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Accueil > Départements > Biochimie, Biophysique et Biologie Structurale > Stéphane BRESSANELLI : Interactions et mécanismes d’assemblage des protéines et des peptides

Publications de l’équipe


  • K. Ben Ouirane, Y. Boulard, et S. Bressanelli, « The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif », The Journal of Biological Chemistry, vol. 294, nᵒ 19, p. 7573-7587, mai 2019.
    Résumé : RNA viruses synthesize new genomes in the infected host thanks to dedicated, virally-encoded RNA-dependent RNA polymerases (RdRps). As such, these enzymes are prime targets for antiviral therapy, as has recently been demonstrated for hepatitis C virus (HCV). However, peculiarities in the architecture and dynamics of RdRps raise fundamental questions about access to their active site during RNA polymerization. Here, we used molecular modelling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp. Tracing the possible passage of incoming UTP or GTP through the RdRp-specific entry tunnel, we found two successive checkpoints that regulate nucleotide traffic to the active site. We observed that a magnesium-bound nucleotide first binds next to the tunnel entry, and interactions with the triphosphate moiety orient it such that its base moiety enters first. Dynamics of the RdRp motifs F1 + F3 then allow the nucleotide to interrogate the RNA template base prior to nucleotide insertion into the active site. These dynamics are finely regulated by a second magnesium dication, thus coordinating the entry of a magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. The findings of our work suggest that some at least of these features are general to viral RdRps and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses.
    Mots-clés : B3S, catalysis, complex, crystal-structure, fidelity, IMAPP, insights, mechanism, molecular dynamics, nucleoside, nucleoside/nucleotide transport, nucleotide transport, positive-sense RNA virus, protein motif, RNA virus, RNA-dependent RNA polymerase (RdRp), simulations, Single-stranded, Single-stranded, positive-sense RNA virus, structural basis, structural biology, viral polymerase.

  • P. Chervy, C. Petcut, D. Rault, C. Meriadec, T. Bizien, K. François, J. Richard, C. Chassaing, N. Benamar, F. Artzner, et M. Paternostre, « Organic Nanoscrolls from Electrostatic Interactions between Peptides and Lipids: Assembly Steps and Structure », Langmuir, vol. 35, nᵒ 32, p. 10648-10657, août 2019.
    Résumé : An important aspect of cells is their shape flexibility that gives them motion but also a high adaptation versatility to their environment. This shape versatility is mediated by different types of protein–membrane interactions among which electrostatic plays an important role. In the present work we examined the interaction between a small dicationic peptide, that possesses self-assembly properties, and lipid model membranes. The peptide, lanreotide, spontaneously forms nanotubes in water that have a strictly uniform diameter. In the current work, we show that the interaction between the cationic peptide and negatively charged bilayers of lipids induces the formation of myelin sheath-like structures that we call nanoscrolls. By deciphering the different steps of formation and the molecular structure of the self-assembly, we show how electrostatics modify the spontaneous peptide and lipid way of packing.
    Mots-clés : B3S, IMAPP.

