Axe thématique " Immunité et Interactions Hôte-Pathogènes"
IBS – Salle 012
Innate immunity relies upon the ability of pattern recognition molecules to sense conserved molecular markers exposed on microbial surfaces, and to elicit effector mechanisms providing a first line of defense. Among these molecules are the ficolins, a family of proteins conserved through evolution from invertebrates to mammals, which can trigger the lectin pathway of complement. Human ficolins are soluble oligomeric proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. To decipher the molecular mechanisms underlying their sensing properties, the X-ray structures of the H-, L- and M-ficolin recognition domains, alone and in complex with various ligands, have been recently solved [1, 2]. As shown on Figure 1, these domains have three-lobed structures. The binding sites experimentally observed in the three ficolins will be described and compared, in relation to their sensing properties.
An outer binding site S1, homologous to the GlcNAc binding pocket of the invertebrate tachylectin 5A, is present in the human ficolins. It is more preserved in M-ficolin and shows structural modulations of its specificity in ficolins. Unexpectedly, the structure of this site can be disrupted in M-ficolin by a pH-dependent conformational switch [2]. Three additional sites, S2, S3, S4, were found in L-ficolin. The more extended β-D-glucan ligand, a marker of yeast surfaces, interacts with both S3 and S4 (Fig1B). These new S2 to S4 sites define together an unpredicted continuous recognition surface able to sense various acetylated and neutral carbohydrate markers in the context of extended polysaccharides, as found on microbial or apoptotic surfaces [1].
IBS Seminar Room
The first ABC (‘ATP-Binding Cassette’) transporter responsible for the resistance of cancer cells to the chimio-therapeutic treatments, known as a MDR (‘MutliDrug Resistance’) phenotype, was discovered more than 30 years ago. Since then, many ABC transporters have been identified in all living organisms and are essential to the transport or a wide range of molecules, from nutrients to toxic waste. Multidrug ABC transporters have now been identified in many pathogenic microorganisms where they confer resistance towards antibiotic, antifungus or antiparisitic medicines, broadening the threat that these transporters pose to human health. Our group has been involved in the study of two bacterial multidrug ABC transporters to understand how they work at the molecular level, and I will summarize our current view of their catalytic mechanism in the context of several recent 3-D structures obtained for related transporters.
IBS Seminar Room
– Abstract
Hosted by Wai Li Ling (IBS)
where?: Institut Jean Roget, Salle de Conférence du 5ème Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Partnership for Structural Biology
ILL Chadwick amphitheatre
Session 1, chair: Sean McSweeney (ESRF)
– 13h30 Matthew Bowler (ESRF): The mechanism of phosphoryl hydrolysis studied by 19F-NMR and
X-ray crystallography
– 13h50 Bruno Franzetti (IBS): Structures, mode of action and cellular role of the TET polypeptides destruction machines
– 14h10 Franck Tarendeau (EMBL): Influenza polymerase PB2
– 14h30 Wim Burmeister (UVHCI) : Structure of Epstein-Barr virus exonuclease
– 14h50 Phil Callow (ILL): Small Angle Neutron Scattering Studies of the Human Pyruvate Dehydrogenase Complex
15h10 – 15h40 Coffee break
Session 2, chair: Darren Hart (EMBL)
– 15h40 Ganesh Natrajan (ESRF): Structure of HobA: a new regulator of DNA replication in Helicobacter pylori
– 16h00 Dimitrios Skoufias (IBS): The A and B in spindle localization of auroras; a single amino acid makes the difference in centrosome versus inner centromere localization of aurora kinases
– 16h20 Juan Sanchez Weatherby (EMBL): Online crystal humidifier
– 16h40 Suman Lata (UVHCI): ESCRT-III nano-coils are disassembled by VPS4
– 17h00 Susana Teixeira (ILL): Neutron crystallography at the Deuteration Laboratory - a few examples
PSB seminar series, host: Winfried Weisenhorn
IBS seminar room
– IBS seminar Room
PhD Defense: Le passage sélectif d’ions et de métabolites à travers les membranes biologiques est essentiel à de nombreux processus cellulaires fondamentaux. Au niveau de la membrane interne de la mitochondrie, la communication cellulaire et les processus d’échanges sont principalement assurés par les transporteurs mitochondriaux. Ces protéines membranaires jouent un rôle clef dans les fonctions métaboliques des cellules eucaryotes et leur dysfonctionnement est à l’origine d’un certain nombre de maladies graves chez l’homme
Parmi les transporteurs mitochondriaux, deux familles ont été étudiées au cours de ce travail : les AACs (ADP/ATP Carriers) et les UCPs (UnCoupling Proteins). Deux systèmes de production hétérologue de ces transporteurs ont été mis en place : la synthèse in vitro et l’expression chez E.coli de protéines de fusion. Le premier a permis la production et la purification d’environ 0,6 mg de protéine par mL de réaction et le deuxième a été exploité afin de réaliser des caractérisations fonctionnelles des transporteurs ADP/ATP. Un test fonctionnel pour la protéine découplante a également été mis au point. Ce test, basé sur la mesure directe des courants électriques associés à l’activité de transport de l’UCP, à permis la caractérisation fonctionnelle de la protéine UCP1 native.
EMBL seminar room
Chadwick Amphitheatre, ILL
Chadwick Amphitheatre (ILL)
Biology can only exist by enclosing its contents, otherwise the contents would be washed away. Gram negative bacteria have two cell walls, an outer and an inner membrane. In addition to holding contents in and poisons out, the cell wall must allow passage of nutrients and waste products. The lecture will discuss an outer membrane protein, Wza which is responsible for the export of carbohydrate polymers. We have determined its structure to high resolution. The inner membrane of bacteria is subject to enormous osmotic pressure when bacteria move from one environment to another. Failure to release pressure will cause cell death. This tightly regulated system senses pressure. I will present a conformationally trapped structure that explains the basis of opening and closing by mechanosensitive channels. These channels are embedded in the inner membrane.
Hosted by Sean McSweeney (ESRF)
Chadwick Amphitheatre (ILL)
The VS ribozyme is the largest of the nucleolytic ribozymes, and the only member of the class for which there is no crystal structure. We have used small-angle X-ray solution scattering in an ab initio structural reconstruction of the complete VS ribozyme, and its components. The structure of the ribozyme is based around a core comprising a coaxial stack of three helices. Two further helices extend laterally, organized by two three-way helical junctions. An additional three-way junction formed by an auxiliary helix directs the substrate stem-loop, juxtaposing the cleavage site with the A730 internal loop of helix VI to create the active complex. We have identified a guanine (G638) and an adenine (A756) nucleobase as critical to the rate of central conversion of substrate to product and proposed a chemical mechanism for the ribozyme that involves general acid-base catalysis by the combined action of these nucleobases. This is supported by the pH dependence of the reaction rate for the natural substrate and those modified at position 638, and by the observation that A756 can be replaced with an imidazole nucleotide analog with preservation of activity. From recent experiments we conclude that A756 is the general acid in the cleavage reaction, leaving G638 as the base that removes the proton from the 2’-O in the cleavage reaction.
The proposed mechanism is closely similar to the probable mechanism of the hairpin ribozyme. The striking similarity of the two nucleolytic ribozymes has probably arisen by convergent evolution. Single-molecule experiments showing active hairpin ribozyme carrying out cleavage and ligation reactions will be shown.
Hosted by Trevor Forsyth (ILL)
CIBB seminar room
Based on the natural example of KATP channels in which a "receptor" intimately regulates an ion channel (Kir6.2), we physically coupled two different human GPCRs with Kir6.2, in order to create electrical probes for GPCR ligands, called ICCRs (Ion Channel Coupled Receptors). The electrical nature of the signal allows real-time measurements with high signal/noise ratio in in vivo and cell-free conditions, and it avoids the use of labelled ligands.
First ICCRs were made by fusion of the human muscarinic M2 receptor with Kir6.2. The M2-Kir6.2 fusion proteins were heterologously expressed in Xenopus oocytes and characterized electrophysiologically with the two-electrode voltage-clamp technique. Acetylcholine did not significantly activate the simple M2-Kir6.2 fusion protein in spite of the fact that the fused receptor is fully active as proved with co-expressed G-protein activated channels. After intensive protein engineering, we created optimized muscarinic ICCRs that were reversibly activated by acetylcholine, indicating a regulation of the Kir6.2 gating by the GPCR in active-state. We demonstrated i) that the current amplitude was correlated to agonist concentrations, ii) that optimized M2-Kir6.2 ICCRs were also inhibited by addition of antagonist, iii) that ACh-induced Kir6.2 activation was G-proteins independent as confirmed with co-expressed Pertussis toxin, and iv) that fusion proteins were functional in cell-free conditions as observed in patch-clamp recordings. Swapping the M2 receptor with the long D2 receptor, provided a dopaminergic ICCR specifically sensitive to its agonists and antagonists, but, unexpectedly, dopaminergic agonists inhibited D2-Kir6.2 currents.
In conclusion, we demonstrated that at least two GPCRs directly, reversibly and proportionally regulate the gating of a linked ion channel, by their ligand-induced conformational changes. Extended to others GPCRs, these ICCRs would be useful for complementary structure-function studies of GPCRs, and, in interface with microelectronics, they appear as promising tools for high throughput drug screenings and point-of-care in vitro diagnostics.
Moreau C. et al. (2008) Coupling ion channels to receptors for biomolecule sensing. Nature Nanotechnology. In press.
Hosted by Laurence Serre (ESRF)
CIBB seminar room
Hosted by Winfried Weissenhorn
EMBL seminar room
The combination of X-ray crystallography and rapid cryo-trapping methods have enabled the visualisation of catalytic intermediates in a variety of enzyme systems. However, the resolution of the X-ray experiment is not always sufficient to precisely place the structure on the reaction pathway. In addition, many trapped intermediates are X-ray sensitive and can decay during diffraction data collection, resulting in a final structure that may not be representative of the initial trapped species.
Complementary methods, such as single crystal spectroscopy, provide a means to precisely identify the cryo-trapped species as well as detect any X-ray induced changes during diffraction data collection.
I will present examples of the use of single crystal spectroscopy to both identify trapped intermediates as well as follow changes in redox state during X-ray exposure. I will also discuss new developments in the instrumentation available for single crystal spectroscopy at synchrotron sources.
Hosted by ILL College VIII
EMBL seminar Room
IBS Seminar Room
Since the binding of the human growth hormone (hGH) to a homodimeric hGH receptor (hGHR)
was shown, the mechanism of activation of hGHR has remained controversial. The model for
activation was originally proposed as a hormone-induced sequential dimerization of the receptor
subunits and has been supported by several in vitro and in vivo studies.
However, there has been increasing evidence that hGHR would in fact exist as a preformed dimer
on the surface of cells in the absence of a ligand. The binding of hGH onto hGHR extracellular
domain follows a two-step mechanism where hGH fi rst binds to a receptor subunit and then to the
second one. The association of the two dimerization domains between the two receptor subunits
is essential to signal transduction to the receptor intracellular domain through the membrane. If
the hGHR monomers dimerize because of hGH binding, the activation process basically consists
in bringing the subunits together. However, if the hGHR exists as a constitutive dimer on the
cell surface, its activation must be mediated by a hGH binding-induced conformational change.
Waters and co-workers proposed a mechanism which supports this model and involves a relative
rotation and translation of the subunits within the dimeric receptor (Nat. Struct. Mol. Biol. (2005)
12, 814-821). Here, I will present the fi rst atomistic model for hGHR activation using molecular
dynamics simulations. The simulations show that after removing hGH from its complex with a
dimeric hGHR, the receptor subunits exhibit a relaxation involving a relative rotation of the two
subunits. We also fi nd new interaction interfaces between the subunits in both the cytokine-bound
and unliganded hGHR states. The results from the simulations bring new perspectives on the
mechanism of transduction of the signal through the plasma membrane from the extracellular to
the intracellular domains of cytokine receptors related to hGHR.
Hosted by M. Field (IBS)
hosted by Christine Ebel
EMBL seminar Room
EMBL Seminar Room
ILL4 Seminar Room 125
see Abstract
CIBB Seminar Room
Förster Resonance Energy Transfer (FRET) allows measuring the distance between two spectrally distinct fluorophores, in the 20-100 Å range. When monitored at the single molecule level, smFRET is useful in resolving subpopulations, or observing conformational changes as a function of time within single macromolecular complexes in vitro. I will describe here the methodologies used to label proteins and nucleic acids with fluorescent dyes, and measure FRET accurately on the labelled complexes, freely diffusing in solution or immobilized on surfaces. I will focus on the study of complexes involved in prokaryotic transcription initiation and termination (helicases and polymerases). Finally, I will discuss how information gathered from smFRET experiments could be used to complement other high- or low-resolution methods in structural biology.
single-molecule biophysics at Montpellier
ILL Chadwick Amphitheatre
EMBL Seminar Room
IBS Seminar Room
EMBL Seminar room
Group A Streptococcus (GAS, S. pyogenes), the major causative agent of pharyngitis, impetigo, necrotizing fasciitis, rheumatic fever and Streptococcal toxic shock syndrome (STSS), is a life threatening pathogen. M protein, a major virulence factor of all pathogenic GAS located on the bacterial surface, modulates host invasion as well as evasion from host defense. This dimeric coiled-coil protein contains a hypervariable domain defining more than 120 different serotypes. Among them, M1 is the leading cause of invasive infections, making it an important serotype to study. In patients with STSS, human fibrinogen (Fg), the glycoprotein precursor of fibrin, may associate with M1 following infection. The molecular pathogenesis of STSS is initiated by the binding of the soluble form of M1 to Fg, triggering vascular leakage through release of intermediate Heparin-Binding Proteins (Herwald et al, 2004).
