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3. Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A

Author

Gaucher, Jean-François, Reille-Seroussi, Marie, Gagey-Eilstein, Nathalie, Broussy, Sylvain, Coric, Pascale, Seijo, Bili, Lascombe, Marie-Bernard, Gautier, Benoît, Liu, Wang-Quing, Huguenot, Florent, Inguimbert, Nicolas, Bouaziz, Serge, Vidal, Michel, Broutin, Isabelle, Lascombe, Marie, Permyakov, Eugene, Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Pharmacochimie Moléculaire et Cellulaire (PMC - UMR_S 648), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Böttger, Sonja, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Synthèse et structure de molécules d'interet pharmacologique (SSMIP), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre des Matériaux des Mines d'Alès (C2MA), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Université Sorbonne Paris Cité (USPC), Laboratoire de Chimie des Biomolécules et de l'Environnement (LCBE), Université Montpellier 1 (UM1)-Université de Perpignan Via Domitia (UPVD), Unité de Pharmacologie Chimique et Génétique (UPCG - UMR_S 640/UMR 8151), Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)

Subjects
0301 basic medicine, Vascular Endothelial Growth Factor A, Dimer, lcsh:Medicine, Plasma protein binding, 01 natural sciences, Physical Chemistry, chemistry.chemical_compound, Chemical Precipitation, Receptor, lcsh:Science, Multidisciplinary, Crystallography, Chemistry, MESH: Protein Multimerization, Physics, Chemical Reactions, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Condensed Matter Physics, Molecular Docking Simulation, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Zinc, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biochemistry, Physical Sciences, Crystal Structure, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Crystallization, Dimerization, Binding domain, Protein Binding, Research Article, Chemical Elements, Cadmium, Cations, Divalent, Materials by Structure, Chemical physics, Materials Science, Context (language use), Crystals, 03 medical and health sciences, Cations, MESH: Cations, Divalent, Enzyme-linked receptor, Extracellular, MESH: Molecular Docking Simulation, Humans, Solid State Physics, MESH: Protein Binding, Binding site, Ions, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Binding Sites, Vascular Endothelial Growth Factor Receptor-1, MESH: Humans, MESH: Vascular Endothelial Growth Factor Receptor-1, 010405 organic chemistry, MESH: Vascular Endothelial Growth Factor A, lcsh:R, Dimers (Chemical physics), 0104 chemical sciences, 030104 developmental biology, Chemical Properties, MESH: Binding Sites, Biophysics, lcsh:Q, Protein Multimerization
Abstract

International audience; Angiogenesis is tightly regulated through the binding of vascular endothelial growth factors (VEGFs) to their receptors (VEGFRs). In this context, we showed that human VEGFR1 domain 2 crystallizes in the presence of Zn 2+ , Co 2+ or Cu 2+ as a dimer that forms via metal-ion interactions and interlocked hydrophobic surfaces. SAXS, NMR and size exclusion chromatography analyses confirm the formation of this dimer in solution in the presence of Co 2+ , Cd 2+ or Cu 2+ . Since the metal-induced dimerization masks the VEGFs binding surface, we investigated the ability of metal ions to displace the VEGF-A binding to hVEGFR1: using a competition assay, we evidenced that the metals displaced the VEGF-A binding to hVEGFR1 extracellular domain binding at micromolar level.

Published
2016

4. Biophysical Studies of the InducedDimerization of Human VEGF Receptor 1Binding Domain by Divalent MetalsCompeting with VEGF-A

Author

Gaucher, Jean-François, Reille-Seroussi, Marie, Gagey-Eilstein, Nathalie, Broussy, Sylvain, Coric, Pascale, Seijo, Bili, Lascombe, Marie-Bernard, Gautier, Benoit, Liu , Wang-Quing, Huguenot, Florent, Inguimbert, Nicolas, Bouaziz, Serge, Vidal, Michel, Broutin, Isabelle, Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5) - Centre National de la Recherche Scientifique (CNRS), Chimie Organique, Médicinale et Extractive et Toxicologie Expérimentale (COMETE - UMR 8638), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD) - École pratique des hautes études (EPHE) - Centre National de la Recherche Scientifique (CNRS), Pharmacochimie Moléculaire et Cellulaire (PMC - UMR_S 648), and Centre National de la Recherche Scientifique (CNRS) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Université Paris Descartes - Paris 5 (UPD5)

Subjects
[SDV.IB] Life Sciences [q-bio]/Bioengineering, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences
Abstract