  • L. Marichal, G. Giraudon--Colas, F. Cousin, A. Thill, J. Labarre, Y. Boulard, J. - C. Aude, S. Pin, et J. P. Renault, « Protein–Nanoparticle Interactions: What Are the Protein–Corona Thickness and Organization? », Langmuir, vol. 35, nᵒ 33, p. 10831-10837, août 2019.
    Résumé : Protein adsorption on a surface is generally evaluated in terms of the evolution of the proteins’ structures and functions. However, when the surface is that of a nanoparticle, the protein corona formed around it possesses a particular supramolecular structure that gives a “biological identity” to the new object. Little is known about the actual shape of the protein corona. Here, the protein corona formed by the adsorption of model proteins (myoglobin and hemoglobin) on silica nanoparticles was studied. Small-angle neutron scattering and oxygenation studies were combined to assess both the structural and functional impacts of the adsorption on proteins. Large differences in the oxygenation properties could be found while no significant global shape changes were seen after adsorption. Moreover, the structural study showed that the adsorbed proteins form an organized yet discontinuous monolayer around the nanoparticles.
    Mots-clés : B3S, BIM, DBG, IMAPP, PEPS.
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  • M. Chevreuil, D. Law-Hine, J. Chen, S. Bressanelli, S. Combet, D. Constantin, J. Degrouard, J. Möller, M. Zeghal, et G. Tresset, « Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte », Nature Communications, vol. 9, nᵒ 1, p. 3071, août 2018.
    Résumé : The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape.
    Mots-clés : B3S, cryoelectron microscopy, disassembly, IMAPP, kinetic pathway, mechanism, Modeling, nanoparticles, pathway, plant-virus, protein, reconstruction, rna, templates, time-resolved small-angle X-ray scattering, Virus, virus-like particles.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, M. Desmadril, N. Nhiri, A. Van Dorsselaer, S. Cianferani, E. Jacquet, T. Meinnel, et C. Giglione, « Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts », Biochimica Et Biophysica Acta, vol. 1866, nᵒ 2, p. 348-355, févr. 2018.
    Résumé : Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 specific activity to values similar to those of bacterial PDFs. We next show that Vp16PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
    Mots-clés : AMIG, B3S, DBG, Enzyme mechanism, IMAPP, MIP, N-terminal methionine excision, Peptide deformylase, PF, PIM, PROMTI, Structure, Virus.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Localizing Conformational Hinges by NMR: Where Do Hepatitis B Virus Core Proteins Adapt for Capsid Assembly? », Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, vol. 19, nᵒ 11, p. 1336-1340, juin 2018.
    Résumé : The hepatitis B virus (HBV) icosahedral nucleocapsid is assembled from 240 chemically identical core protein molecules and, structurally, comprises four groups of symmetrically nonequivalent subunits. We show here that this asymmetry is reflected in solid-state NMR spectra of the capsids, in which peak splitting is observed for a subset of residues. We compare this information to dihedral angle variations from available 3D structures and also to computational predictions of "dynamic" domains and molecular hinges. We find that although, at the given resolution, dihedral angles variations directly obtained from the X-ray structures are not precise enough to be interpreted, the chemical-shift information from NMR correlates, and interestingly goes beyond, information from bioinformatics approaches. Our study reveals the high sensitivity with which NMR can detect the residues allowing the subtle conformational adaptations needed in lattice formation. Our findings are important for understanding the formation and modulation of protein assemblies in general.
    Mots-clés : asymmetric unit, B3S, core protein, hepatitis B virus, IMAPP, nucleocapsid, solid-state NMR.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Solid-state [13C-15N] NMR resonance assignment of hepatitis B virus core protein », Biomolecular NMR assignments, vol. 12, nᵒ 1, p. 205-214, avr. 2018.
    Résumé : Each year, nearly 900,000 deaths are due to serious liver diseases caused by chronic hepatitis B virus infection. The viral particle is composed of an outer envelope and an inner icosahedral nucleocapsid formed by multiple dimers of a ~ 20 kDa self-assembling core protein (Cp). Here we report the solid-state 13C and 15N resonance assignments of the assembly domain, Cp149, of the core protein in its capsid form. A secondary chemical shift analysis of the 140 visible residues suggests an overall alpha-helical three-dimensional fold matching that derived for Cp149 from the X-ray crystallography of the capsid, and from solution-state NMR of the Cp149 dimer. Interestingly, however, at three distinct regions the chemical shifts in solution differ significantly between core proteins in the capsid state versus in the dimer state, strongly suggesting the respective residues to be involved in capsid assembly.
    Mots-clés : AMIG, Assignments, B3S, Core protein, Hepatitis B virus, IMAPP, Nucleocapsid, Solid-state NMR.

  • L. Marichal, J. - P. Renault, S. Chédin, G. Lagniel, G. Klein, J. - C. Aude, C. Tellier-Lebegue, J. Armengaud, S. Pin, J. Labarre, et Y. Boulard, « Importance of Post-translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica surfaces », Langmuir: the ACS journal of surfaces and colloids, vol. 34, nᵒ 18, p. 5312-5322, mai 2018.
    Résumé : Understanding the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest for both basic research and practical applications involving nanotechnology. From the list of cellular proteins with the highest affinity for silica nanoparticles, we highlighted the group of proteins containing arginine-glycine-glycine (RGG) motifs. Biochemical experiments confirmed that RGG motifs interact strongly with the silica surfaces. The affinity of these motifs is further increased when the R residue is asymmetrically, but not symmetrically, dimethylated. Molecular dynamics simulations show that the asymmetrical dimethylation generates an electrostatic asymmetry in the guanidinium group of the R residue, orientating and stabilizing it on the silica surface. The RGG motifs (methylated or not) systematically target the siloxide groups on the silica surface through an ionic interaction, immediately strengthened by hydrogen bonds with proximal silanol and siloxane groups. Given that, in vivo, RGG motifs are often asymmetrically dimethylated by specific cellular methylases, our data add support to the idea that this type of methylation is a key mechanism for cells to regulate the interaction of the RGG proteins with their cellular partners.
    Mots-clés : B3S, BIM, DBG, IMAPP, PEPS.

