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Accueil > Plateformes > Mesures d’interactions protéine-protéine

Publications

2017


  • T. Di Meo, W. Ghattas, C. Herrero, C. Velours, P. Minard, J. - P. Mahy, R. Ricoux, et A. Urvoas, « αRep A3: A versatile artificial scaffold for metalloenzyme design », Chemistry (Weinheim an Der Bergstrasse, Germany), 2017.
    Résumé : αRep is a new family of artificial proteins based on a thermostable alpha-helical repeated motif. One of its members, αRep A3, forms a stable homo-dimer with a wide cleft that is able to receive metal complexes and thus appears as suitable for generating new artificial biocatalysts. Based on the crystal structure of αRep A3, two positions (F119 and Y26) were chosen and changed independently into cysteine residues. A phenanthroline ligand was covalently attached to the unique cysteine of each protein variant and the corresponding biohybrids were purified and characterized. Once mutated and coupled to phenanthroline, the protein remained folded and dimeric. Copper(II) was bound specifically by the two biohybrids with two different binding modes and, in addition, the holo biohybrid A3F119NPH was found to be able to catalyze enantioselectively the Diels-Alder (D-A) cycloaddition with up to 62% ee. This study validates the choice of the αRep A3 dimer as a protein scaffold and provides a new promising route for the design and production of new enantioselective biohybrids based on entirely artificial proteins issued from a highly diverse library.
    Mots-clés : artificial repeat proteins, B3S, Diels-Alder reaction, Enantioselective Catalysis, MIP, PF, PIM.


  • J. Lang, A. Vigouroux, A. El Sahili, A. Kwasiborski, M. Aumont-Nicaise, Y. Dessaux, J. A. Shykoff, S. Moréra, et D. Faure, « Fitness costs restrict niche expansion by generalist niche-constructing pathogens », The ISME Journal, vol. 11, nᵒ 2, p. 374-385, 2017.
    Mots-clés : B3S, MESB3S, MICROBIO, PBI, PF, PIM.

  • L. Loiseau, C. Fyfe, L. Aussel, M. Hajj Chehade, S. B. Hernández, B. Faivre, D. Hamdane, C. Mellot-Draznieks, B. Rascalou, L. Pelosi, C. Velours, D. Cornu, M. Lombard, J. Casadesús, F. Pierrel, M. Fontecave, et F. Barras, « The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ », The Journal of Biological Chemistry, 2017.
    Résumé : Ubiquinone (UQ), also referred to as coenzyme Q, is a widespread lipophilic molecule in both prokaryotes and eukaryotes in which it primarily acts as an electron carrier. Eleven proteins are known to participate in UQ biosynthesis in Escherichia coli, and we recently demonstrated that UQ biosynthesis requires additional, nonenzymatic factors, some of which are still unknown. Here, we report on the identification of a bacterial gene, yqiC, which is required for efficient UQ biosynthesis, and which we have renamed ubiK. Using several methods, we demonstrated that the UbiK protein forms a complex with the C-terminal part of UbiJ, another UQ biogenesis factor we previously identified. We found that both proteins are likely to contribute to global UQ biosynthesis rather than to a specific biosynthetic step, since both ubiK and ubiJ mutants accumulated octaprenylphenol, an early intermediate of the UQ biosynthetic pathway. Interestingly, we found that both proteins are dispensable for UQ biosynthesis under anaerobiosis, even though they were expressed in the absence of oxygen. We also provide evidence that the UbiK-UbiJ complex interacts with palmitoleic acid, a major lipid in E. coli. Last, in Salmonella enterica, ubiK was required for proliferation in macrophages and virulence in mice. We conclude that although the role of the UbiK-UbiJ complex remains unknown, our results support the hypothesis that UbiK is an accessory factor of Ubi enzymes and facilitates UQ biosynthesis by acting as an assembly factor, a targeting factor, or both.
    Mots-clés : bioenergetics, coenzyme Q10 (CoQ10), Electron transfer, Escherichia coli (E. coli), Microbiology, PF, PIM, SICAPS, Ubiquinone.


  • P. V. Sauer, J. Timm, D. Liu, D. Sitbon, E. Boeri-Erba, C. Velours, N. Mücke, J. Langowski, F. Ochsenbein, G. Almouzni, et D. Panne, « Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1 », eLife, vol. 6, mars 2017.
    Mots-clés : AMIG, B3S, PF, PIM.


  • A. Talagas, L. Fontaine, L. Ledesma-García, J. Mignolet, I. Li de la Sierra-Gallay, N. Lazar, M. Aumont-Nicaise, M. J. Federle, G. Prehna, P. Hols, et S. Nessler, « Correction: Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS », PLOS Pathogens, vol. 13, nᵒ 2, p. e1006208, févr. 2017.
    Mots-clés : B3S, FAAM, PF, PIM.