International audience; Angiogenesis is tightly regulated through the binding of vascular endothelial growth factors(VEGFs) to their receptors (VEGFRs). In this context, we showed that human VEGFR1domain 2 crystallizes in the presence of Zn 2+ , Co 2+ or Cu 2+ as a dimer that forms via metal-ion interactions and interlocked hydrophobic surfaces. SAXS, NMR and size exclusion chro-matography analyses confirm the formation of this dimer in solution in the presence of Co 2+ ,Cd 2+ or Cu 2+ . Since the metal-induced dimerization masks the VEGFs binding surface, weinvestigated the ability of metal ions to displace the VEGF-A binding to hVEGFR1: using acompetition assay, we evidenced that the metals displaced the VEGF-A binding tohVEGFR1 extracellular domain binding at micromolar level.

Published
2016

5. New OprM structure highlighting the nature of the N-terminal anchor

Author

Monlezun, Laura, Phan, Gilles, Benabdelhak, Houssain, Lascombe, Marie-Bernard, Enguéné, Véronique, Picard, Martin, Broutin, Isabelle, Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Système membranaires, photobiologie, stress et détoxication (SMPSD), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
efflux pump, post-translational modification, multidrug resistance, [SDV]Life Sciences [q-bio], lipoyl, efflux pump, membrane protein, X-ray structure, Microbiology, Original Research
Abstract

International audience; Among the different mechanisms used by bacteria to resist antibiotics, active efflux plays a major role. In Gram-negative bacteria, active efflux is carried out by tripartite efflux pumps that form a macromolecular assembly spanning both membranes of the cellular wall. At the outer membrane level, a well-conserved outer membrane factor (OMF) protein acts as an exit duct, but its sequence varies greatly among different species. The OMFs share a similar tri-dimensional structure that includes a beta-barrel pore domain that stabilizes the channel within the membrane. In addition, OMFs are often subjected to different N-terminal post-translational modifications (PTMs), such as an acylation with a lipid. The role of additional N-terminal anchors is all the more intriguing since it is not always required among the OMFs family. Understanding this optional PTM could open new research lines in the field of antibiotics resistance. In Escherichia coli, it has been shown that CusC is modified with a tri-acylated lipid, whereas TolC does not show any modification. In the case of OprM from Pseudomonas aeruginosa, the N-terminal modification remains a matter of debate, therefore, we used several approaches to investigate this issue. As definitive evidence, we present a new X-ray structure at 3.8 Å resolution that was solved in a new space group, making it possible to model the N-terminal residue as a palmitoylated cysteine.

Published
2015

6. Crystal structure of the allergen Equ c 1. A dimeric lipocalin with restricted IgE-reactive epitopes

Author

Lascombe, Marie-Bernard, Grégoire, Christophe, Poncet, Pascal, Tavares, Gisele, Rosinski-Chupin, Isabelle, Rabillon, Jacques, Goubran-Botros, Hany, Mazié, Jean-Claude, David, Bernard, Alzari, Pedro, Biochimie Structurale, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Immuno-Allergie, Institut Pasteur [Paris], Génétique et Biochimie du Développement, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Anticorps (plate-forme) - Antibody Engineering (Platform), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
Models, Molecular, Protein Conformation, MESH: Sequence Homology, Amino Acid, MESH: Protein Structure, Secondary, MESH: Amino Acid Sequence, Crystallography, X-Ray, Protein Structure, Secondary, MESH: Antibodies, Monoclonal, MESH: Recombinant Proteins, Mice, MESH: Protein Conformation, MESH: Animals, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH: Immunoglobulin E, Antibodies, Monoclonal, Lipocalins, Recombinant Proteins, MESH: Mutagenesis, Site-Directed, MESH: Lipocalins, Dimerization, MESH: Models, Molecular, MESH: Allergens, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Molecular Sequence Data, MESH: Glycoproteins, MESH: Sequence Alignment, MESH: Carrier Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [CHIM.CRIS]Chemical Sciences/Cristallography, Animals, Point Mutation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Horses, MESH: Horses, MESH: Mice, Glycoproteins, MESH: Point Mutation, Binding Sites, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, Allergens, Immunoglobulin E, MESH: Crystallography, X-Ray, MESH: Dimerization, MESH: Binding Sites, Mutagenesis, Site-Directed, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Carrier Proteins, Sequence Alignment
Abstract