  • T. Tubiana, J. - C. Carvaillo, Y. Boulard, et S. Bressanelli, « TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries », Journal of Chemical Information and Modeling, vol. 58, nᵒ 11, p. 2178-2182, nov. 2018.
    Résumé : It is extremely helpful to be able to partition the thousands of frames produced in molecular dynamics simulations into a limited number of most dissimilar conformations. While robust clustering algorithms are already available to do so, there is a distinct need for an easy-to-use clustering program with complete user control, taking as input a trajectory from any molecular dynamics (MD) package and outputting an intuitive display of results with plots allowing at-a-glance analysis. We present TTClust (for Trusty Trajectory Clustering), a python program that uses the MDTraj package to fill this need.
    Mots-clés : B3S, dynamics, IMAPP.


  • E. Baquero, A. A. Albertini, H. Raux, A. Abou‐Hamdan, E. Boeri‐Erba, M. Ouldali, L. Buonocore, J. K. Rose, J. Lepault, S. Bressanelli, et Y. Gaudin, « Structural intermediates in the fusion‐associated transition of vesiculovirus glycoprotein », The EMBO Journal, vol. 36, nᵒ 5, p. 679-692, mars 2017.
    Mots-clés : B3S, conformational change, CRYOEM, glycoprotein, IMAPP, intermediate structures, membrane fusion, PF, RHABDO, Vesiculovirus, VIRO, VIROEM.

  • S. Y. Doerflinger, M. Cortese, I. Romero-Brey, Z. Menne, T. Tubiana, C. Schenk, P. A. White, R. Bartenschlager, S. Bressanelli, G. S. Hansman, et V. Lohmann, « Membrane alterations induced by nonstructural proteins of human norovirus », PLoS pathogens, vol. 13, nᵒ 10, p. e1006705, oct. 2017.
    Résumé : Human noroviruses (huNoV) are the most frequent cause of non-bacterial acute gastroenteritis worldwide, particularly genogroup II genotype 4 (GII.4) variants. The viral nonstructural (NS) proteins encoded by the ORF1 polyprotein induce vesical clusters harboring the viral replication sites. Little is known so far about the ultrastructure of these replication organelles or the contribution of individual NS proteins to their biogenesis. We compared the ultrastructural changes induced by expression of norovirus ORF1 polyproteins with those induced upon infection with murine norovirus (MNV). Characteristic membrane alterations induced by ORF1 expression resembled those found in MNV infected cells, consisting of vesicle accumulations likely built from the endoplasmic reticulum (ER) which included single membrane vesicles (SMVs), double membrane vesicles (DMVs) and multi membrane vesicles (MMVs). In-depth analysis using electron tomography suggested that MMVs originate through the enwrapping SMVs with tubular structures similar to mechanisms reported for picornaviruses. Expression of GII.4 NS1-2, NS3 and NS4 fused to GFP revealed distinct membrane alterations when analyzed by correlative light and electron microscopy. Expression of NS1-2 induced proliferation of smooth ER membranes forming long tubular structures that were affected by mutations in the active center of the putative NS1-2 hydrolase domain. NS3 was associated with ER membranes around lipid droplets (LDs) and induced the formation of convoluted membranes, which were even more pronounced in case of NS4. Interestingly, NS4 was the only GII.4 protein capable of inducing SMV and DMV formation when expressed individually. Our work provides the first ultrastructural analysis of norovirus GII.4 induced vesicle clusters and suggests that their morphology and biogenesis is most similar to picornaviruses. We further identified NS4 as a key factor in the formation of membrane alterations of huNoV and provide models of the putative membrane topologies of NS1-2, NS3 and NS4 to guide future studies.
    Mots-clés : B3S, IMAPP.