Structural and mutational analyses of an M1 fragment carried out in our laboratory show that non-canonical residues in the Fg-binding region disrupt the coiled-coil packing, leading to dissociation of the helices in this region, which impairs Fg binding (McNamara et al, 2008). The structural characterization of the complex between M1 and a Fg fragment would lead us to a better understanding of the neutrophils activation and a better development of new vaccines.
Herwald H, Cramer H, Mörgelin M, Russell W, Sollenberg U, Norrby-Teglund A, Flodgaard H, Lindbom L, Björck L. Cell. (2004) 116:367-79.
CIBB Seminar Room
Global warming and the progressive depletion of fossil fuels has led the financing agencies of developed countries to promote “clean energy vector†research. Consequently, there has been a renewed interest in this field. One possibility is the generation of molecular hydrogen from solar energy. There are basically two options to generate H2 from the Sun: photovoltaic cells and micro-organisms. Anaerobic microbes can generate hydrogen through fermentation of biomass and photosynthesis. In both cases, they use oxygen-sensitive enzymes called hydrogenases that catalyze the following reversible reaction: 2H+ + 2e- = H2. Over the last decade, we have solved the three-dimensional structures of representatives of the two classes of hydrogenases present in sulfate-reducing bacteria. These studies have revealed complex buried organometallic active sites, connected to the molecular surface by hydrophobic channels. Recently, site-directed mutagenesis based on hydrogenase structures has been used to try to obtain oxygen-resistant enzymes in order to couple hydrogen production to photosynthesis. An alternative approach has been the search for naturally oxygen-resistant enzymes present in aerophilic micro-organisms.
One effective way of probing hydrogenases for oxygen resistant is electro-chemistry. The enzyme is adsorbed onto a graphite electrode and current production in the presence of H2 is studied as a function of changing potentials. The effect of other gases, such as O2 and CO can then be studied. This approach also leads to the use of hydrogenase in bio-fuel cells.
During my talk I will address these different aspects of hydrogenase research.
IBS seminar Room
IBS seminar room
CIBB seminar Room
The myelin sheath, a multilayered membrane structure wrapped around the
axons, allows for the rapid transmission of nerve impulses in vertebrates. Several nervous system diseases are linked to deficiencies in myelin formation and structure. Biochemically, the myelin membrane is unique, and it contains several proteins not found in other tissues. However, relatively little is known about the structural properties of myelin-specific proteins and their complexes with ligands. We aim at obtaining a better understanding of the myelin sheath via detailed structural and biochemical studies on its protein components.
IBS seminar Room
hosted by C. Ebel (LBM/IBS)
CIBB seminar Room
organised by ILL College-8
ESRF Auditorium, Central Building
Coffee will be served at 3.30 pm in the entrance hall on the ground floor of the Central Building
hosted by Sine Larsen (ESRF)
IBS seminar Room
Influenza virus is a serious disease that affects and kills many people every winter. There exist only a few drugs against the virus and drug resistance is a significant problem. In order to determine new drug targets, research into the structure and function of the viral RNA-dependent RNA polymerase was necessary. The polymerase consists of 3 subunits; the real polymerase subunit PB1, the PB2 subunit that is involved in “Cap-snatching†necessary for the production of viral mRNAs and the PA subunit for which no function was known.
Until 2007 no structural information on the polymerase was known apart from a low-resolution EM 3-D reconstruction. In collaboration with the groups of Darren Hart and Stephen Cusack, and also with the NMR group of IBS, a major effort has now led to the structures of 3 domains of PB2 and one domain of PA. The structure of another domain of PA was determined by Chinese and Japanese groups. The structures and the functions of all domains will be discussed. The structures have also shed light on some of the mutations that occur when avian influenza virus adapts to humans.
РThe cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. (2009) Nature Dias A, Bouvier D, Cr̩pin T, McCarthy AA, Hart DJ, Baudin F, Cusack S, Ruigrok RW.
– Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. (2008) PLoS Pathog. Tarendeau F, Crepin T, Guilligay D, Ruigrok RW, Cusack S, Hart DJ.
– The structural basis for cap binding by influenza virus polymerase subunit PB2. (2008) Nat Struct Mol Biol. Guilligay D, Tarendeau F, Resa-Infante P, Coloma R, Crepin T, Sehr P, Lewis J, Ruigrok RW, Ortin J, Hart DJ, Cusack S.
– Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit. (2007) Nat Struct Mol Biol. Tarendeau F, Boudet J, Guilligay D, Mas PJ, Bougault CM, Boulo S, Baudin F, Ruigrok RW, Daigle N, Ellenberg J, Cusack S, Simorre JP, Hart DJ.
Room 337, ESRF Central Building
Photosystem II (PSII) is a membrane protein complex involved in the process of oxygenic photosynthesis. PSII has a double function: the oxidation of the water molecule delivering molecular oxygen and the harvesting of light converting the photonic energy trough the equivalent excitonic form into chemical energy. In green organisms the coordination of these two PSII functions and the functional integration of the PSII activity with the other thylakoid membrane protein complexes results in the ability of energy conversion and chemical energy accumulation delivering oxygen as a secondary product. Currently several high resolution structures of PSII from cyanobacteria are available but none from green algae and higher plants has been described. Several lines of evidence suggest not only similarities but also important differences between prokaryotic and eukaryotic PSII especially regarding the processes of photo-protection and of excitonic energy transfer. Furthermore the process that, via the Oxygen Evolving Complex, is responsible for the splitting of the water molecule delivering oxygen, is in general still not completely understood.
In this short speech I will report a new approach for the purification, characterization and crystallization of PSII from a transplastomic strain on Nicotiana tabacum.
IBS seminar room
Nous développons un nouveau projet depuis début 2006 au PSB et à l’IBS : Nous nous intéressons tout particulièrement au processus de phagocytose des cellules apoptotiques effectué par un certain nombre de cellules de l’immunité et aux voies de signalisation qui mènent aux modifications dynamiques du cytosquelette d’actine au cours de ce processus.
Les cellules apoptotiques créent de très nombreux déchets cellulaires (plusieurs milliards par jour) pouvant provoquer des réactions inflammatoires. Il est donc essentiel que ces corps apoptotiques soient internalisés par les cellules phagocytaires de l’organisme et déclenchent en parallèle des mécanismes anti-inflammatoires. Les cellules apoptotiques présentent à leur surface des structures moléculaires particulières qui sont reconnues par les récepteurs du phagocyte, soit directement, soit par l’intermédiaire de molécules aidant à la reconnaissance (Complément, anticorps, …). Ces interactions, déjà largement étudié à l’IBS (LEM – équipe de G. Arlaud) sont la clef du déclenchement des réactions anti-inflammatoires et du remodelage du cytosquelette d’actine conduisant à l’internalisation. Toutefois, les molécules et les bases moléculaires et structurales impliquées dans les processus de signalisation sont très mal connues à l’heure actuelle.
Récemment, un tandem de protéines multi-domaine, le couple ELMO/DOCK, a été identifié comme un effecteur clef des voies de signalisation initiant l’ingestion des cellules apoptotiques par les phagocytes. Ce complexe est un nouveau type de Facteur d’Echange de Guanine (GEF) capable d’activer la GTPase Rac1 qui conduit au remodelage du cytosquelette d’Actine.
A l’heure actuelle, les quelques données disponibles sur le fonctionnement de ce complexe et de ses partenaire au niveau cellulaire et structural sont très élusives.
Depuis 3 ans, nous avons entrepris l’étude par la combinaison d’approches cellulaires et fonctionnelles, de biologie moléculaire et de biochimie ainsi que différentes approches de biologie structurale. Lors de mon exposé orienté comme un rapport d’avancement, j’aborderai les différentes techniques et difficultés que nous rencontrons ainsi que les différentes pistes de recherche sur lesquelles nous nous engageons
IBS seminar Room
The talk will describe the role of protein crystallography in the pharmaceutical drug discovery process. I will cover:
– molecular basis of drug action
– overview of the pharmaceutical drug discovery & development process
– goals for structural research in a pharmaceutical project
– structure-based hit validation
– optimization of molecular interactions
– the structure-based drug design cycle
– fragment based screening
EMBL seminar Room
EMBL seminar Room
– 9:30 to 9:35
Methods for simultaneous X-ray diffraction studies on mutliple single crystals and absorbed dose calculations for macromolecular crystals -
by Karthik Paithankar
– 09:35 to 10:10
Solving a novel protein structure by sulphur SAD
by Cristofer Enroth
– 10:30 to 11:05
Getting RIPped with Radiation Damage
by Max Nanao
– 11:05 to 11:40
Title forthcoming
by G. Natrajan
EMBL seminar Room
IBS seminar Room
IBS seminar Room
– CIBB seminar room
Lipid bilayers, which provide valuable model systems for biomembranes, display a variety of polymorphic phases, depending on their molecular structure and environmental conditions, such as pH, ionic strength, temperature and pressure. By using calorimetric, spectroscopic and diffraction techniques, the temperature and pressure dependent structure and phase behavior of lipid systems, differing in chain configuration and headgroup structure has been studied. Moreover, neutron small-angle scattering and two-photon excited fluorescence microscopy have been used to study the lateral organization of phase-separated lipid membranes and raft mixtures as well as the influence of peptide and protein incorporation on membrane structure and dynamics, also under high pressure conditions. Furthermore, we discuss pressure as a kinetic variable. Applying the pressure-jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of various lipid mesophase phase transformations was investigated, including studies of membrane fusion processes. The technique has also been applied for studying polymer phase transitions and protein folding reactions. We present data on the pressure-induced un/refolding of proteins using small-angle scattering and Fourier-transform infrared spectroscopy, which monitor changes in the tertiary and secondary structural properties of the proteins upon pressurization or depressurization. A thermodynamic approach is introduced for determining the stability of proteins as a function of both temperature and pressure and express it as a three-dimensional free energy surface. By combining small-angle scattering with liquid state theoretical approaches, also the effects of molecular crowding and pressure on the intermolecular interaction potential and solvational properties of proteins has been investigated. Finally, recent advances in using pressure for studying misfolding and aggregation (amyloidogenesis) of proteins will be discussed.
– salle de conference de l’IAB
– EMBL Seminar Room
EMBL Seminar Room
– External visitors may ask for a site access to Karine Sultan (sultan@ill.fr).
CIBB seminar room
The formulator machine has been specifically designed to speed up the production of crystallisation refinement screens.
This machine will be available at the CIBB next Tuesday and Wednesday.
If you are interested in testing it yourself please contact Jose A Marquez (EMBL)
ILL Chadwick Amphitheatre
IBS Seminar Room
CIBB Seminar room
CIBB Seminar Room
Institut Jean Roget (Grenoble)
salle de conference, 5ème ét.,
Domaine de la Merci,
La Tronche
Contact: C.Bisanz : 04.76.63.74.74
ESRF Auditorium
Since the discovery of the green fluorescent protein (GFP) in 1962, many developments allowed improving the use of this naturally light-emitting protein as a powerful tool for tracking proteins or organelles of interest within living cells and organisms. At the beginning of the 21st century, the discovery of photoactivatable fluorescent proteins (PAFPs), notably from Anthozoan species, triggered a revolution in the field of FP technology. Some PAFPs are capable of being irreversibly photoconverted from a green- to a red-emitting form while other ones can be reversibly switched on and off, depending on specific excitation wavelengths. These proteins are being extensively used in optical microscopy techniques, particularly in “nanoscopy†, which provides optical resolution 10 fold beyond the theoretical Abbe limit. In order to further develop these techniques, notably in term of time-resolution, the need to obtain brighter fluorescent probes that photoconvert or photoswitch efficiently is crucial. At the same time, fluorescent highlighters generally need to be monomeric and photostable. In order to better understand the mechanisms of phototransformations in PAFPs, three members of the family have been studied: EosFP, Dendra2 and IrisFP. The phenomena of green-to-red photoconversion, reversible photoswitching and non-reversible photobleaching have been studied by a combination of X-ray crystallography and microspectrophotometry using the Cryobench laboratory of the ESRF/IBS. Together, the results have allowed us to propose a mechanism for the photoconversion of EosFP and Dendra2 and to discover and characterize IrisFP, the first PAFP combining both properties of photoconversion and photoswitching. The structural modifications of the chromophore associated with an X-ray induced radical state, likely to be involved in the photobleaching pathway of PAFPs, were also characterized.