International audience; The three-dimensional structure of the major horse allergen Equ c 1 has been determined at 2.3 A resolution by x-ray crystallography. Equ c 1 displays the typical fold of lipocalins, a beta-barrel flanked by a C-terminal alpha-helix. The space between the two beta-sheets of the barrel defines an internal cavity that could serve, as in other lipocalins, for the binding and transport of small hydrophobic ligands. Equ c 1 crystallizes in a novel dimeric form, which is distinct from that observed in other lipocalin dimers and corresponds to the functional form of the allergen. Binding studies of point mutants of the allergen with specific monoclonal antibodies raised in mouse and IgE serum from horse allergic patients allowed to identify putative B cell antigenic determinants. In addition, total inhibition of IgE serum recognition by a single specific monoclonal antibody revealed the restricted nature of the IgE binding target on the molecular surface of Equ c 1.

Published
2000

16. Structure of sylvaticin, a new α-elicitin-like protein from Pythium sylvaticum.

Author

Lascombe, Marie-Bernard, Retailleau, Pascal, Ponchet, Michel, Industri, Benoît, Blein, Jean-Pierre, and Prangé, Thierry

Subjects
*PROTEINS, *AMINO acids, *PYTHIUM, *LIPIDS, *STEROLS, *OOMYCETES
Abstract

The structure of sylvaticin, a 10 kDa major pythin protein excreted by the parasitic oomycete Pythium sylvaticum, has been determined. Although closely related to α-elicitins in its biological response, toxicity and overall structure, sylvaticin presents a number of structural features that make it an unusual member of the elicitin class. Elicitins possess a large hydrophobic cavity and the mechanism of the systemic acquired resistance induced in planta is known to proceed through lipid transport and complexation within this cavity. Unlike other elicitins, sylvaticin contains tryptophan residues, one of which points inwards towards the central cavity, thus limiting access to sterols. In the case of sylvaticin, the sterol-transport mechanism is likely to be of less importance compared with other members of the elicitin family and still remains to be fully characterized. [ABSTRACT FROM AUTHOR]

Published
2007
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17. Expression, purification, crystallization and preliminary X-ray studies of the outer membrane efflux proteins OprM and OprN from Pseudomonas aeruginosa.

Author

Broutin, Isabelle, Benabdelhak, Houssain, Moreel, Xavier, Lascombe, Marie-Bernard, Lerouge, Dimitri, and Ducruix, Arnaud

Subjects
PSEUDOMONAS aeruginosa, MEMBRANE proteins, PSEUDOMONAS, CRYSTALLIZATION, ESCHERICHIA coli, AFFINITY chromatography
Abstract

OprM and OprN belong to the outer membrane factor family proteins. These ∼52 kDa proteins are part of the tripartite efflux pumps found in Pseudomonas aeruginosa and are responsible in part for the antibiotic resistance observed in these bacteria. Both proteins have been expressed in Escherichia coli as His-tag proteins and purified accordingly by affinity chromatography in the presence of n-octyl-β-D-glucopyranoside detergent. OprM and OprN were crystallized using PEG 20 000/ammonium citrate and ammonium sulfate as precipitating agents, respectively. Crystals belong to space group C2, with unit-cell parameters a = 152.6, b = 87.9, c = 355.9 Å, βe = 98.9° and a = 151.3, b = 87.6, c = 356.5 Å, = 98.1° for OprM and OprN, respectively. Using the ESRF synchrotron- radiation source, OprM diffraction data extended to 3.4 Å. [ABSTRACT FROM AUTHOR]

Published
2005
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18. Crystallization of DIR1, a LTP2-like resistance signalling protein from Arabidopsis thaliana.

Author

Buhot, Nathalie, Bakan, Bénédicte, Lamb, Chris J., Marion, Didier, Lascombe, Marie-Bernard, Blein, Jean Pierre, and Prangé, Thierry

Subjects
ARABIDOPSIS thaliana, CRYSTALLIZATION, CRYSTALS, SPACE groups, ARABIDOPSIS, CRYSTALLOGRAPHY
Abstract

DIR1, a putative LTP2 protein from Arabidopsis thaliana implicated in systemic acquired resistance in planta, has been crystallized in space group P212121 with one molecule per asymmetric unit. The crystals diffract to a resolution of 1.6 Å. [ABSTRACT FROM AUTHOR]

Published
2006
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19. Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum.