  • S. Fieulaine, R. Alves de Sousa, L. Maigre, K. Hamiche, M. Alimi, J. - M. Bolla, A. Taleb, A. Denis, J. - M. Pagès, I. Artaud, T. Meinnel, et C. Giglione, « Corrigendum: A unique peptide deformylase platform to rationally design and challenge novel active compounds », Scientific Reports, vol. 7, p. 39365, janv. 2017.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, W. V. Bienvenut, C. Dian, T. Meinnel, et C. Giglione, « The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation », Scientific Reports, vol. 7, nᵒ 1, p. 11041, sept. 2017.
    Résumé : Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.
    Mots-clés : B3S, DBG, IMAPP, PROMTI.

  • I. Jupin, M. Ayach, L. Jomat, S. Fieulaine, et S. Bressanelli, « A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase », PLOS Pathogens, vol. 13, nᵒ 11, p. e1006714, nov. 2017.
    Mots-clés : Algorithms, Animals, Arabidopsis thaliana, B3S, Chemistry, Physical, Chickens, crystal structure, Crystallization, Crystallography, X-Ray, crystals, Data Collection, IMAPP, Leaves, Microbial mutation, Models, Molecular, Molecular dynamics, Molecular Structure, Muramidase, Physicochemical Phenomena, Protein Conformation, Synchrotrons, Viral Replication.

  • E. Karakas, C. Taveneau, S. Bressanelli, M. Marchi, B. Robert, et S. Abel, « Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA », Journal of Biomolecular Structure and Dynamics, vol. 35, nᵒ 1, p. 159-181, janv. 2017.
    Mots-clés : Amber, B3S, Dimethylamines, fluorescence spectroscopy, IMAPP, LBMS, LDAO surfactant, lipid kinase PI4KA, Lipids, MD simulation, micelle, Micelles, Minor Histocompatibility Antigens, Molecular Conformation, Molecular Dynamics Simulation, molecular modeling, Phosphotransferases (Alcohol Group Acceptor), Protein Binding, Proteins, Static Electricity, Surface-Active Agents.

  • P. K. Mandal, D. Shukla, V. Govind, Y. Boulard, et L. Ersland, « Glutathione Conformations and Its Implications for in vivo Magnetic Resonance Spectroscopy », Journal of Alzheimer's disease: JAD, mai 2017.
    Résumé : Glutathione (GSH) is a major antioxidant in humans that is involved in the detoxification of reactive radicals and peroxides. The molecular structural conformations of GSH depend on the surrounding micro-environment, and it has been experimentally evaluated using NMR and Raman spectroscopic techniques as well as by molecular dynamics simulation studies. The converging report indicates that GSH exists mainly in two major conformations, i.e., "extended" and "folded". The NMR-derived information on the GSH conformers is essential to obtain optimal acquisition parameters in in vivo MRS experiments targeted for GSH detection. To further investigate the implications of GSH conformers in in vivo MRS studies and their relative proportions in healthy and pathological conditions, a multi-center clinical research study is necessary with a common protocol for GSH detection and quantification.
    Mots-clés : Antioxidant, B3S, Brain, conformation, Glutathione, IMAPP, Magnetic Resonance Spectroscopy, molecular dynamics, nuclear magnetic resonance.