Institut Albert Bonniot
CIBB Seminar Room
L-Asparaginases hydrolyze L-asparagine to L-aspartate and ammonia. However, due to posttranslational modifications of asparagine (glycosylation, isomerization to beta-aspartyl residues), specialized enzymes are required for the hydrolysis of the beta-amide bond in the general scheme of asparagine metabolism. In E. coli, there are two classic L-asparaginases. The homotetrameric periplasmic enzyme (EcAII), but not the homodimeric EcAI found in the cytoplasm, is a potent antileukemic agent. In plants, L-asparaginases are essential for nitrogen circulation. There are two types of plant asparaginases, with or without potassium dependence. E. coli expresses a protein (EcAIII) with intriguing sequence similarity to the plant enzymes. It is structurally unrelated to the classic bacterial enzymes but belongs to the family of N-terminal nucleophile (Ntn) hydrolases. We have shown that EcAIII and its yellow lupine homolog (LlA) are more active as isoaspartyl aminopeptidases. This dual activity is important in seeds where efficient supply of nitrogen is necessary during the synthesis of storage proteins and for the removal of toxic beta-aspartyl protein aberrations. The crystal structures of LlA and EcAIII show (alpha/beta)2 heterotetramers composed of alpha and beta subunits generated on autoproteolytic activation, which liberates a Thr nucleophile at the N-terminus of subunit beta. A sodium-binding loop with conserved main-chain coordination is necessary for proper positioning of all components of the active site. Despite sequence homology and structural similarity to human and bacterial aspartylglucosaminidases, LlA and EcAIII are unable to hydrolyze glycosylated asparagine. Unexpectedly, the structure of the plant-type enzymes bears resemblance to threonine aspartase (taspase), which hydrolyzes the alpha-peptide bonds of two Asp-Gly peptides of MLL, a protein implicated in some human leukemias. There are several unclear aspects of the catalytic mechanism of Ntn-hydrolases in general and plant-type L-asparaginases in particular. They are especially puzzling with respect to the autoproteolytic activation event, in which the same catalytic Thr residue is supposed to carry out the reaction before the active site is actually formed as a result of this reaction. We have generated and crystallized an inactive Thr -> Ala mutant of EcAIII which is unable to cleave itself and remains in the single-chain precursor form. The mutant is also not cleaved in the presence of catalytic amounts of active EcAIII, demonstrating the cis character of the autoproteolytic activation. Comparisons of the crystal structures of the mutant protein and the active enzyme (i) demonstrate the spatial relation and stereochemical requirements of the two catalytic processes, (ii) reveal a dual role of the sodium-coordinating loop, and (iii) indicate two different oxyanion hole areas. There are also interesting implications regarding the identification of a general-base residue supposed to activate the Thr nucleophile.
hosted By Dominique Housset (IBS)
CIBB seminar room
Recent progress in nuclear magnetic resonance (NMR) spectroscopy and advancements in specific isotope labelling have enabled the high resolution structure determination of biomolecular complexes as well as the studies of challenging interactions in high molecular weight assemblies (up to 1 Mda). These latest developments made at PSB will be presented and illustrated with application to HIV and HCV RNA complexes, large biological machineries involved in microRNAs processing and protein quality control.
IBS seminar room
Light can have a manyfold of effects on proteins, ranging from photodamage to serving as (co)substrate for catalysis. Another aspect is the use of light for investigation of functional processes in proteins by a host of optical spectroscopy methods.
Both aspects can be exemplified by our work on DNA photolyase, a light-dependent DNA repair enzyme. The enzyme contains an FAD cofactor that, depending on its redox state, upon optical excitation donates or accepts an electron.
Both reactions trigger a cascade of further events on the picosecond to millisecond timescales. Existing time resolved spectroscopy setups allowed to disentangle some of these (e.g., intraprotein electron transfer chain or substrate handling). Others (photorepair or deprotonation) fall in the time window of few nanoseconds that is difficult to address by both "classical" and pump/probe transient absorption techniques and call for a dedicated effort to be tracked down.
The talk will concentrate on non-standard ways of using light to gain access to photolyase’s functional features.
hosted by D. Bourgeois and M. Weik (IBS)
IBS Seminar Room
IBS seminar Room
IBS seminar room
hosted by Martin Blackledge (IBS)
IBS Seminar Room
hosted by Nicole Thielens (IBS)
Amphithéâtre 15 de l’école PHELMA – Polygone
more information on the talk and speaker
EMBL seminar room
hosted by Andrew Mc Carthy (EMBL)
IBS seminar room
La plupart des protéines sont (faiblement) fluorescentes grâce aux tryptophanes qui tiennent lieu de chromophores, et dont les propriétés de fluorescence sont contrôlées par les interactions avec l’environnement protéique. Ces propriétés de fluorescence sont exaltées dans un petit nombre de protéines qui incorporent des chromophores exogènes (chlorophylle, hème) ou endogènes (acides aminés cyclisés). Dans cet exposé, nous montrerons comment l’étude structurale d’une protéine par cristallographie aux rayons X couplée à des méthodes complémentaires (spectroscopie de fluorescence, simulation par dynamique moléculaire) permet de progresser dans la compréhension du mécanisme de fluorescence. En particulier, l’antenne collectrice de lumière LHC-II de plante est une protéine photosynthétique localisée dans les membranes des thylakoïdes, rendue fluorescente par ses molécules de chlorophylle. Nous avons cherché à comprendre dans quelle mesure le contrôle des propriétés de fluorescence était déterminant pour l’efficacité de l’activité photosynthétique. D’autre part, les protéines fluorescentes cyan dérivées de la GFP sont très utilisées en biologie cellulaire pour la mesure d’interactions protéines-protéines par FRET. Nous avons mis en évidence comment les interactions hydrophobes du chromophore avec son environnement contrôlent le niveau de fluorescence de ces protéines. Enfin, en nous basant sur la structure cristallographique d’un phytochrome de D. radiodurans, nous avons fait évoluer un fragment de la protéine par mutagenèse dirigée pour détourner ses propriétés de transduction de signal en propriétés de fluorescence dans l’infrarouge, et obtenir ainsi un marqueur codé génétiquement utile pour l’imagerie du corps entier.
IBS seminar Room
Cdc25 phosphatases are key regulators of cell-cycle check-points. This talk will first present computer simulations for the dephosphorylation reaction of Cdc25B with its natural substrate, the Cdk2-pTpY/CycA protein complex. Then, the talk will present small-molecule binding to an ensemble of Cdc25B conformations, generated with a coarse-grained model of the protein backbone. Formerly unknown binding modes that may uncover the mechanism of inhibition are proposed. Structural characteristics previously treated as artifacts in analysis of x-ray crystallography data are suggested as features of the thermal ensemble.
Hosted by Martin Field (IBS/LDM)
IBS seminar room
The first ABC (‘ATP-Binding Cassette’) transporter responsible for the resistance of cancer cells to the chimio-therapeutic treatments, known as a MDR (‘MutliDrug Resistance’) phenotype, was discovered more than 30 years ago. Since then, many ABC transporters have been identified in all living organisms and are essential to the transport or a wide range of molecules, from nutrients to toxic waste. Multidrug ABC transporters have now been identified in many pathogenic microorganisms where they confer resistance towards antibiotic, antifungus or antiparisitic medicines, broadening the threat that these transporters pose to human health. Our group has been involved in the study of two bacterial multidrug ABC transporters to understand how they work at the molecular level, and I will summarize our current view of their catalytic mechanism in the context of several recent 3-D structures obtained for related transporters.
IBS seminar room
Inappropriate cell recruitment is a hallmark of all autoimmune, allergic and inflammatory diseases. The prevention of inflammation by interfering with cellular recruitment by neutralization of cytokines and adhesion molecules has proven to be successful in the clinic. Chemokines are important potential targets due to the central role they play in the cell recruitment process. Chemokines are unique amongst cytokines as they signal through 7 transmembrane (7TM) receptors, allowing the identification of small molecule inhibitors through high throughput screening. The object of this presentation is to discuss the validity and feasibility of targeting several points of therapeutic intervention offered by the chemokine system, and to assess the state of play within the field to date. Although some trials disappointingly did not achieve their goal, nature has devised strategies to inhibit the chemokine system highlighting the relevancy of these targets.
Blood sucking parasites such as ticks feed for extended periods on their hosts without eliciting an immune response. They secrete a battery of anti-coagulant, anti-pain and anti-inflammatory molecules in their saliva in order to remain undetected by the host. We have confirmed the presence of anti-chemokine activity in tick saliva and have cloned three distinct chemokine binding proteins from a cDNA library constructed from tick salivary glands, which we have named Evasins. As opposed to viral chemokine binding proteins which have very broad specificities, the Evasins are highly selective. We have characterized them both in vitro and in vivo, where they show potent anti-inflammatory activities. We have solved the structure of two of these proteins which display novel folds with no homologues in the PDB database. These surprisingly small proteins, smaller than the single chain nanobodies or camelids, provide novel scaffolds for anti-inflammatory binding proteins.
Hosted by H. Lortat-Jacob (IBS)
EMBL Seminar Room
Secretory and membrane proteins are transported through a conserved
heterotrimeric membrane-bound protein complex, the Sec61 or SecY complex.
In bacteria, the SecY complex provides a membrane channel that opens in
response to the binding of preprotein substrate and the SecA ATPase. The
questions addressed in my laboratory concern the stoichiometry of the
complex with the motor protein, the ionic (im)permeability of the channel
during preprotein transport, and the control of the SecY biogenesis by the
protein Syd. We reconstitute these interactions using Nanodiscs,
water-soluble particles that mimic a small patch patch of membrane lipid
bilayer.
Hosted By Christiane Schaffitzel (EMBL/UVHCI)
IBS Seminar Room
Protein translocation across membranes is a pathway of utmost biological importance. The canonical pathway of protein translocation and membrane insertion is facilitated by SecYEG or Sec61 in bacteria or eukaryotes, respectively. Besides this canonical family of protein-conducting channels, the YidC/Oxa1/Alb3 family is involved in the co-translational membrane insertion of specific proteins in prokaryotes, mitochondria and chloroplasts.
We solved the structures of SecYEG (1) and of YidC (2) bound to ribosome-nascent peptide complexes by cryo-EM. Importantly, both SecYEG and YidC form dimers on the ribosome. Although both families are not homologues, they share a common overall architecture. In bacteria, SecYEG and YidC are part of the holo-translocon which is responsible for insertion, folding and assembly of membrane proteins. Recently, we succeeded for the first time to express and purify this six membered membrane protein complex (3).
References:
1.Mitra, K., Schaffitzel, C., et al. (2005) Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438, 318-324.
2.Kohler, R. et al. (2009) YidC and Oxa1 form dimeric insertion pores on the translating ribosome. Mol. Cell 34, 344-353.
3.Bieniossek, C. et al. (2009) Automated unrestricted multigene recombineering for multiprotein complex production. Nat. Methods 6, 447-450.
EMBL Seminar Room
ILL Chadwick Amphitheatre.
CIBB Seminar room.
DNA denaturation is known to occur locally (fluctuational “bubble†-like opening of a
cluster of base pairs) or globally (complete separation of the two strands, “melting†).
Both processes can be described in terms of the Peyrard-Bishop-Dauxois (PBD)
model, which is known to provide a valid mesoscopic description of long DNA chains
in the ordered phase in terms of the nonlinear lattice dynamics of a single
(transverse) degree of freedom per base-pair.
The statistical properties of denaturation bubbles have recently been analyzed1 and
shown to reflect the existence of an exact thermodynamic phase transition. A similar
analysis can be performed for (typically larger) clusters of bound base pairs; the latter
give rise to coherent scattering from neutrons.
I will present some data recently obtained2 by neutron diffraction from deuterated
DNA fibers. The data exhibit a very sharp thermodynamic transition, observed for the
first time in fiber samples. I will argue that the basic features of the data can be
understood in terms of the PBD model.
ESRF Common Building, COM 106
for more information contact claudine.romero
Institut Albert Bonniot, Salle de Conférences
for more information, contac Marie-Odile Fauvarque
ESRF Central Building, room 248A
for more information, contact Isabelle Combe
Amphi. 15 PHELMA/Minatech
for more information, contact stephanie.monfront
IBS seminar Room
IBS Seminar Room
Living cells exhibit exceptional dynamical properties, caused by the presence of ATP-driven processes. We focus on two aspects of cell-generated stochasticity: the sub-cellular motion of tracer particles, and cell migration. The intracellular transport of cargos proceeds by successive phases of diffusion and active movement along microtubules by the means of dynein and kinesin motors. In living cell microrheology studies, the tracking of single particles is used for mapping such a cytoplasmic transport. We developed an automated and reliable time-resolved algorithm identifying the motility state signatures of colloidal probes engulfed by Dictyostelium discoideum (Dd) cells. It is based on the analysis of the local MSD and directional persistence of the tracer path, and is able to separate the active and passive motion of particles in cells. We analyze the particle motion in terms of a two-state model: this yields the distribution of active and passive state durations as well as the distribution of the state parameters, i.e. the velocity during active phases and the diffusion coefficient of the passive motion. The distribution of active life times is found to decay exponentially with a characteristic time T = 0.65 s. The velocity distribution of active events exhibits several peaks, revealing the signature of a finite number of molecular motors working collectively. In contrast, after depolymerization of the microtubule network, the analyzed paths exhibit no significant active event, proving that active states are due to tracer transport along the microtubules exclusively. On the other hand, migration can be observed on the whole cell level, and the characteristics of cellular motion as a function of the environment can be retrieved. We use microstructured surfaces made of a silicon elastomer (PDMS) as a control substrate to study the influence of the topography on Dd motility. Cell shape, velocity and migration-mode are significantly modified by the presence of micron-scale structures.
hosted by Dominique Bourgeois (IBS)
EMBL Seminar Room
hosted by Jose A Marquez (EMBL/UVHCI)
ILL Chadwick Amphitheatre
Similar to proteins, most membrane lipids are transported by carriers (vesicles or tubules) with typical 50-100nm diameters that bud off from a donor membrane. During budding, sorting occurs: some lipids and proteins are selectively incorporated into these transport intermediates. It has been proposed that constituents can be dynamically sorted due to membrane curving during coat formation. In order to test this hypothesis, we have pulled membrane nanotubes from Giant Vesicles (GUV) with a controlled diameter (15-500 nm). We will show that curvature-induced lipid sorting only occurs if the membrane is close to a demixing point. In addition, for these compositions, lipid sorting is further amplified when even a low fraction of lipids is clustered upon cholera toxin binding suggesting that lipid-clustering proteins may play an important role in curvature-induced sorting in biological membranes
Another aspect of the role of curvature in membrane trafficking can be studied with these nanotubes. Dynamin is a protein, which assembles in helical structures around the neck of vesicles during budding and induces fission upon GTP hydrolysis. We will show that dynamin assembly can occur only when the neck diameter is below a threshold value. This curvature-dependent polymerization mechanism guaranties a correct timing for carrier budding.