2016



  • S. Ahmad, L. Pecqueur, B. Dreier, D. Hamdane, M. Aumont-Nicaise, A. Plückthun, M. Knossow, et B. Gigant, « Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin », Scientific Reports, vol. 6, p. 28922, juill. 2016.
    Mots-clés : B3S, MIKICA, PF, PIM.

  • D. Hamdane, C. Velours, D. Cornu, M. Nicaise, M. Lombard, et M. Fontecave, « A chemical chaperone induces inhomogeneous conformational changes in flexible proteins », Physical chemistry chemical physics: PCCP, vol. 18, nᵒ 30, p. 20410-20421, 2016.
    Résumé : Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the conformation of the marginally stable LPPs to avoid their inappropriate protein/protein interactions and aggregation.
    Mots-clés : PF, PIM, SICAPS.

  • L. Marty, A. Vigouroux, M. Aumont-Nicaise, Y. Dessaux, D. Faure, et S. Moréra, « Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens », The Journal of Biological Chemistry, vol. 291, nᵒ 43, p. 22638-22649, 2016.
    Résumé : Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. Opines are either sugar phosphodiesters or the products of condensed amino acids with ketoacids or sugars. They are Agrobacterium nutrients and imported into the bacterial cell via periplasmic-binding proteins (PBPs) and ABC-transporters. Mannopine, an opine from the mannityl-opine family, is synthesized from an intermediate named deoxy-fructosyl-glutamine (DFG), which is also an opine and abundant Amadori compound (a name used for any derivative of aminodeoxysugars) present in decaying plant materials. The PBP MotA is responsible for mannopine import in mannopine-assimilating agrobacteria. In the nopaline-opine type agrobacteria strain, SocA protein was proposed as a putative mannopine binding PBP, and AttC protein was annotated as a mannopine binding-like PBP. Structural data on mannityl-opine-PBP complexes is currently lacking. By combining affinity data with analysis of seven x-ray structures at high resolution, we investigated the molecular basis of MotA, SocA, and AttC interactions with mannopine and its DFG precursor. Our work demonstrates that AttC is not a mannopine-binding protein and reveals a specific binding pocket for DFG in SocA with an affinity in nanomolar range. Hence, mannopine would not be imported into nopaline-type agrobacteria strains. In contrast, MotA binds both mannopine and DFG. We thus defined one mannopine and two DFG binding signatures. Unlike mannopine-PBPs, selective DFG-PBPs are present in a wide diversity of bacteria, including Actinobacteria, α-,β-, and γ-proteobacteria, revealing a common role of this Amadori compound in pathogenic, symbiotic, and opportunistic bacteria.
    Mots-clés : ABC transporter, B3S, Crystal Structure, DFG, host-pathogen interaction, isothermal titration calorimetry (ITC), mannopine, MESB3S, opine, periplasmic binding protein, PF, PIM, plant pathogen, x-ray crystallography.


  • A. Talagas, L. Fontaine, L. Ledesma-Garca, J. Mignolet, I. Li de la Sierra-Gallay, N. Lazar, M. Aumont-Nicaise, M. J. Federle, G. Prehna, P. Hols, et S. Nessler, « Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS », PLOS Pathogens, vol. 12, nᵒ 12, p. e1005980, déc. 2016.
    Mots-clés : B3S, FAAM, PF, PIM.

2015



  • A. Chevrel, A. Urvoas, I. L. de la Sierra-Gallay, M. Aumont-Nicaise, S. Moutel, M. Desmadril, F. Perez, A. Gautreau, H. van Tilbeurgh, P. Minard, et M. Valerio-Lepiniec, « Specific GFP-binding artificial proteins ( Rep): a new tool for in vitro to live cell applications », Bioscience Reports, vol. 35, nᵒ 4, p. e00223-e00223, août 2015.
    Mots-clés : B3S, FAAM, MIP, PF, PIM.


  • A. El Sahili, A. Kwasiborski, N. Mothe, C. Velours, P. Legrand, S. Moréra, et D. Faure, « Natural Guided Genome Engineering Reveals Transcriptional Regulators Controlling Quorum-Sensing Signal Degradation », PLOS ONE, vol. 10, nᵒ 11, p. e0141718, nov. 2015.
    Mots-clés : 4-Butyrolactone, Amino Acid Sequence, Amino Acid Substitution, B3S, Bacterial Proteins, Carboxylic Ester Hydrolases, Circular Dichroism, Crystallography, X-Ray, Directed Molecular Evolution, Gene Expression Regulation, Bacterial, Homoserine, Lactones, MESB3S, MICROBIO, Molecular Sequence Data, Mutation, Mutation, Missense, PBI, PF, PIM, Point Mutation, Polymorphism, Single Nucleotide, Protein Conformation, Protein Folding, Quorum Sensing, Rhodococcus, Transcription Factors, Transcription, Genetic.