  • L. Moriceau, L. Jomat, S. Bressanelli, C. Alcaide-Loridan, et I. Jupin, « Identification and Molecular Characterization of the Chloroplast Targeting Domain of Turnip yellow mosaic virus Replication Proteins », Frontiers in Plant Science, vol. 8, p. 2138, 2017.
    Résumé : Turnip yellow mosaic virus (TYMV) is a positive-strand RNA virus infecting plants. The TYMV 140K replication protein is a key organizer of viral replication complex (VRC) assembly, being responsible for recruitment of the viral polymerase and for targeting the VRCs to the chloroplast envelope where viral replication takes place. However, the structural requirements determining the subcellular localization and membrane association of this essential viral protein have not yet been defined. In this study, we investigated determinants for the in vivo chloroplast targeting of the TYMV 140K replication protein. Subcellular localization studies of deletion mutants identified a 41-residue internal sequence as the chloroplast targeting domain (CTD) of TYMV 140K; this sequence is sufficient to target GFP to the chloroplast envelope. The CTD appears to be located in the C-terminal extension of the methyltransferase domain-a region shared by 140K and its mature cleavage product 98K, which behaves as an integral membrane protein during infection. We predicted the CTD to fold into two amphipathic α-helices-a folding that was confirmed in vitro by circular dichroism spectroscopy analyses of a synthetic peptide. The importance for subcellular localization of the integrity of these amphipathic helices, and the function of 140K/98K, was demonstrated by performing amino acid substitutions that affected chloroplast targeting, membrane association and viral replication. These results establish a short internal α-helical peptide as an unusual signal for targeting proteins to the chloroplast envelope membrane, and provide new insights into membrane targeting of viral replication proteins-a universal feature of positive-strand RNA viruses.
    Mots-clés : amphipathic helix, B3S, chloroplast envelope membrane, IMAPP, membrane targeting, replication protein, RNA viruses, TYMV, viral replication, viral replication complexes.

  • T. Tubiana, Y. Boulard, et S. Bressanelli, « Dynamics and asymmetry in the dimer of the norovirus major capsid protein », PloS One, vol. 12, nᵒ 7, p. e0182056, 2017.
    Résumé : Noroviruses are the major cause of non-bacterial acute gastroenteritis in humans and livestock worldwide, despite being physically among the simplest animal viruses. The icosahedral capsid encasing the norovirus RNA genome is made of 90 dimers of a single ca 60-kDa polypeptide chain, VP1, arranged with T = 3 icosahedral symmetry. Here we study the conformational dynamics of this main building block of the norovirus capsid. We use molecular modeling and all-atom molecular dynamics simulations of the VP1 dimer for two genogroups with 50% sequence identity. We focus on the two points of flexibility in VP1 known from the crystal structure of the genogroup I (GI, human) capsid and from subsequent cryo-electron microscopy work on the GII capsid (also human). First, with a homology model of the GIII (bovine) VP1 dimer subjected to simulated annealing then classical molecular dynamics simulations, we show that the N-terminal arm conformation seen in the GI crystal structure is also favored in GIII VP1 but depends on the protonation state of critical residues. Second, simulations of the GI dimer show that the VP1 spike domain will not keep the position found in the GII electron microscopy work. Our main finding is a consistent propensity of the VP1 dimer to assume prominently asymmetric conformations. In order to probe this result, we obtain new SAXS data on GI VP1 dimers. These data are not interpretable as a population of symmetric dimers, but readily modeled by a highly asymmetric dimer. We go on to discuss possible implications of spontaneously asymmetric conformations in the successive steps of norovirus capsid assembly. Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein.
    Mots-clés : B3S, Crystallography, X-Ray, fluorescence spectroscopy, Hepacivirus, IMAPP, LDAO surfactant, lipid kinase PI4KA, MD simulation, micelle, Molecular modeling, Protein Structure, Secondary, RNA Replicase, RNA, Viral, Surface Plasmon Resonance, Transcription, Genetic, Virus Replication.


  • A. Akil, J. Peng, M. Omrane, C. Gondeau, C. Desterke, M. Marin, H. Tronchère, C. Taveneau, S. Sar, P. Briolotti, S. Benjelloun, A. Benjouad, P. Maurel, V. Thiers, S. Bressanelli, D. Samuel, C. Bréchot, et A. Gassama-Diagne, « Septin 9 induces lipid droplets growth by a phosphatidylinositol-5-phosphate and microtubule-dependent mechanism hijacked by HCV », Nature Communications, vol. 7, p. 12203, juill. 2016.

  • A. Breiman, S. Fieulaine, T. Meinnel, et C. Giglione, « The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks », Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol. 1864, nᵒ 5, p. 531-550, 2016.
    Mots-clés : B3S, Co-translational folding, Co-translational modifications, Co-translational targeting, DBG, IMAPP, Macromolecular Substances, plants, PROMTI, Protein Biosynthesis, Protein Folding, Protein Processing, Post-Translational, Proteolysis, Ribosome, Ribosome-associated protein biogenesis factors, Ribosomes.