– Speaker invited by Nicolas Martinelli (PhD Student, UVHCI)
CIBB seminar room
– Mimivirus, a virus infecting amoebae of the acanthamoeba genus, is the prototype member of the Mimiviridae, the latest addition to the family of the nucleocytoplasmic large DNA viruses, already including the Poxviridae, the Iridoviridae, the Asfarviridae, and the Phycodnaviridae. Because of the size of its particle-a fiber-covered icosahedral protein capsid 0.75 microm in diameter-Mimivirus was initially mistaken for a parasitic bacterium. Its 1.2-Mb genome sequence encodes more than 900 proteins, many of them associated with functions never before encountered in a virus, such as four aminoacyl-tRNA synthetases. These findings revived the debate about the origin of DNA viruses and their possible role in the emergence of the eukaryotic nucleus. The recent isolation of a new type of satellite virus, called a virophage, associated with a second strain of Mimivirus, confirmed its unique position within the virus world. Post genomic studies are now in progress slowly shedding some light on the physiology of the most complex virus isolated to date.
Hosted By Laurence Serre
CIBB seminar Room
Bacteria which form part of our normal microbial flora have evolved a number of
protective measures which ensure their survival against attack by our own antimicrobial
defenses. One such non-specific defense against infection is the presence within mucosa
and skin surfaces of antimicrobial peptides (AMPs). These peptides have generated a
huge amount of interest recently as potential candidates for novel antimicrobial
therapeutics. However, it is thought that a number of bacteria are able to resist the
activity of AMPs through modification their membrane lipids, although the precise
mechanisms by which such resistance is achieved have yet to be elucidated. This talk will
outline the how use of biophysical techniques, including neutron scattering, can help to
shed light upon the role played by modified membrane lipids in bacterial resistance to
AMPs.
EMBL seminar room
IBS Seminar Room
– In spite the robustness and perfection of their mechanism of action, proteins posses a remarkable ability to rapidly change and adopt new functions. I will describe experimental work aimed at reproducing the evolution of new proteins in the laboratory, and unraveling their traits of evolvability. Specifically, I will describe how the functional promiscuity of proteins, their conformational plasticity, and their modularity of fold, accelerate their rate of evolution. I will address the issue of neutral (or actually, seemingly neutral) mutations, and neutral networks, as facilitators of protein evolution. Finally, I will address mechanisms for buffering and compensating the deleterious effects of mutations, including compensatory stabilizing mutations and chaperones, that can greatly accelerate the rate of protein evolution
Hosted by Martin Weik (IBS)
Auditorium - ESRF Central Building
J. Murray Gibson, Director of the Advanced Photon Source (APS), will visit the ESRF and give a talk at 16.00 on “The Renewal of the APS, and US activities for Future Light Source developments†.
– Coffee and tea will be served as of 15.30 hours.
– Advance registration is required by sending an e-mail to Chantal Argoud (argoud@esrf.fr).
– If the number of registered participants exceeds 30 persons, the seminar will be moved into the Auditorium.
CTRM Control Room
– Abstract and information
EMBL Seminar Room
– Positive-strand RNA viruses, a large group including human pathogens
such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of
infected host cells. Their replication complexes are commonly
associated with modified host cell membranes. Membrane structures
supporting viral RNA synthesis range from distinct spherular membrane
invaginations to more elaborate webs of packed membranes and vesicles.
Generally, their ultrastructure, morphogenesis, and exact role in viral
replication remain to be defined. Poorly characterized double-membrane
vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis.
We have now applied electron tomography of cryofixed infected cells for
the three-dimensional imaging of coronavirus-induced membrane
alterations at high resolution. Our analysis defines a unique
reticulovesicular network of modified endoplasmic reticulum that
integrates convoluted membranes, numerous interconnected DMVs (diameter
200-300 nm), and "vesicle packets" apparently arising from DMV merger.
The convoluted membranes were most abundantly immunolabeled for viral
replicase subunits. However, double-stranded RNA, presumably revealing
the site of viral RNA synthesis, mainly localized to the DMV interior.
Since we could not discern a connection between DMV interior and
cytosol, our analysis raises several questions about the mechanism of
DMV formation and the actual site of SARS-CoV RNA synthesis. Our data
document the extensive virus-induced reorganization of host cell
membranes into a network that is used to organize viral replication and
possibly hide replicating RNA from antiviral defense mechanisms.
Together with biochemical studies of the viral enzyme complex, our
ultrastructural description of this "replication network" will aid to
further dissect the early stages of the coronavirus life cycle and its
virus-host interactions.
Hosted by Christiane Schaffitzel (EMBL)
ILL Chadwick Amphitheatre
Hosted By Daniel Panne (EMBL/UVHCI)
ESRF Auditorium
Solid-State NMR is a well-established technique for determining structural and dynamic features in molecular systems of modest size. Recently, great progress has been made in the development of methods for NMR applied to the study of solid proteins. This has led to the first complete structure determinations, to studies of dynamics, and to studies of a range of biophysical properties including hydration or ligand binding. We will describe the state of the art in this domain, covering diamagnetic and paramagnetic micro-crystalline proteins, fibrils, and notably recent work on membrane proteins by solid-state NMR.
more information on Lyndon Emsley and on the Centre de Resonance Magnetique Nucleaire
for an entrance badge, please contact in advance Mary-Jane Villot
hosted by Jose A Marquez (EMBL/UVHCI)
CIBB Seminar Room
– Branched polymers encompass several classes of different topology. The present consideration is confined to:
1.
Randomly branched structures of covalently bound repeat units and reversibly linked unimers.
2.
Hyperbranched structures on the basis of amylopectin, the branched component of starch, and their fragments.
3.
More complex structures based on chain rigidity, mainly from protein filamens.
Randomly branched materials are commonly taken as well understood by the Stockmayer-Flory and percolation theories. Surprisingly a significant influence on the angular dependence of the scattered light was found from excluded volume interaction among segments. Comparison was made with randomly crosslinked 3- arm star molecules of materials which were connected via covalent bonds and with those linked via physical bonds. No gelation could be obtained with physically linked structures in contrast to covalently bound samples where gelation took place as expected.
Most organic syntheses of hyperbranched samples gave too small particles for a comprehensive analysis via light scattering . Large hyperbranched structures are obtained by the combination of two specific enzymes in starch acting on chain growth and branching respctively. Glycogen and amylopectin aroused special interest. The light scattering properties of amylopectin and fragments of it are discussed at detail. Compared to theoretical prediction a much lower branching density was observed than predicted. The deviations from theory arise from branching heterogeneity. An unexpected hyperbranched supramolecular structure was obtained with a starch fragment which contained an aliphatic amine chain attached to the reducing end group (focal endgroup).
Branching and network formation is frequent with filaments from polysaccharides and proteins. Examples will be shown, and the reason for branching and network formation will be discussed. The theoretical model resembles a hyerbranched structure where linear AB-units are intercalated between two hyper-branching AB2- units which reduces the branching density. Valuable information is expected from SANS measurements in connection to theoretical approaches.
IBS Seminar Room
– Abstract
IBS Seminar Room
IBS Seminar Room
Hosted by H.Lortat-Jacob (IBS)
CIBB Seminar Room
ILL Chadwick Amphitheatre
ESRF Auditorium
Coffee will be served at 10:00 am in the entrance hall of the ESRF.
Hosted by O. Konovalov (ESRF)
IBS Seminar Room
EMBL Seminar Room
IBS Seminar Room
hosted by Thierry Vernet (IBS)
EMBL Seminar Room
For more information see: chem.usc.edu/faculty/McKenna.html
ILL Chadwick Amphitheatre
more informations on the So Iwata
Membrane proteins are a supreme example where more effort in structural biology is needed. In spite of their abundance and importance, of over 50,000 protein structures in the Protein Data Bank, only some 190 of these proteins are unique membrane proteins. Membrane transporters form the second largest family among these membrane proteins; it is known that 5-12% of genes in the genomes sequenced to date encode membrane transporters. However, the structure determination of membrane transporters remains extremely challenging; the 3D structures of less than 20 such proteins are known. No structures are known for any mammalian solute carriers, except for the ATP/ ADP exchanger from mitochondria. Functional and structural studies of membrane transporters responsible for the uptake and release of various materials including sugars, amino acids, peptides, drugs and ions are essential to our understanding of how the cells and our bodies work.
I will update our effort on structural and functional studies on mammalian solute carriers and their orthologues including lactose permease (1,2) and hydantoin transporter (3) and their molecular transport mechanisms will be discussed based on the crystal structures.
for an entrance badge, please contact in advance Claudine Romero
Hosted By Sean McSweeney (ESRF)
by Nathalie Grandvaux (Faculté de Médecine, Département de Biochimie, Université de Montréal)
Host : F. Fieschi (IBS/M &P Group)
IBS seminar room
– IBS seminar room
– CEA Amphi Dautreppe
Рcontactez Odile Rossignol (t̩l. 04.38.78.45.63 - Email: odile.rossignol@cea.fr).
Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS Seminar Room
hosted by J. Peter (IBS)
– EMBL seminar Room
Please contact Andrew McCarthy for information
– 11:00 EMBL seminar Room
additional information on Bruno Canard’s group and activity
Abstract: The diversity of emerging viruses is impressive, yet there are some common themes in their mechanisms of growth and survival in the infected cell, such as viral RNA replication and RNA
capping.
Studying the viral world at large is now possible due to structural genomics methods, and this should greatly help the design of antiviral
molecules targetting RNA viruses which may emerge in the near future.
In this talk, I will present the VIZIER consortium (2005-2009), which has addressed these viral enzymes as potential drug targets. I will
analyse VIZIER main results, success and failures, and present in detail the structural and mechanistic analysis of two enzymes discovered and characterized during the program.
Hosted by Ivan Ivanov (UVHCI/ILL)
IBS Seminar Room
CIBB Seminar Room
hosted by Jean-Pierre Simorre (IBS)
CIBB Seminar Room
Hosted by the College 8
IBS seminar Room
CIBB Seminar Room
Hosted By Jo Zaccai (ILL)
EMBL Seminar Room
CIBB Seminar Room
Abstract
hosted by ILL College 8
IBS Seminar Room
ILL Chadwick Amphitheatre
10:00 - Mechanisms of tubulin assembly and of microtubule destabilizing inhibitors.
– By Marcel Knossow (L.E.B.S. , C.N.R.S. Gif sur Yvette)
11:00 - Bacterial cell wall architecture: strength by design.
– By Simon J. Foster (University of Sheffield, UK)
Organizing committee: Ramesh Pillai (EMBL/UVHCI) Dimitrios Skoufias (IBS) Thierry Vernet (IBS) Andre Zapun (IBS)
IBS seminar Room
– 10:00: Molecular anatomies in subcellular proteomics
By Johan Malmström (Department of Immunotechnology, Lund University, Sweden)
– 11:00: Divide and conquer: strategies for the analysis of complex proteomes.
By Jeroen Krigsveld (EMBL, Heidelberg, Germany)
ILL Chadwick Amphitheatre 13:300 to 17:30
IBS seminar Room
IBS Seminar Room
– The same redox chemistry makes transition metals such as copper both essential in numerous enzymatic reactions and highly toxic for the cell, whenever their concentration exceeds the required intracellular levels. Therefore, all living organisms have developed mechanisms to control intracellular metal concentrations. Cupriavidus metallidurans CH34 is a β-proteobacterium found in industrial biotopes and, because of its adaptation to these harsh environments, became a model system for the study of heavy metal resistance. I will report on the structural and metal-binding studies on two periplasmic protein compounds, most probably involved in periplasmic copper and silver trafficking. The solution structures of apo and Cu(I)-bound CopK were solved using NMR spectroscopy and high-resolution information on its metal-binding site was obtained from X-ray absorption spectroscopy (XAS). Both techniques demonstrate that Cu(I) is coordinated in a tetrathioether site. I will also report on the C-terminal domain of SilB, a membrane-fusion protein that belongs to the RND system silABC. This 82 residue domain closely ressembles CusF with respect to its primary sequence and to its three-dimensional structure.
IBS seminar Room
– With recent advances in both, experiment and computer simulations, it has become possible to investigate the dynamics of small molecules in heterogeneous environments. This is of particular interest because small ligands can be used as an experimental probe to investigate the interior of proteins or other disordered materials.