Author

Lascombe, Marie-Bernard, Ponchet, Michel, Cardin, Loic, Milat, Marie-Louise, Blein, Jean-Pierre, and Prangé, Thierry

Subjects
*MICROBIAL proteins, *PYTHIUM, *PROTEINS, *PYTHIACEAE, *CRYSTALLIZATION, *CRYSTALLOGRAPHY
Abstract

Analyzes the purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum. Precipitant agent used in the presence of nickel chloride; Diffraction date recorded to 2.1 A resolution at a synchrotron-radiation source.

Published
2004
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20. The Crystal Structure of a Family 5 Endoglucanase Mutant in Complexed and Uncomplexed Forms Reveals an Induced Fit Activation Mechanism

Author

Domínguez, Roberto, Souchon, Hélène, Lascombe, Marie-Bernard, and Alzari, Pedro M.

Abstract

The structures of the Glu140→Gln mutant ofClostridium thermocellumendoglucanase CelC in unliganded form (CelCE140Q) and in complex with cellohexaose (CelCE140Q– Glc6) have been refined to crystallographicR-factors of 19.4% at 1.9 Å and 17.8% at 2.3 Å resolution, respectively. The structure of CelCE140Q– Glc6complex shows two

Published
1996
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21. Crystallization and preliminary X-ray studies of oligandrin, a sterol-carrier elicitor from Pythium oligandrum.

Author

Lascombe, Marie-bernard, Mitat, Marie-louise, Btein, Jean-pierre, Panabieres, Franck, Ponchep, Michet, and Prangrl, Thierry

Subjects
PYTHIUM, CARRIER proteins, CELL culture, PARASITIC plants, CRYSTALLIZATION, PATHOGENIC microorganisms
Abstract

The article presents information on the crystallization and preliminary X-ray studies of oligandrin, a sterol-carrier elicitor from Pythium oligandrum. Phytophtora and Phytium spp. fungi are micromycetes, parasites of many economically important crops. They produce proteins that induce leaf necrosis and further a systemic acquired resistance against a wide range of other pathogens, including fungal and bacterial species. In the case of the low-temperature form, the unit-cell parameters are still indicative of a multimeric protein in the crystal.

Published
2000
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22. Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A.

Author

Gaucher JF, Reille-Seroussi M, Gagey-Eilstein N, Broussy S, Coric P, Seijo B, Lascombe MB, Gautier B, Liu WQ, Huguenot F, Inguimbert N, Bouaziz S, Vidal M, and Broutin I

Subjects
Binding Sites, Humans, Protein Binding drug effects, Vascular Endothelial Growth Factor A metabolism, Vascular Endothelial Growth Factor Receptor-1 metabolism, Cations, Divalent pharmacology, Molecular Docking Simulation, Protein Multimerization, Vascular Endothelial Growth Factor A chemistry, Vascular Endothelial Growth Factor Receptor-1 chemistry
Abstract

Angiogenesis is tightly regulated through the binding of vascular endothelial growth factors (VEGFs) to their receptors (VEGFRs). In this context, we showed that human VEGFR1 domain 2 crystallizes in the presence of Zn2+, Co2+ or Cu2+ as a dimer that forms via metal-ion interactions and interlocked hydrophobic surfaces. SAXS, NMR and size exclusion chromatography analyses confirm the formation of this dimer in solution in the presence of Co2+, Cd2+ or Cu2+. Since the metal-induced dimerization masks the VEGFs binding surface, we investigated the ability of metal ions to displace the VEGF-A binding to hVEGFR1: using a competition assay, we evidenced that the metals displaced the VEGF-A binding to hVEGFR1 extracellular domain binding at micromolar level., Competing Interests: The authors have declared that no competing interests exist.

Published
2016
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23. Crystallization of DIR1, a LTP2-like resistance signalling protein from Arabidopsis thaliana.

Author

Lascombe MB, Buhot N, Bakan B, Marion D, Blein JP, Lamb CJ, and Prangé T

Subjects
Arabidopsis immunology, Arabidopsis Proteins isolation & purification, Carrier Proteins isolation & purification, Crystallization, Crystallography, X-Ray, Fatty Acid-Binding Proteins, Signal Transduction, Arabidopsis chemistry, Arabidopsis Proteins chemistry, Carrier Proteins chemistry, Plant Proteins chemistry
Abstract

DIR1, a putative LTP2 protein from Arabidopsis thaliana implicated in systemic acquired resistance in planta, has been crystallized in space group P2(1)2(1)2(1) with one molecule per asymmetric unit. The crystals diffract to a resolution of 1.6 angstroms.

Published
2006
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