  • S. Fieulaine, R. Alves de Sousa, L. Maigre, K. Hamiche, M. Alimi, J. - M. Bolla, A. Taleb, A. Denis, J. - M. Pagès, I. Artaud, T. Meinnel, et C. Giglione, « A unique peptide deformylase platform to rationally design and challenge novel active compounds », Scientific Reports, vol. 6, p. 35429, oct. 2016.

  • G. Klein, S. Devineau, J. C. Aude, Y. Boulard, H. Pasquier, J. Labarre, S. Pin, et J. P. Renault, « Interferences of Silica Nanoparticles in Green Fluorescent Protein Folding Processes », Langmuir: the ACS journal of surfaces and colloids, vol. 32, nᵒ 1, p. 195-202, janv. 2016.
    Résumé : We investigated the relationship between unfolded proteins, silica nanoparticles and chaperonin to determine whether unfolded proteins could stick to silica surfaces and how this process could impair heat shock protein activity. The HSP60 catalyzed green fluorescent protein (GFP) folding was used as a model system. The adsorption isotherms and adsorption kinetics of denatured GFP were measured, showing that denaturation increases GFP affinity for silica surfaces. This affinity is maintained even if the surfaces are covered by a protein corona and allows silica NPs to interfere directly with GFP folding by trapping it in its unstructured state. We determined also the adsorption isotherms of HSP60 and its chaperonin activity once adsorbed, showing that SiO2 NP can interfere also indirectly with protein folding through chaperonin trapping and inhibition. This inhibition is specifically efficient when NPs are covered first with a layer of unfolded proteins. These results highlight for the first time the antichaperonin activity of silica NPs and ask new questions about the toxicity of such misfolded proteins/nanoparticles assembly toward cells.
    Mots-clés : B3S, DBG, Green Fluorescent Proteins, IMAPP, Nanoparticles, PEPS, Protein Folding, Silicon Dioxide.

  • G. Klein, C. Mathé, M. Biola-Clier, S. Devineau, E. Drouineau, E. Hatem, L. Marichal, B. Alonso, J. - C. Gaillard, G. Lagniel, J. Armengaud, M. Carrière, S. Chédin, Y. Boulard, S. Pin, J. - P. Renault, J. - C. Aude, et J. Labarre, « RNA-binding proteins are a major target of silica nanoparticles in cell extracts », Nanotoxicology, vol. 10, nᵒ 10, p. 1555-1564, déc. 2016.
    Résumé : Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics and mixtures of soluble proteins prepared either from yeast cells or from alveolar human cells, we observed that proteins with large unstructured region(s) are more prone to bind on silica NPs. These disordered regions provide flexibility to proteins, a property that promotes their adsorption. The statistical analyses also pointed to a marked overrepresentation of RNA-binding proteins (RBPs) and of translation initiation factors among the adsorbed proteins. We propose that silica surfaces, which are mainly composed of Si-O(-) and Si-OH groups, mimic ribose-phosphate molecules (rich in -O(-) and -OH) and trap the proteins able to interact with ribose-phosphate containing molecules. Finally, using an in vitro assay, we showed that the sequestration of translation initiation factors by silica NPs results in an inhibition of the in vitro translational activity. This result demonstrates that characterizing the protein corona of various NPs would be a relevant approach to predict their potential toxicological effects.
    Mots-clés : B3S, BIM, DBG, IMAPP, intrinsically disordered protein, PEPS, Protein corona, proteomics, RNA binding protein, silica nanoparticles.

  • D. Law-Hine, M. Zeghal, S. Bressanelli, D. Constantin, et G. Tresset, « Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch », Soft Matter, vol. 12, nᵒ 32, p. 6728-6736, 2016.