Atomistic Simulations are an established computational method to investigate gas- and condensed-phase systems. Recent extensions to force fields incorporate more details in capturing electrostatic interactions and allow to more quantitatively understand particular processes. Here, I will describe some of these methods and their use to understand the energetics, [vibrational]spectroscopy and reactions in biological and physico-chemical systems. For myoglobin interacting with diatomic ligands the vibrational spectroscopy of the ligand and its rebinding kinetics are long-standing problems in biophysics which continue to attract the attention of experimentalists and computational chemists. The relationship between spectroscopy and structure is an interesting problem in the physical chemistry of doped ices which play an important role in astrophysics.
hosted by Martin Field (IBS)
IBS Seminar Room
– Streptococcus pneumoniae (le pneumocoque) est une bacteÌ rie responsable de maladies non-invasives (otites, pneumonie) et invasives (septiceÌ mie, meÌ ningite). Elle tue 1,6 millions de personnes par an aÌ€ travers le monde. La recrudescence des pheÌ nomeÌ€nes de reÌ sistance aux antibiotiques existants, ainsi que la couverture reÌ duite des vaccins actuels, imposent la recherche et la caracteÌ risation de cibles theÌ rapeutiques innovantes. Nos travaux se sont concentreÌ s sur les proteÌ ines de la surface du pneumocoque AdcAII et PhtD dont les fonctions ne sont pas connues. L’affiniteÌ et la speÌ cificiteÌ de AdcAII pour le zinc ont eÌ teÌ deÌ montreÌ es par des meÌ thodes biophysiques. Nous avons ensuite pu deÌ montrer que AdcAII eÌ tait une proteÌ ine homologue aux parties extracellulaires des ABC transporteurs chargeÌ s de l’import du zinc, ion vital pour la bacteÌ rie. Pour cela, des eÌ tudes phylogeÌ neÌ tiques ont eÌ teÌ meneÌ es et la structure de la proteÌ ine a eÌ teÌ reÌ solue par cristallographie aux rayons X, aÌ€ une reÌ solution de 2,4 AÌŠ. Les expeÌ riences in vivo, portant sur les mutants de deÌ leÌ tion ΔadcAII, ainsi que l’eÌ tude de l’organisation geÌ neÌ tique de adcAII laissent cependant supposer que AdcAII n’intervient pas dans l’import du zinc. Les fortes identiteÌ s de seÌ quence de AdcAII avec des proteÌ ines de streptocoques impliqueÌ es dans l’adheÌ rence bacteÌ rienne aÌ€ la laminine humaine nous ont pousseÌ aÌ€ tester ses proprieÌ teÌ s d’adheÌ rence. Des expeÌ riences d’interactions aÌ€ des proteÌ ines extracellulaires de l’hoÌ‚te, et aÌ€ la laminine en particulier, ont eÌ teÌ meneÌ es avec la proteÌ ine recombinante AdcAII en fonction du zinc, ainsi qu’avec les souches sauvage ou muteÌ e ΔadcAII de pneumocoques. Des doutes sont exprimeÌ s quant au fait que l’adheÌ rence de AdcAII aÌ€ la laminine repreÌ sente sa fonction premieÌ€re. La co-transcription et la co-reÌ gulation par le zinc des proteÌ ines AdcAII et PhtD ont eÌ teÌ Ì tablies, indiquant une possible relation fonctionnelle entre les deux proteÌ ines. La caracteÌ risation de PhtD a permis de deÌ montrer sa capaciteÌ aÌ€ fixer le zinc, meÌ canisme qui est accompagneÌ de reÌ arrangements conformationnels. Des eÌ tudes par RMN et des mesures de la stabiliteÌ thermique des proteÌ ines par « thermal shift assay » notamment ont permis d’eÌ tablir une interaction entre PhtD et AdcAII, qui ne serait effective que dans des conditions de deÌ ficit en zinc.
IBS Seminar Room
– DNA damage is a common occurrence that compromises the functional integrity of DNA. Well over 10,000 DNA damages are estimated to occur daily in every human cell. The causative agents of these damages are mainly free radicals, which are normally produced as natural by-products of food metabolism. If damaged DNA is left unrepaired, it generates mutations, replication errors, persistent DNA damage and genomic instability, which ultimately is associated with cancer and aging. DNA repair pathways are ubiquitous and the principles of damage recognition are conserved from bacteria to humans. A better understanding of the mechanisms and principles underlying damage recognition in simple organisms such as bacteria is thus an essential step towards obtaining a complete overview of the more complex human DNA repair systems. I will present our work on the structural and functional characterisation of three of the major DNA repair pathways found in the extreme radiation-resistant bacterium Deinococcus radiodurans. This Gram-positive eubacterium displays an extraordinary resistance to a wide-range of DNA-damaging agents, such as ionising radiation and desiccation. Ionising radiation induces the most lethal form of DNA damage, namely DNA double-strand breaks (DSBs). Whilst in most species only a few DSBs can be tolerated and repaired, D. radiodurans can withstand and repair over 100 DSBs in its genomic DNA. Initial investigations support the view that the extreme radiation resistance of D. radiodurans is complex and is most likely determined by a combination of factors including genome packing, cell structure and importantly a highly efficient DNA repair machinery.
hosted by B. Franzetti (IBS)
EMBL Seminar Room
link to H.E.J. Research Institute of Chemistry (Univ. of Karachi)
read more about Muhammad Iqbal Choudhary
– ILL Chadwick Amphitheatre
The high resolution structures of the 30S subunit and more recently the entire ribosome have shed light on how the ribosome ensures the fidelity of translation. We will describe our studies on the nature of the recognition of codon-anticodon base pairing by the 30S ribosomal subunit, and how this leads to a series of conformational changes that results in the hydrolysis of GTP by elongation factor Tu, leading to the acceptance of the new amino acyl tRNA for the formation of a peptide bond.
Hosted by Jo Zaccai (ILL)
ILL Chadwick Amphitheatre
РOrganised by Bridgette Connell (IBS), Shona Gillespie (ILL), Thierry Izore (IBS), Nikolaos Mathioudakis (EMBL), Deeska Munnur (ILL), Yan Nie (EMBL), Simone Pellegrino (ESRF), Marion S̩vajol (IBS), Eric Thierry (UVHCI).
12:30 Poster Session & Welcome Buffet in the ILL Entrance Hallway
13:30 Short Introduction (Thierry Izore)
· First Session chaired by Bridgette Connell
– 13:35 Structure and Function of CHMP Proteins and their ligands involved in HIV budding.
By Nicolas Martinelli (UVHCI)
– 14:00 Understanding the role of RecN in the extreme radio-resistant
bacterium Deinococcus radiodurans.
By Simone Pellegrino (ESRF)
– 14:25 X-ray and neutron characterisation of self assembling filamentous structure.
By Estelle Mossou (ILL)
– 14:50 -15:20 First Year PhD Students. Two-minute clips
– 15:20 – 15:50: Coffee Break - Poster Session
· Second Session chaired by Yan Nie
– 15:50 Design of biosensors based on the covalent assembly of Gprotein coupled receptors and potassium channels.
By Lydia Caro (IBS)
– 16:15 Structural studies on RIG-I, a receptor for intracellular viral
RNA.
By Eva Kowalinski (EMBL)
– 16:40-17:10 First Year PhD Students. Two-minute clips
– 17:10 – 18:00: Poster Session and Best Poster Prize
– 18:00 Closing Session
ILL Chadwick Amphitheatre
– 10:00 Yuichiro Takagi (USA) :
Mediator of transcription regulation: structure and functional interactions
– 11:00 Timothy J. Richmond (Switzerland) :
Structure and Interactions of the Chromatin Remodeling Factor ISW1a
hosted by Imre Berger (EMBL/UVHCI)
EMBL seminar Room
EMBL Seminar Room
ILL Chadwick Amphitheatre
web-page:www.ill.eu/news-events/events/mam2010/
application deadline: 30th November 2009
– Organisers
Guiseppe Zaccaï and Andrew Harrison
– Secretary
Karine Sultan - contact email: mam2010@ill.eu
EMBL Seminar Room
Structural and mechanistic studies of the anaphase promoting complex – a multi-subunit cell cycle regulator The anaphase promoting complex (APC) is a multi-subunit cullin-RING E3 ubiquitin ligase that regulates progression through the mitotic phase of the cell cycle and controls entry into S phase by catalysing the ubiquitylation of cell cycle regulatory proteins such as cyclin B and securin. Selection of APC/C targets is achieved through recognition of short destruction motifs, predominantly the D-box and KEN-box. The APC is assembled from over 12 individual subunits. Many of the APC,s core proteins comprise multiple repeat motifs whose principle function is to provide a molecular scaffold, but whose exact biological role is not well understood. The best characterised APC subunits are the cullin and RING proteins Apc2 and Apc11 that generate the catalytic centre, and the TPR subunit Apc3/Cdc27 that interacts simultaneously with co-activator and the APC subunit Apc10 (also known as Doc1). Substrate recognition is known to involve a co-activator protein (either Cdc20 or Cdh1) together with core APC subunits, although the structural basis for substrate recognition and ubiquitylation is not understood. We are investigating the structure and mechanism of the APC using a combination of biochemical, crystallographic and electron microscopy approaches. I will describe our recent work, addressing the basis for co-activator dependent substrate recognition based on a 14 Å resolution cryo-EM maps of the APC in complex with co-activator and substrate.
– more about David Barford...
Invited by Eva Kowalinski (EMBL PhD student)
– EMBL Seminar Room
Structural characterisation of proteins is often hindered by insufficient
amounts of soluble material. A common approach addressing this problem is to isolate their separate domains, classically done by time-consuming iterations of design, generation and testing of constructs. An alternative approach is to generate a random library of all possible constructs by enzymatic DNA truncation and test them in one experiment for expressionand solubility. In this work, the novel, directed evolution-type method Expression of Soluble Proteins by Random Incremental Truncations (ESPRIT) was used to explore the definition of protein domains. The biological focus was a set of multidomain protein kinases that has previously resisted soluble over-expression and structural characterisation.
EMBL Seminar Room
more information on Stefan Knapp
Selected Publications:
* Barr, AJ, Ugochukwu, E, Lee, W-H., King, O, Filippakopoulos, P, Alfano, I, Savitsky, P, Burgess-Brown, N, Muller S, Knapp, S (2009). Structural and Functional analysis of the classical protein tyrosine phosphatase family (PTPome). Cell, 136(2):352-26
* Filippakopoulos, P, Kofler, M, Gish, GD, Salah, E, Neudecker, P, Kay, LE, Turk , BE, Pawson, T and Knapp, S. (2008) Structure of the Fps/Fes tyrosine kinase reveals cooperative interactions between the SH2-kinase domains and substrate. Cell, 134(5):793-803.
* Baumli, S., Lolli, G., Lowe, ED., Troiani, S., Rusconi, L., Bullock, AN., Debreczeni, JE., Knapp, S., Johnson LN. (2008). The structure of P-TEFb (cdk9/cyclin T), its complex with flavopiridol and regulation by phosphorylation. EMBO J. 27,(13), 1907-1918.
* Marsden, B.D., and Knapp, S. (2008). Doing more than just the structure-structural genomics in kinase drug discovery. Current Opinion in Chemical Biology, 12, 40-45.
Hosted by Darren Hart (EMBL/UVHCI)
– IBS Seminar Room
Le travail de thèse s’est articulé autour de deux axes : l’étude d’inhibiteurs peptidiques anti-Fur et la caractérisation de Fur d’Helicobacter pylori.
Avec l’apparition de souches pathogènes multi résistantes, de nouveaux antibactériens doivent être développés. Le régulateur principal du transport du fer bactérien Fur (Ferric Uptake regulator) est une cible potentielle. En effet, il régule des fonctions essentielles et est spécifique des procaryotes. Quatre aptamères peptidiques (F1 à F4) dirigés contre Fur d’Escherichia coli ont été isolés précédemment au laboratoire. Les aptamères peptidiques sont des protéines combinatoires constituées d’une plate-forme protéique constante dans laquelle est insérée une boucle variable de 13 acides aminés qui constitue la partie active. Les peptides linéaires pF1 à pF4, correspondant aux parties variables de F1 à F4 ont été testés in vitro pour leur capacité à inhiber la liaison de Fur à l’ADN. Des variants mutés et/ou tronqués ont aussi été étudiés. Des tests double hybride chez la levure ont été réalisés afin d’étudier in vivo l’interaction de Fur avec les peptides pF1 à pF4, et l’interaction des aptamères F1 à F4 avec les protéines Fur d’autres souches pathogènes, dont Helicobacter pylori.
H.pylori est une bactérie qui colonise la muqueuse gastrique chez l’homme. La protéine Fur d’H.pylori a été purifiée, elle est nativement un dimère contenant un zinc par sous-unité. Ses propriétés de métallation et de liaison à l’ADN ont été étudiées, et les cystéines impliquées dans la liaison du zinc ont été identifiées. La structure tridimensionnelle du double mutant C78S C150S a été résolue en collaboration avec l’ESRF
– IBS Seminar Room
Abstract:Membrane proteins constitute one of the most fascinating classes of biological macromolecules. In a typical genome, roughly 30% of the genes code for proteins associated with membranes, but since these proteins are present on the cell surface they are of extremely high importance efor pharmaceutical applications. Over half of currently available drugs target membrane proteins, and in terms of market value it is close to 80%. Due to difficulties in overexpression and crystallization there are still only a couple of hundred membrane protein structures known, and for this reason sequence-based modeling of membrane proteins has received a lot of attention.
While most transmembrane segments in proteins are clearly hydrophobic, there are surprisingly enough a number of exceptions where marginally stable or even hydrophilic segments appear in the hydrophobic region. Many of these are critically important, for instance the S4 segments of voltage-gated ion channels - it is the charged residues inside these protein that causes the channel to open and close in response to voltages, which we need for every nerve impulse and heart beat. There has been significant debate between experimental results that claim insertion for these is quite cheap, and theoretical calculations claiming it is prohibitively expensive.
We use a fairly wide combination methods to study these systems, ranging from bioinformatics through modeling and molecular simulations all the way to in vitro experiments. I will discuss these methods and talk about recent work where we have shown that the hydrophobicity values derived from experimental insertion is amazingly efficient at predicting insertion, how this can be used to understand (and predict) helix-helix interactions in membranes, and how we now likely can explain the molecular step of the insertion. I will also discuss how this related to some of our very recent results on structural changes in ion channel gating, where the charged S4 residues play a crucial role.
Biography
Erik Lindahl is Associate Professor in Computational Stuctural Biology in the Department of Biochemistry and Biophysics at Stockholm University. The overall goal of his research is use large-scale modeling and simulation techniques to better understand how proteins fold, interact and function, with an emphasis on membrane proteins. Apart from this application work, Erik is a pioneer in the development of high performance biocomputational software. He is one of the co-authors of the widely-used Gromacs simulation program and participates in the folding@home project based at Stanford University.
– More information on Center for biomembrane research and Erik Lindahl research group
Hosted by Martin Field (IBS)
– IBS Seminar Room
– room 03-1-14, Experimental Hall
– Abstract
Hosted by Sean McSweeney
ILL Amphitheatre
Room 03-1-15, Experimental Hall (ESRF)
– PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Hosted By Antoine Royant
Room 337, ESRF Central Building
– PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
hosted by Antoine Royant
IBS Seminar Room
Hosted By Bruno Franzetti (IBS)
CTRM Control Room
– PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Hosted by Antoine Royant
IBS Seminar Room
Solution Nuclear Magnetic Resonance spectroscopy represents a powerful tool to study the structure, function and dynamics of biological molecules. Over the last decade, technological advances and isotope labeling techniques have expanded the range of tractable targets by at least an order of magnitude.