  • L. Garcia, F. Cisnetti, N. Gillet, R. Guillot, M. Aumont-Nicaise, J. - P. Piquemal, M. Desmadril, F. Lambert, et C. Policar, « Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I) », Journal of the American Chemical Society, vol. 137, nᵒ 3, p. 1141-1146, 2015.
    Résumé : The idea of a possible control of metal ion properties by constraining the coordination sphere geometry was introduced by Vallee and Williams with the concept of entasis, which is frequently postulated to be at stake in metallobiomolecules. However, the interactions controlling the geometry at metal centers remain often elusive. In this study, the coordination properties toward copper ions—Cu(II) or Cu(I)—of a geometrically constrained glycoligand centered on a sugar scaffold were compared with those of an analogous ligand built on an unconstrained alkyl chain. The sugar-centered ligand was shown to be more preorganized for Cu(II) coordination than its open-chain analogue, with an unusual additional stabilization of the Cu(I) redox state. This preference for Cu(I) was suggested to arise from geometric constraints favoring an optimized folding of the glycoligand minimizing steric repulsions. In other words, the Cu(I) d(10) species is stabilized by valence shell electron pair repulsion (VSEPR). This idea was rationalized by a theoretical noncovalent interactions (NCI) analysis. The cumulative effects of weak forces were shown to create an efficient buckle as in a hook-and-loop fastener, and fine structural features within the glycoligand reduce repulsive interactions for the Cu(I) state. This study emphasizes that monosaccharide platforms are appropriate ligand backbones for a delicate geometric control at the metal center, with a network of weak interactions within the ligand. This structuration availing in glycoligands makes them attractive for metallic entasis.
    Mots-clés : Carbohydrates, Copper, Ligands, Models, Molecular, Molecular Structure, Organometallic Compounds, PF, PIM.

  • 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.

  • M. Jose, S. Tollis, D. Nair, R. Mitteau, C. Velours, A. Massoni-Laporte, A. Royou, J. - B. Sibarita, et D. McCusker, « A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis », Molecular Biology of the Cell, vol. 26, nᵒ 13, p. 2519-2534, 2015.
    Résumé : The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4∆ and bud6∆ alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.
    Mots-clés : Cell Polarity, Endocytosis, Exocytosis, Metabolic Networks and Pathways, PF, PIM, Protein Transport, Saccharomyces cerevisiae Proteins, Saccharomycetales.

  • D. Proença, C. Velours, C. Leandro, M. Garcia, M. Pimentel, et C. São-José, « A two-component, multimeric endolysin encoded by a single gene », Molecular Microbiology, vol. 95, nᵒ 5, p. 739-753, 2015.
    Résumé : Bacteriophage endolysins are bacterial cell wall degrading enzymes whose potential to fight bacterial infections has been intensively studied. Endolysins from Gram-positive systems are typically described as monomeric and as having a modular structure consisting of one or two N-terminal catalytic domains (CDs) linked to a C-terminal region responsible for cell wall binding (CWB). We show here that expression of the endolysin gene lys170 of the enterococcal phage F170/08 results in two products, the expected full length endolysin (Lys170FL) and a C-terminal fragment corresponding to the CWB domain (CWB170). The latter is produced from an in-frame, alternative translation start site. Both polypeptides interact to form the fully active endolysin. Biochemical data strongly support a model where Lys170 is made of one monomer of Lys170FL associated with up to three CWB170 subunits, which are responsible for efficient endolysin binding to its substrate. Bioinformatics analysis indicates that similar secondary translation start signals may be used to produce and add independent CWB170-like subunits to different enzymatic specificities. The particular configuration of endolysin Lys170 uncovers a new mode of increasing the number of CWB motifs associated to CD modules, as an alternative to the tandem repetition typically found in monomeric cell wall hydrolases.
    Mots-clés : Amino Acid Sequence, Bacteriophages, Binding Sites, Cell Wall, Computational Biology, Endopeptidases, Enterococcus, Escherichia coli, Multiprotein Complexes, PF, PIM, Protein Binding, Protein Multimerization, Protein Structure, Tertiary, Protein Subunits, Sequence Homology, Amino Acid.


  • N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, et F. Ochsenbein, « Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork », Nucleic Acids Research, vol. 43, nᵒ 3, p. 1905-1917, févr. 2015.
    Mots-clés : AMIG, B3S, PF, PIM.


  • F. Samazan, B. Rokbi, D. Seguin, F. Telles, V. Gautier, G. Richarme, D. Chevret, P. F. Varela, C. Velours, et I. Poquet, « Production, secretion and purification of a correctly folded staphylococcal antigen in Lactococcus lactis », Microbial Cell Factories, vol. 14, nᵒ 1, 2015.


  • M. Valerio-Lepiniec, A. Urvoas, A. Chevrel, A. Guellouz, Y. Ferrandez, A. Mesneau, I. L. de la Sierra-Gallay, M. Aumont-Nicaise, M. Desmadril, H. van Tilbeurgh, et P. Minard, « The αRep artificial repeat protein scaffold: a new tool for crystallization and live cell applications », Biochemical Society Transactions, vol. 43, nᵒ 5, p. 819-824, oct. 2015.
    Mots-clés : B3S, FAAM, MIP, PF, PIM.
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