  • M. Ayach et S. Bressanelli, « Crystallization of mutants of Turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition », Acta Crystallographica. Section F, Structural Biology Communications, vol. 71, nᵒ Pt 4, p. 405-408, avr. 2015.
    Résumé : Processing of the polyprotein of Turnip yellow mosaic virus is mediated by the protease PRO. PRO cleaves at two places, one of which is at the C-terminus of the PRO domain of another polyprotein molecule. In addition to this processing activity, PRO possesses an ubiquitin hydrolase (DUB) activity. The crystal structure of PRO has previously been reported in its polyprotein-processing mode with the C-terminus of one PRO inserted into the catalytic site of the next PRO, generating PRO polymers in the crystal packing of the trigonal space group. Here, two mutants designed to disrupt specific PRO-PRO interactions were generated, produced and purified. Crystalline plates were obtained by seeding and cross-seeding from initial `sea urchin'-like microcrystals of one mutant. The plates diffracted to beyond 2 Å resolution at a synchrotron source and complete data sets were collected for the two mutants. Data processing and analysis indicated that both mutant crystals belonged to the same monoclinic space group, with two molecules of PRO in the asymmetric unit.
    Mots-clés : Amino Acid Sequence, B3S, Crystallization, Hydrolases, IMAPP, Molecular Sequence Data, Mutation, self-processing viral cysteine proteinase, Tymovirus, ubiquitin, ubiquitin hydrolase, Ubiquitin-Specific Proteases.

  • E. Baquero, A. A. Albertini, H. Raux, L. Buonocore, J. K. Rose, S. Bressanelli, et Y. Gaudin, « Structure of the Low pH Conformation of Chandipura Virus G Reveals Important Features in the Evolution of the Vesiculovirus Glycoprotein », PLOS Pathogens, vol. 11, nᵒ 3, p. e1004756, mars 2015.
    Mots-clés : B3S, Evolution, Molecular, Humans, Hydrogen-Ion Concentration, IMAPP, Nucleocapsid, Protein Structure, Tertiary, RHABDO, Vesiculovirus, Viral Fusion Proteins, VIRO.

  • S. Bressanelli, « Kickstarting a viral RNA polymerase », Science, vol. 347, nᵒ 6223, p. 715-716, févr. 2015.

  • C. Giglione, S. Fieulaine, et T. Meinnel, « N-terminal protein modifications: Bringing back into play the ribosome », Biochimie, vol. 114, p. 134-146, 2015.
    Mots-clés : Amidohydrolases, Amino Acid Sequence, Animals, B3S, Co-translational modifications, DBG, Humans, IMAPP, Methionine aminopeptidase, Methionyl Aminopeptidases, Molecular Sequence Data, N-myristoyltransferase, N-terminal, N-α-acetyltransferase, Peptide deformylase, PROMTI, Protein Biosynthesis, Protein Processing, Post-Translational, Ribosomes.

  • 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.

  • D. Law-Hine, A. K. Sahoo, V. Bailleux, M. Zeghal, S. Prevost, P. K. Maiti, S. Bressanelli, D. Constantin, et G. Tresset, « Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates », The Journal of Physical Chemistry Letters, vol. 6, nᵒ 17, p. 3471-3476, sept. 2015.

  • T. Michon, J. Sturgis, et S. Bressanelli, « Ingénierie des protéines : construire en 3D avec des protéines », in Synthèse 2014, Micro et Nanotechnologies : Avancées, tendances et perspectives, Observatoire des Micro et NanoTechnologies., 2015, p. 40-42.

  • N. Scrima, J. Lepault, Y. Boulard, D. Pasdeloup, S. Bressanelli, et S. Roche, « Insights into herpesvirus tegument organization from structural analyses of the 970 central residues of HSV-1 UL36 protein », The Journal of Biological Chemistry, vol. 290, nᵒ 14, p. 8820-8833, avr. 2015.
    Résumé : The tegument of all herpesviruses contains a capsid-bound large protein that is essential for multiple viral processes, including capsid transport, decapsidation at the nuclear pore complex, particle assembly, and secondary envelopment, through mechanisms that are still incompletely understood. We report here a structural characterization of the central 970 residues of this protein for herpes simplex virus type 1 (HSV-1 UL36, 3164 residues). This large fragment is essentially a 34-nm-long monomeric fiber. The crystal structure of its C terminus shows an elongated domain-swapped dimer. Modeling and molecular dynamics simulations give a likely molecular organization for the monomeric form and extend our findings to alphaherpesvirinae. Hence, we propose that an essential feature of UL36 is the existence in its central region of a stalk capable of connecting capsid and membrane across the tegument and that the ability to switch between monomeric and dimeric forms may help UL36 fulfill its multiple functions.
    Mots-clés : Amino Acid Sequence, B3S, Cell Line, Transformed, Crystal Structure, Dimerization, herpesvirus, Herpesvirus 1, Human, HSV1, Humans, IMAPP, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Structural Biology, Tegument, ul36, Viral Proteins, VIRO, VIROEM, Virus Assembly, Virus Structure, vp1/2.