Here we briefly describe the methodological advances that allow NMR spectroscopy of high molecular weight proteins and present the applications of this new methods to the TET2 protein, an aminopeptidase involved in peptide degradation, forming a homododecamer of 468 kDa.
IBS Seminar Room
All major branches of the bacterial sub-kingdom possess a cell wall containing peptidoglycan (PG), which is a huge mesh-like network that covers the whole surface of the cell. PG consists of long glycan strands cross linked by peptide bridges. The precursors for PG are made inside the cell and then polymerized on the outside by the action of penicillin-binding proteins (PBPs). Autolytic enzymes cleave bonds in the PG in a controlled manner to allow orderly growth of the cell. The walls of Gram positive bacteria contain an almost equal mass of one or more anionic polymers called teichoic acids, the functions of which remain poorly understood. The cell wall is a crucial structure for bacteria because it opposes the cytoplasmic turgor pressure on the cytoplasmic membrane, preventing the cell from bursting, as well as providing protection from mechanical damage. The wall is also the target for the best of our antibiotics, particularly b-lactams and glycopeptides. Despite many decades of research, many features of cell wall biogenesis remain poorly understood.
hosted by T. Vernet (IBS)
EMBL Seminar Room
Amphithéâtre du LPSC ( 53 rue des Martyrs, Grenoble)
Cette année de double anniversaire (bicentenaire de la naissance de Darwin et de la publication de la philosophe zoologique de Lamarck), est l’occasion de revenir sur les contributions respectives de ces deux naturalistes.
"Selection naturelle" et "hérédité des caractères acquis" : ces deux expressions résument l’opposition entre deux théories évolutives. Si cette opposition doit être relativisée (aucun des deux auteurs ne peut se réduire à ces mots), elle a néanmoins marqué la recherche en biologie de ces deux derniers siècles. L’objet de cette communication est de présenter, brièvement, un état de la recherche en biologie de l’évolution centré sur la discipline Evo-Devo (de l’anglais Evolutionary Developmental biology). L’accent sera mis sur les concepts actuels qui remettent l’opposition entre Lamarck et Darwin au goût du jour. Darwin avait bien raison quant au mécanisme fondamental moteur de l’évolution, et Lamarck tort. Pourtant, la synthèse évolutive des années 40 était limitée par un rejet trop systématique de données considérées comme "non orthodoxes" "néo-Lamarckiennes". L’Evo Devo, en intégrant des données écologiques et développementales nous permet de dépasser cette limite. Nous tenterons de montrer que, sans une certaine ironie, c’est en partie grâce à la renaissance de Lamarck que la théorie de Darwin est plus vivante que jamais.
– room 500 - 501, Central Building
– Abstract
Sean McSweeney (seanmcs@esrf.fr)
salle de Conférence de l’IAB
The activity state of a gene is determined by a complex regulatory network of co-acting factors (including small RNAs) affecting the structure of the chromatin into which the gene is embedded. The control of gene expression and differentiation are particularly interesting in the parasite model Toxoplasma gondii, as the apparent lack of large families of recognizable transcription factors typically found in other eukaryotic organisms suggests that they may be unusually reliant on epigenetic mechanisms. Based on this hypothesis, our lab and others brought evidences that the parasite possesses a sophisticated ‘histone code’ that rivals those described in higher eukaryotic cells. We showed how active domains in chromatin are established and altered during parasite differentiation by generating high-resolution genome-wide maps of histone modifications using ChIP-on-chip. We confirmed that chromatin regulators make suitable targets for development of therapeutic drugs and dissect how a new histone deacetylase inhibitor is acting on parasites. Finally, we show that the small RNA repertoire of Toxoplasma is exceptionally diverse and includes conspicuous populations of microRNAs, as well as a variety of short interfering RNAs. We are now in a process to delineate the mechanisms by which the parasite genome is silenced through small regulatory RNAs and histone code.
– CIBB Seminar Room
Both proteins and RNAs can form specifically packed and catalytically active structures, but RNAs do so with a limited “alphabet†of only 4 different bases, whereas proteins are made of 20 chemically diverse amino acids. Could a protein form a stable and uniquely folded structure with a set of amino acids as limited as the alphabet of RNA? In this talk, I will describe the characterization of a family of twenty residue peptides called “KIA7†with the sequence:
Ala-Lys-Ala-Ala-Ala-Ala-Ala-Ile-Lys-Ala-Ile-Ala-Ala-Ile-Ile-Lys-Ala-Gly-Gly-X where X is an aromatic amino acid. These peptides adopt well folded four helix bundle proteins with a specifically packed core as determined by NMR spectroscopy, even though their composition of amino acids and set of stabilizing interactions is very limited. The stability of the folded four helix bundle structure increases with the size and hydrophobicity of the C-terminal group: KIA7His < KIA7Tyr ≤ KIA7Phe < KIA7Trp. KIA7His is composed of just five different amino acids all of which form under the same set of putative prebiotic Earth conditions. KIA7His, in the presence of certain divalent cations, can specifically cleave RNA hairpins. This suggests that proto-ribonucleases might have co-inhabited and influenced the evolution of the RNA World.
Hosted by Marc Jamin (UVHCI)
– EMBL seminar room
EMBL Seminar Room
– Very often, the positions of flexible domains within macromolecules as well as within macromolecular complexes cannot be determined by standard structural biology methods. To overcome this problem, we developed a method that uses probabilistic data analysis to combine single-molecule measurements with X-ray crystallography data. The method determines not only the most likely position of a fluorescent dye molecule attached to the domain but also the complete three-dimensional probability distribution depicting the experimental uncertainty. With this approach, single-pair fluorescence resonance energy transfer measurements can now be used as a quantitative tool for investigating the position and dynamics of flexible domains within macromolecular complexes. We applied this method to find the position of the 5’ end of the nascent RNA exiting transcription elongation complexes of yeast (Saccharomyces cerevisiae) RNA polymerase II and studied the influence of transcription factor IIB on the position of the RNA. This work lays the foundation for the development of the fluorescence nano-positioning system.
Nature Methods. 2008 Nov;5(11):965-71
Nucleic Acids Res. 2009 Sep;37(17):5803-9.
Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):135-40
hosted by Daniel Panne (EMBL)
IBS seminar Room
– Because fossils from the time when cellular life originated and diversified are scant and difficult to interpret, alternative means to investigate the ecology of the Last Universal Common Ancestor (LUCA) and of the ancestors of the three domains of life are of great scientific value. It was recently recognized that footprints of the effect of temperature on ancestral organisms could be uncovered in extant genomes. Accordingly, analyses of resurrected proteins predicted that the bacterial ancestor was thermophilic and that Bacteria subsequently adapted to lower temperatures. Since the archaeal ancestor is also thought to have been thermophilic, LUCA was parsimoniously inferred as thermophilic too. However, an analysis of ribosomal RNAs supported the hypothesis of a non-hyperthermophilic LUCA. We show that both rRNA and protein sequences analysed with advanced, realistic models of molecular evolution provide independent support for two phases in the history of environmental temperature changes over the tree of life: in the first period, thermotolerance increased from a mesophilic LUCA to thermophilic ancestors of Bacteria and of Archaea-Eukaryota; in the second period, it decreased. Therefore, the two lineages descending from LUCA and leading to the ancestors of Bacteria and Archaea-Eukaryota convergently adapted to high temperatures, maybe in response to a climate change of the early Earth, and/or aided by the transition from an RNA genome in LUCA to organisms with more thermostable DNA genomes. This analysis unifies apparently contradictory results into a coherent depiction of the evolution of an ecological trait over the entire tree of life.
IBS Seminar Room
– ABC drug transporters play an important role in cancer drug resistance, protection against xenobiotics, and in general in the passage of drugs through cellular and tissue barriers. Characterization of a compound as an ABC transporter substrate or inhibitor bears significant consequences in drug development, the selection of dosing regimens, the anticipation of toxic effects and the potential for drug-drug interactions. The pharmacological relevance of ABC transporters has promoted efforts to establish in vitro systems for testing drug-transporter or drug-drug interactions. The talk will review how the expression and function of human ATP-Binding Cassette (ABC) transporters modulate the pharmacological effects of various drugs, and how this predictable ADME-TOX modulation can be used during the process of drug discovery and development. The use of the in vitro, in vivo, in silico models, their combination, and the emerging clinical information will be evaluated with respect to their potential application in early drug screening.
– IBS seminar room
G protein-coupled receptors (GPCR) constitute the largest and a highly diverse family of
integral membrane proteins that transmit signals inside cells in response to a variety of
extracellular stimuli. Strategic location of GPCRs on the cell surface and their participation
in crucial physiological processes turn these proteins into prominent drug targets. Structure
determination of GPCRs remains challenging, and many essential aspects, related to
the mechanism of signal transduction and ligand specificity and selectivity, are poorly
understood.
Here we will present recently determined structures of the human CXCR4 chemokine G
protein-coupled receptor bound to a small molecule and a cyclic peptide antagonists;
and a structure of the dopamine D3 receptor in complex with an antagonist. CXCR4
structures reveal a receptor homodimer and provide insights into chemokine signaling
and HIV-1 recognition. Structural details of the dopamine D3 receptor help to understand
pharmacological specificity between dopamine D2 and D3 receptors.
Host : Valentin Gordeliy (IBS)
– seminar room, 1st floor ILL4.
The use of gels as a medium for growing high quality crystals is well established.Furthermore, it has been shown that the gel environment is able to alter the habitof crystals and induce different polymorphs and enantiomorphs compared with thosegrown from solution.
More recently, a new class of gelators has emerged based on low-molecular weight compounds which self assemble into supramolecular networks capable of forming gels.The reversible nature of supramolecular gels can be utilised to allow easy recovery of crystals whilst the diverse array of chemical functionalities that can be introduced allows for tuning of interactions between the gel and growing crystal.
We have demonstrated ‘proof of principle’ for the crystallisation of a wide range of pharmaceutical compounds from a series of bis-urea based gelators in a variety of solvent systems. Addition of TBA-Acetate was found to break down the gels allowing the crystals to be isolated in many cases. A number of differences in crystal habit and polymorphism between crystals grown in gels and from solution were observed. Work is continuing to match the functionality and properties of gelators with crystallisation systems of interest.
J. A. Foster, M-O. M. Piepenbrock, G. O. Lloyd, N. Clarke, J. A. K. Howard and J. W. Steed, Nature Chemistry, 2010, awaiting publication
Hosted by the ILL Students
EMBL seminar Room
For the first 30 years since its discovery, reversible protein acetylation has been studied and understood almost exclusively in the context of histone modification and gene transcription. With the discovery of non-histone acetylated proteins and acetylation-modifying enzymes in cellular compartments outside the nucleus, the regulatory potential of reversible acetylation has slowly been recognized in the last decade. Protein acetylation/deacetylation events are involved in a number of important biological processes including cellular differentiation, proliferation, embryonic development and tumor formation. The recent development of new technology has enabled, for the first time, the identification and quantification of the acetylome, acetylation events at the whole-proteome level. These efforts have uncovered a stunning complexity of the acetylome that potentially rivals that of the phosphoproteome. We will discuss the roles of histone deacetylases in signal transduction, their relevance to disease and pharmaceutical targeting.
– Dr Tso-Pang Yao, is Associate Professor in the Department of Pharmacology and Cancer Biology (Duke University). He received his PhD in Biomedical Science (Dr. Ronald Evans’ laboratory) from the Salk Institute, San Diego and was a Postdoctoral fellow in the laboratory of Dr. David Livingston (Dana Farber Cancer Institute, Boston).
– References: EMBO J. 2010 Jan 14. Science Signaling 2009; Nov 17 Cancer Res. 2008 Sep 15 Nature. 2007 Jun 14
– more information on Tso-Pang Yao
Hosted by Danielle Desravines (EMBL PhD Student)
– IBS Seminar Room
Protein function critically depends on the synergy of structure and dynamics, so-called structural dynamics. This is particularly true for acetylcholinesterase (AChE) that displays a high catalytic turnover despite the buried nature of its active site.
Structural dynamics are not readily accessible to conventional X-ray crystallography. Yet, the advent of third generation synchrotron sources has brought exiting new possibilities to study macromolecular structural dynamics by kinetic crystallography, aiming at the observation of e.g. enzymes in action.
We developed and employed several kinetic-crystallography approaches to gain insight into molecular motions involved in substrate and product traffic within Torpedo californica AChE (TcAChE). As a first step, substrate and product binding within the active site gorge was experimentally elucidated by solving the crystal structures of TcAChE complexed with the substrate acetylthiocholine, the product thiocholine and a non-hydrolysable substrate analogue. Molecular ‘breathing’ motions involving the entire enzyme during product clearance from the active site were identified by a combination of temperature-controlled crystallography and radiolysis or laser-photolysis of precursors of the enzymatic product choline. Taken together, these crystallographic snapshots might be part of a molecular movie showing acetylcholinesterase at work. Multiple MD simulations were used to fill-in the gap between the crystallographically characterized intermediate steps, and were surprisingly able to reproduce all experimental results.
In the future, we plan to use similar methodologies to study other proteins involved in e.g. Alzheimer disease and antibiotic resistance. We will give a brief overview on these new and/or on-going projects.
