ribosome.
Khatter H, Myasnikov AG, Mastio L, Billas IM, Birck C, Stella S, Klaholz BP
Nucleic Acids Res 2014 Apr;42:e49

Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes.
Robin G, Sato Y, Desplancq D, Rochel N, Weiss E, Martineau P
J Mol Biol 2014 Nov 11;426:3729-43

Structural insight into arginine methylation by the mouse protein arginine methyltransferase 7: a zinc finger freezes the mimic of the dimeric state into a single active site.
Cura V, Troffer-Charlier N, Wurtz JM, Bonnefond L, Cavarelli J
Acta Crystallogr D Biol Crystallogr 2014 Sep;70:2401-12

Structural insights into the molecular mechanism of vitamin D receptor activation by lithocholic acid involving a new mode of ligand recognition.
Belorusova AY, Eberhardt J, Potier N, Stote RH, Dejaegere A, Rochel N
J Med Chem 2014 Jun 12;57:4710-9

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.
Myasnikov AG, Afonina ZA, Ménétret JF, Shirokov VA, Spirin AS, Klaholz BP
Nat Commun 2014 Nov 7;5:5294

The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning.
Maletta M, Orlov I, Roblin P, Beck Y, Moras D, Billas IM, Klaholz BP
Nat Commun 2014 Jun 19;5:4139

2013 publications

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms.
Simonetti A, Marzi S, Fabbretti A, Hazemann I, Jenner L, Urzhumtsev A, Gualerzi CO, Klaholz BP
Acta Crystallogr D Biol Crystallogr 2013 Jun;69:925-33