  • J. Stojko, S. Fieulaine, S. Petiot-Bécard, A. Van Dorsselaer, T. Meinnel, C. Giglione, et S. Cianférani, « Ion mobility coupled to native mass spectrometry as a relevant tool to investigate extremely small ligand-induced conformational changes », Analyst, vol. 140, nᵒ 21, p. 7234-7245, 2015.
    Mots-clés : Amidohydrolases, Anti-Bacterial Agents, Arabidopsis, B3S, Binding, Competitive, Buffers, Crystallography, X-Ray, DBG, IMAPP, Ions, Kinetics, Ligands, Mass Spectrometry, PROMTI, Protein Binding, Protein Conformation, Proteins.

  • C. Taveneau, K. Blondeau, et S. Bressanelli, « Definition and expression in E. coli of large fragments from the human lipid kinase phosphatidylinositol 4-kinase type III alpha, and purification of a 1100-residue N-terminal module », Protein Expression and Purification, vol. 114, p. 121-127, 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

  1. Tassali, N. ; Kotera, N. ; Boutin, C. ; Léonce, E. ; Boulard, Y. ; Rousseau, B. ; Dubost, E. ; Taran, F. ; Brotin, T. ; Dutasta, J.-P. ; Berthault, P. Smart Detection of Toxic Metal Ions, Pb2+ and Cd2+, Using a 129Xe NMR-Based Sensor. Anal. Chem. 2014, 86 (3), 1783–1788.
  2. Rieille, N. ; Bressanelli, S. ; Freire, C. C. ; Arcioni, S. ; Gern, L. ; Péter, O. ; Voordouw, M. J. Prevalence and Phylogenetic Analysis of Tick-Borne Encephalitis Virus (TBEV) in Field-Collected Ticks (Ixodes Ricinus) in Southern Switzerland. Parasit Vectors 2014, 7 (1), 443.
  3. Harak, C. ; Radujkovic, D. ; Taveneau, C. ; Reiss, S. ; Klein, R. ; Bressanelli, S. ; Lohmann, V. Mapping of Functional Domains of the Lipid Kinase Phosphatidylinositol 4-Kinase Type III Alpha Involved in Enzymatic Activity and Hepatitis C Virus Replication. J. Virol. 2014, 88 (17), 9909–9926.
  4. Gobeaux, F. ; Tarabout, C. ; Fay, N. ; Meriadec, C. ; Ligeti, M. ; Buisson, D.-A. ; Cintrat, J.-C. ; Artzner, F. ; Paternostre, M. Directing Peptide Crystallization through Curvature Control of Nanotubes. J. Pept. Sci. 2014, 20 (7), 508–516.
  5. Fieulaine, S. ; Desmadril, M. ; Meinnel, T. ; Giglione, C. Understanding the Highly Efficient Catalysis of Prokaryotic Peptide Deformylases by Shedding Light on the Determinants Specifying the Low Activity of the Human Counterpart. Acta Cryst. D 2014, 70 (Pt 2), 242–252.
  6. Duriez, M. ; Thouard, A. ; Bressanelli, S. ; Rossignol, J.-M. ; Sitterlin, D. Conserved Aromatic Residues of the Hepatitis B Virus Precore Propeptide Are Involved in a Switch between Distinct Dimeric Conformations and Essential in the Formation of Heterocapsids. Virology 2014, 462-463C, 273–282.
  7. Dubost, E. ; Dognon, J.-P. ; Rousseau, B. ; Milanole, G. ; Dugave, C. ; Boulard, Y. ; Léonce, E. ; Boutin, C. ; Berthault, P. Understanding a Host-Guest Model System through ¹²⁹Xe NMR Spectroscopic Experiments and Theoretical Studies. Angew. Chem. Int. Ed. Engl. 2014, 53 (37), 9837–9840.
  8. Caillet-Saguy, C. ; Lim, S. P. ; Shi, P.-Y. ; Lescar, J. ; Bressanelli, S. Polymerases of Hepatitis C Viruses and Flaviviruses : Structural and Mechanistic Insights and Drug Development. Antiviral Res. 2014, 105, 8–16.

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