– EMBL seminar Room
INTRACT, a novel small molecule assay technology will be presented that enables extremely fast and highly sensitive screening of small molecule fragments in solution. INTRACT is based on measuring minute perturbations in the hydration shell of a target molecule as a consequence of ligand binding. Rapid assay set-up, direct and easy access to accurate information on fragment Kd, binding mode and the straightforward identification of badly behaved aggregating compounds enable informed decision making. In this way only the best, most promising fragment hits from a fragment library screen are being progressed. Together with a proprietary fragment collection, this screening technique forms the core of SEEDS, our fragment based drug discovery service offerings. by Executive Director ,
– ILL Chadwick Amphitheatre
hosted by Imre Berger (EMBL) and Michael Plevin (IBS)
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Eva Jahn-Feppon tel +33 (0)476 88-26-19.
Requests made by e-mail will be confirmed. If you do not receive a confirmation e-mail, please contact us by phone.
– CIBB Seminar Room
Many experimental evidence support the view that growth and survival of cancer cells rely on the aberrant activation of several signaling pathways in which protein-kinases play a key role. Therefore, the implication of these enzymes in deregulated signaling pathways together with their susceptibility to small molecule inhibitors make them the first choice for a « Signal Transduction Therapy ».
Protein-kinase CK2 is a pleiotropic, constitutively active Ser/Thr protein-kinase, whose level is unvariably elevated in cancer cells, providing a favourable environnement for tumor progression. Consequently, CK2 has recently emerged as a relevant therapeutic target and its pharmacological inhibition appears as a promissing strategy. To date more than forty crystal structures of CK2 have been deposited in the Protein Data Base establishing a strong basis for the rational design of effective CK2 inhibitors. I will show that similar to other kinases, a number of ATP competitive inhibitors targeting its active site have been identified, some of them exhibiting anti-tumoral activity. Moreover, it has been revealed that the molecular architecture of this multi-subunit enzyme could offer opportunities to develop alternative strategies to inhibit CK2 functions. Using high-throughput and structure-based virtual screening approaches, we have identified different classes of small molecules targeting different surface area such as exosites on CK2a or at the CK2a/CK2b interface.
These exosite-targeting inhibitors promise exciting opportunities by exploiting new mechanisms of action that may allow greater specificity.
References
– Filhol O, Martiel JL, Cochet C. (2004) Protein kinase CK2: A new view of an old molecular complex. EMBO Reports, 5: 351-355 .
– Niefind K, Guerra B, Ermakova I, Issinger OG. (2001) Crystal structure of human protein kinase CK2 : insights into basic properties of the CK2 holoenzyme. EMBO J, 20 : 5320-5331.
– Chantalat L, Leroy D, Filhol O, Nueda A, Benitez MJ, Chambaz EM, Cochet C, Dideberg O.. Crystal structure of the human protein kinase CK2 regulatory subunit reveals its zinc finger-mediated dimerization. EMBO J., 1999, 18, 2930-2940.
– Laudet B, Barette C, Dulery V, Renaudet O, Dumy P, Metz A, Prudent R, Deshiere A, Dideberg O, Filhol O, Cochet C. (2007) Structure-based design of small peptide inhibitors of protein-kinase CK2 subunit interaction. Biochem J, 408: 363-373
– Laudet B, Moucadel V, Prudent R, Filhol O, Wong YS, Royer D, Cochet C. (2008) Identification of chemical inhibitors of Protein-Kinase CK2 subunit interaction. Mol Cell Biochem, 316: 63-69.
РPrudent R, Moucadel V, Laudet B, Barette C, Lafanech̬re L, Hasenknopf B, Li J, Bareyt S, Lac̫te E, Thorimbert S, Malacria M, Gouzerh P, Cochet C. (2008) Identification of Polyoxometalates as nanomolar non-competitive inhibitors of Protein Kinase CK2. Chemistry & Biology, 15: 683-691.
– Prudent R, Cochet C. (2009) New protein kinase CK2 inhibitors: jumping out of the catalytic box. Chemistry & Biology, 16 : 112-120.
РLopez-Ramos M, Prudent R, Moucadel V, Sautel, C, Barette C, Lafanech̬re L, Mouawad L, Schmidt F, GriersonD, Florent JC, Filippakopoulos P, Bullock AN, Knapp S, Reiser JP, Cochet C.
New Potent inhibitors of CK2 and Pim kinases : Discovery and Structural Insights. FASEB J. 2010, (in press).
hosted by JB Reiser (IBS)
– EMBL Seminar Room
Throughout evolution, proteins have sought a balance between flexibility and thermal stability, which allows them to achieve their biological function and, at the same time, to preserve a well-defined average structure. As a result, most of functional proteins are not rigid or static objects but experience local and global movements at different timescales. Their environment plays an essential role in this context. In particular, it is well-known that water molecules located in the vicinity of a solute show differences in their organization and hence in their thermodynamic, dynamic, and electrostatic properties, when compared to bulk waters. The water behavior at a molecular level is strongly affected by the presence of cosolvents, and this is also critical for the dynamics of macromolecules. In the middle 1980s, Zaks and Klivanov observed that the catalytic activity of several proteins, when they are suspended in hydrophobic solvents at low water concentration, is comparable or even higher than in aqueous solution. It has been proposed that water acts as a lubricant, forming hydrogen bonds with accessible groups of enzymes and providing them with the flexibility necessary for catalysis. Such explanations are generally accepted although no direct evidence has been provided. The activity of enzymes under those conditions, or when they are trapped in reverse micelles, became more than a curiosity when several biotechnological applications were proposed, taking advantage of this alternative. To date, no experimental technique has been able to provide a detailed structural-dynamics description of this phenomenon. In the present work a comprehensive study of the triosephosphate isomerase from the parasite Trypanosoma cruzi in several water/decane mixtures was performed using molecular dynamics simulations at the time scale of 40 ns. The structure and dynamics of the enzyme, as well as the solvent molecules’ distribution and mobility were analyzed in detail. Our results suggest that the presence of organic solvent molecules located at specific sites of the enzyme accelerates its internal movements, although a minimum number of waters is needed for the protein to keep its structure and dynamics.
– External visitors may ask for a site access to Karine Sultan (sultan@ill.fr).
– IBS Seminar Room
Dans le cadre de la manipulation des protéines membranaires en solution aqueuse, les tensioactifs fluorés ont été dessinées comme alternative aux détergents pour être les moins dénaturantes possible, et donc pour maintenir les protéines membranaires en conditions natives sur les grandes plages de temps nécessaires pour les études biochimiques, biophysiques et structurales. L’idée de base est l’introduction d’atomes de fluor dans la chaîne hydrophobe de tensioactifs de structure par ailleurs classique, ce qui diminue leur miscibilité avec les lipides et leur caractère dissociant. Après de longues années de tâtonnements afin d’obtenir une structure chimique compatible avec les exigences des chimistes (simple et pas trop coûteuse à synthétiser et à purifier), et du biochimiste (chimiquement défini, stable dans le temps, soluble à suffisamment haute concentration, cmc relativement basse, formant des micelles monodisperse, et surtout, maintenant en solution sous forme homogène et active les protéines membranaires), nous nous rapprochons de molécules remplissant tous les critères. Alors que l’effet stabilisant de ces molécules a bien été démontré, s’ouvre maintenant la phase d’exploration des différentes applications pour lesquelles les tensioactifs fluorés pourraient spécifiquement être utilisés. Je détaillerai quelques exemples se basant sur des résultats parfois encore préliminaires.
– EMBL Seminar Room
Our main goal is to understand how cells interpret genetic and
epigenetic information as well as environmental cues to determine
their correct cell fate, i.e. to make the decision to divide, die or
differentiate. For cells to assume their correct fate is essential
for development, epistasis and regeneration of any tissue, organ or
organism. Elucidating the principles and molecular pathways
underlying cell fate decisions is crucial for understanding how
cells become corrupted in disease. The recent discovery of a large
conserved class of small RNA genes, through the study of the control
of developmental timing in the nematode Caenorhabditis elegans,
opened up a new and unexpected dimension of gene regulation.
Although we know very little about the biology of these small RNAs,
the few examples that have been studied suggest that these genes are likely to have a major impact in many areas of biology.
hosted by Stefanie Eckhardt (EMBL)
– IBS seminar Room
Our research interest is in understanding the mechanisms of signalling at a structural with a special focus on sensing processes.We have recently obtained the structure of the Abscisic Acid (ABA) receptor, a hormone regulating the response to environmental stress in plants. This receptor belongs to the so called PYR/PYL/RCAR, family and is able to bind ABA and inhibit the activity of specific protein phosphatases of the type 2C PP2Cs leading to the activation of the signalling pathway controlling the stress response. Our work shows how the hormone binds to the receptor and how this binding orchestrates a series of events that lead to the activation of the ABA signalling cascade. This represents the definitive confirmation of the PYR/PYL/RCAR protein family as ABA receptors, providing insights into the basic mechanisms of sensing and signalling. This work also paves the way for the design of small molecules able to activate the ABA pathway and improve the tolerance of crops to drought an other types of environmental stress.
hosted by Martin Blackledge (IBS)
– IBS seminar room
IBS seminar Room
– ILL Chadwick Amphitheatre
hosted by Celeste Sele (UVHCI)
– ESRF Auditorium
In the summer of 2009, the design of the extension of the ESRF Experimental Hall
started, which is one of three core-deliverables of the ESRF Upgrade Programme.
The "Avant-Projet Sommaire" (APS) is a major project milestone to be completed
in March 2010. It will provide detailed 3-D plans of the buildings both in- and outside
and technical proposals for the building-specific problems of the project. This seminar
will present an overview of the results and details on the proposed solutions for
slab design, heating, ventilation, airco, and electricity, as well as on the risk
management of this project of close to 40 million Euros.
– ESRF Auditorium (to be confirmed)
Larvae infected with insect polyhedrosis viruses become milky white, a result of the formation of masses of intracellular protein crystals. The crystals, or viral polyhedra, consist of a cubic lattice of viral polyhedrin molecules containing thousands of virus particles embedded in the crystalline lattice. Viral polyhedra are remarkably stable, and can remain infectious in soil for years for feeding larvae. Polyhedra survive conditions that would denature most protein molecules, but do dissolve at pH > 10.5 in the mid gut, releasing the embedded virus particles.
We are interested in learning why viral polyhedra are so stable, how they specifically incorporate virus particles inside cells and also in applications e.g. for polyhedra engineered to contain other proteins in place of the embedded virus particles. We developed micro X-ray crystallography techniques to determine the atomic structures of polyhedra produced by the dsRNA virus cypovirus(1) and the DNA virus baculovirus(2), the same virus used in the expression system familiar to molecular biologists. These are amongst the smallest protein crystals ever used for de-novo atomic structure determination. The talk will describe these results, and also our recent work with granulovirus, a type of baculovirus that forms tiny 400nm polyhedra with a crystalline polyhedrin layer only 7 unit cells thick surrounding a single virus particle.
1) The molecular organization of cypovirus polyhedra (2007) Coulibaly F, Chiu E, Ikeda K, Gutmann S, Haebel PW, Schulze-Briese C, Mori H, Metcalf P, Nature. 446, 97-101
2) The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses (2009) Coulibaly F, Chiu E, Gutmann S, Rajendran C, Haebel PW, Ikeda K, Mori H, Ward VK, Schulze-Briese C, Metcalf P, Proc Natl Acad Sci U S A. 106, 22205-10
If you need a badge, please contact Claudine Romero
EMBL seminar Room
hosted by Imre Berger
– IBS seminar Room
The tripartite RND-driven (Resistance Nodulation/cell Division) efflux systems of Gram-negative bacteria play an important role in the cellular defence mechanism against toxic compounds including antibiotics and heavy metals. We are studying two RND-driven heavy metal efflux systems from Cupriavidus metallidurans CH34, a β-proteobacterium having an outstanding ability to grow on harsh environments such as heavy metal contaminated sites. Using different in vivo and in vitro approaches, we are characterizing the different components of these transport complexes in terms of structure-function relationship. The information gained from this study will help us to better understand the metal ion transport mechanism
hosted by B. Bersch and J.Covès (IBS)
– IBS seminar Room
PhD defence
La NADPH oxydase (NOX) est un complexe multienzymatique responsable de la production d’espèces réactives de l’oxygène (ROS) que l’on retrouve dans un grand nombre de types cellulaires. La NOX des neutrophiles est composée de deux protéines transmembranaires (gp91phox et p22phox), qui constituent le site catalytique, et de trois facteurs cytosoliques (p47phox , p67phox et p40phox). Lors de son activation, p47phox subit des changements conformationnels que nous tâchons de définir, afin de mieux comprendre la régulation de ce complexe impliqué dans un grand nombre de pathologies. Dans les neutrophiles, les ROS sont responsables de la destruction de pathogènes phagocytés. Il paraît donc primordial de bien comprendre les bases moléculaires du mécanisme d’activation de la NOX pour envisager sa régulation future.
Au cours de ce travail, des changements conformationnels ont été identifiés sur p47phox par protéolyse ménagée et échange H/D couplés à la spectrométrie de masse (DXMS). Le relargage de l’AIR, entraînant une meilleure accessibilité du site d’interaction avec p22phox, a été confirmé et caractérisé d’un point de vue structural et fonctionnel sur protéine entière. De plus, une surface inédite contrôlant l’état autoinhibé a été mise en évidence. La mutagénèse dirigée au sein de cette surface a permis de confirmer cette hypothèse en identifiant deux résidus clés (R162 et D166) responsables de cette autoinhibition et donc susceptibles d’être de futurs candidats de cibles thérapeutiques. Les propriétés d’interactions relatives des divers mutants avec GST-p22phox Cter et des liposomes ont été testées par BiacoreTM et cosédimentation, respectivement. L’identification de ces résidus a permis de mieux comprendre le mécanisme d’activation de p47phox, et notamment comment le démasquage de l’AIR phosphorylée entraîne celui du domaine PX. Enfin, une étude méthodologique a montré que la plasmepsine 2 de P. falciparum était un nouvel outil susceptible d’améliorer la résolution du DXMS.Axe thématique :Immunité
ILL4 building - meeting room (doors 126/163) - first floor
– ESRF Auditorium, Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
РSalle de conf̩rences, Grenoble Institut des Neurosciences (GIN)
Building. Edmond J. Safra, Chemin Fortune Ferrini CHU, La Tronche. tram stop: Hôpital A. Michallon.
Metabotropic glutamate receptors are GPCRs modulating synaptic transmission either at the pre- or post-synaptic level. They play important roles in the brain, and are the matter of intense research for the discovery of new drugs for the treatment of various psychiatric and neurologic disorders.
Like any other GPCRs, mGluRs possess a 7TM domain responsible for G-protein activation, but the agonist binding site is located in a Venus Flytrap domain (VFT) connected to the 7TM domain via a cystein-rich domain (CRD). Not only are these receptors activated and inhibited by agonists and antagonists, but screening campaigns led to the discovery of highly selective allosteric modulators, either inhibiting or potentiating the action of agonists. The positive allosteric modulators represent an attractive alternative to agonists in drug development.
Within the last years, we have been elucidating the functioning of these receptors at the molecular and structural level, identifying the mechanism of action of both orthosteric and allosteric compounds. Whereas agonists act by stabilizing a closed state of the VFT, positive allosteric modulators stabilize the active state of the 7TM domain. More recently, we identified the mechanism responsible for the allosteric coupling between the VFT and the 7TM domains. We show that the dimeric organization of these receptors is required for function, and that a relative movement of the VFTs is associated with the agonist-induced activation. Then G-protein activation likely requires two important changes in the dimer: a change in conformation in one 7TM, and a change in the relative position of the 7TM domains.
Such a complex functioning of mGluRs offers a number of possibilities to develop new drugs modulating their activity. In collaboration with F Acher (Paris), we are using these information to identify new compounds specifically acting at a specific mGluR subtype, and study its implication in pain (A Eschalier, Clermont-Ferrand) and Parkinson’s disease (M Amalric, Marseille).
– Contact: michel.dewaard@ujf-grenoble.fr
– IBS seminar room
hosted by D. Skoufias (IBS)
– IBS seminar room
hosted by P. Frachet (IBS)
– IBS seminar room
– IBS seminar room
hosted by T. Vernet
– Conf. Room 1st Floor, ILL4
– Computer simulation techniques are an important tool for understanding how the dynamics of a biomolecule leads to its function. All-atom simulations, have developed into an indispensable tool to bridge the gap between theory and experiment, as will be illustrated in this talk. In particular, we focus on the interpretation of X-ray and neutron scattering experiments using normal-mode analysis.
In a first example, we concentrate on the low-frequency lattice vibrations of DNA and relate them to the base-pair opening. Next we address the softening effect of the protein dihydrofolate reductase (DHFR) dynamics upon ligand binding. Based on the quasiharmonic analysis we are also trying to provide the atomic-level explanation of the salt-concentration dependent aggregation mechanism of amyloid-beta protin fibril. At the end of the talk I will briefly present some simulation results on cholesterol/sphingomyelin bilayers suggesting the formation of a liquid-ordered phase above some critical concentration of cholesterol.
– ESRF Central Building room 500/501
– PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Hosted by Alexander Popov (ESRF)
– IBS seminar Room
hosted by M. Blackledge (IBS)
– CIBB Seminar Room
A variety of weak non-covalent interactions exist in biology. These interactions help stabilise secondary and tertiary structures and make critical contributions to biomolecular function. The focus of this talk will be a class of hydrogen bond-like interactions – so-called XH/π interactions – in which the acceptor group is a delocalised system of sp2-hybridised covalent bonds (e.g. aromatic systems, peptide bonds, etc). XH/π interactions were observed in some of the first macromolecular 3D structures and since then their structural and functional roles have been the subject of much debate. However, despite this long-standing interest, it has proven difficult to experimentally characterise these weak yet important interactions.
XH/Ï€ interactions are ideally suited for analysis by NMR spectroscopy. In particular, NMR spectroscopy has a near unique ability to detect and isolate signals arising from multiple different interactions in the same molecule. This capability can allow the donor and acceptor groups to be directly identified, even in the absence of a 3D structure. Furthermore, as each interaction can be monitored separately, it is possible to experimentally determine the functional or structural contribution of a single interaction. This talk will highlight several such approaches for identifying and characterising biologically-relevant XH/Ï€ interactions in proteins.
РAmphith̢̩tre Daniel Dautreppe, CEA Grenoble
On estime que la Terre a 4,5 milliards d’années et que les premiers microorganismes sont apparus environ un milliard d’années plus tard. À cette époque, la composition de l’atmosphère était très différente de celle de maintenant. En effet, le CO2 et le N2 étaient en concentration très importante avec une quantité significative d’H2. Par contre, elle manquait d’O2. Ce gaz est devenu un composant majeur de l’atmosphère uniquement après des éons d’activité photosynthétique par des cyanobactéries. En effet, l’oxygène est un produit secondaire du clivage de l’eau qui a lieu pendant la photosynthèse. Les premiers organismes vivants ont donc évolué dans un milieu anoxique.
Le processus vital dépend principalement de la synthèse de composés carbonés réduits et de leur utilisation pour générer l’énergie nécessaire à la vie. Il y a deux façons de concevoir la génération pré-biotique de ces composés : soit ils ont été synthétisés dans l’espace (ou sur terre par des phénomènes atmosphériques), soit ils ont été synthétisés, entre autre, à partir de la réduction du CO2 couplée à l’oxydation de l’hydrogène. Ces deux alternatives s’appellent respectivement la théorie « hétérotrophe » et la théorie « autotrophe » de l’origine de la vie sur terre.
Au laboratoire, nous avons déterminé la structure tridimensionnelle de plusieurs enzymes à fer-soufre, purifiées à partir de microorganismes anaérobies, qui catalysent des réactions « primordiales » telles que l’oxydation de l’H2 ou la réduction du CO2. Nos travaux favorisent la théorie « autotrophe » et sont aussi en accord avec l’idée que ces réactions ont eu lieu sur des sulfures telles que la pyrite (FeS2) ou la pyrrhotite (FeS). Ces différents points seront abordés au cours du séminaire.
Afin de limiter votre attente si vous venez de l’extérieur du CEA, contactez Odile Rossignol (tel. : 04 38 78 45 63 Email odile.rossignol@cea.fr) en précisant vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. Une autorisation d’entrée sera établie avant votre arrivée. Les auditeurs étrangers (hors CEE) sont invités à demander cette autorisation d’entrée au moins une semaine avant la date du séminaire. N’oubliez pas de vous munir d’une pièce d’identité.
– CIBB Seminar Room
– For an entry badge, please contact villot@embl.fr
– Auditorium, Central Building
– Auditorium, Central Building
– IBS seminar Room
Adaptive immunity plays an essential role protecting vertebrates against a broad range of pathogens and cancer. The major histocompatibility complex (MHC) class I-dependent pathway of antigen presentation represents a sophisticated strategy to recognize and eliminate infected or malignantly transformed cells, taking advantage of the constant proteasomal turnover of the cellular proteome. The transporter associated with antigen processing (TAP1/2, ABCB2/3) is a crucial component of this pathway, catalyzing the peptide translocation and loading of MHC I complexes in the ER-lumen. The peptideloading complex (PLC) consists of the transporter associated with antigen processing TAP1/2, MHC I heavy chain, b2-microglobulin, calreticulin, the disulfide isomerase ERp57, and the adapter protein tapasin. The molecular mechanism of the antigen translocation machinery, the structural organization of the macromolecular peptide-loading complex, and various modes of regulation during differentiation of dendritic cells and by newly identified viral factor will be discussed.
– IBS Seminar Room
Glycerolmonolinolein (MLO), Glycerolmonoolein (GMO), Phytantriol (PT) and a few other
lipophilic molecules self-assemble in bulk in presence of water to form well defined liquid
crystalline phases. Their structure can be tuned by temperature variation and/or by addition
of oils. This leads to gel-like or fluid systems with a large internal interface between water
and oil domains with different viscosities. These nanostructured phases can be dispersed
in the excess water phase by addition of an external stabilizer and energy input leading
to internally self-assembled particles, so-called ISAsomes. These ISAsomes are potential
carrier systems for hydrophilic, amphiphilic and lipophilic functional molecules.
The hierarchical structure can be extended to a next level by gellifying the continuous
aqueous phase by the addition of polymers like k–Carrageenan. This leads to a new type
of hydrogel, loaded with ISAsomes. Differently to the original oil-continuous bulk phase,
the viscosity of this, now water-continuous, system can be varied in a wide range by
composition. These gels can even be dried into foils and re-dispersed.
Finally, we can use the oil-continuous bulk phase to create concentrated, stable water in oil
emulsions having a paste-like consistency with a water content of up to 90% by volume.
The possibilities for applications of the different systems will be discussed.
– IBS seminar room
As a first topic, recent developments in biological neutron and X-ray small angle scattering
(SANS/SAXS) are presented as well as the benefit of combining them with complementary
techniques (with a focus on NMR). The issues of uniqueness, accuracy and exhaustive
sampling of possible structural models will be discussed as a function of structural restraints
available and experimental errors.
As a second topic, the benefit of combining the specific scattering properties of neutrons
and X-rays will be illustrated by a SAXS/SANS study on the interaction of urea with ubiquitin
during the solvent-induced denaturation process.
As a third and last topic, recent developments in neutron spectroscopy for the study
of biomacromolecular and solvent dynamics on the pico/nanosecond timescale and the
Ångström lengthscale will be presented. The possibilities to focus specifically on different
types of atomic motions in complex biological samples (proteins in solution, entire biological
cells) as well as the benefit of combining data from several instruments with different
energy resolutions and wave vector transfers will be discussed.
Finally, future perspectives and possible applications of all three topics will be
presented.
– Institut Jean Roget:
РSalle de Conf̩rence du 5̬me Etage - Campus Sant̩ - Domaine de la Merci - LA TRONCHE
– http://www-ijr.ujf-grenoble.fr/seminars_d.php?oid=467
– Amphitheatre DAUTREPPE (CEA)
– The protein kinase superfamily is one of the largest and most important for biology. These enzymes, which serve as
master switches for regulating a myriad of biological functions, are not only catalysts that mediate the transfer of a
phosphate from ATP to protein substrates but also scaffolds that mediate protein:protein interactions. PKA, one of the
best understood members of this family, serves in many ways as a prototype for the family. The PKA catalytic (C)
subunits are assembled as fully active phosphorylated enzymes that are kept in an inactive state by association with
dimeric regulatory (R) subunits. The tetrameric holoenzyme is activated by the second messenger, cAMP, binding to
the regulatory subunits. With the C subunit we see not only how the enzyme opens and closes as it goes through a
catalytic cycle but also how the presence of a single phosphate assembles a stable, fully active enzyme where the small
and large lobes are linked by a set of two hrydrophobic spines. Although crystal structures of R and C subunits have
been solved previously, recent structures of holoenzyme complexes between R and C subunits demonstrate the
remarkable conformational maleability of the R subunits as they shuttle between two very different but stable
conformational states, one bound to cAMP and the other to the catalytic subunit. These holoenzyme complexes reveal
for the first time how this highly allosteric switch mechanism is mediated. The regulatory subunits not only bind to
cAMP and the catalytic subunits but also to A Kinase Anchoring Proteins (AKAPs) through their dimerization docking
domain. This targeting mechanism localizes PKA to specific sites within the cell.
for a site entry, contact odile.rossignol@cea.fr
– ICMG
РB̢timent E Andr̩ Rassat, Salle de Conf̩rences, rez de chauss̩e, DU
salle de conférence de l’IAB
Amphithéâtre Daniel Dautreppe (CEA)
contact in advance odile.rossignol@cea.fr for a badge
– IBS Seminar Room
Cys-loop receptors mediate neuronal communication in the brain and include nicotinic
acetylcholine, glycine and GABAA receptors. These proteins are integral transmembrane
channels that open in response to neurotransmitter binding. I will present our recent work
on bacterial ancestors of these proteins, their function, X-ray structure, and what can be
deduced regarding their functional architecture and allosteric transitions.
Bocquet et al, Nature, 445: 116-9 (2007)
Bocquet et al, Nature, 457 :111-4 (2009)
Nury et al, J Mol Biol. 395, 1114–1127 (2010)
Nury et al, Proc Natl Acad Sci U S A. 107:6275-80 (2010)
– IBS seminar Room
– CIBB Seminar Room
– EMBL seminar Room
Structure determination of large proteins and protein assemblies is a major challenge in molecular biology. Experiments often yield only low resolution or sparse data, which are not sufficient to fully determine atomistic structures. We have, therefore, developed a general geometry-based algorithm that efficiently refines structures and samples their conformational space under constraints imposed by low-resolution experimental data, in particular, low-resolution electron density maps obtained from electron microscopy or x-ray crystallography experiments. In addition, prior structural knowledge is used to contribute information that is missing from the data and to guide the conformational sampling and refinement; this dramatically reduces the over-fitting problem, which is more severe at low resolution. Applications to protein structure refinement using crystallographic data as well as density maps obtained from single-particle cryo-electron microscopy demonstrate the scope of this approach.
http://www.nature.com/nature/journal/v464/n7292/full/nature08892.html
On the 9th of July at 9:30am in the EMBL seminar room, a ’tutorial’ on DEN refinement with CNS and DEN refinement with DireX will be organised (Gunnnar Schroader’s newly developed program).
hosted by A. McCarthy (EMBL)
– IBS seminar Room
As formalized by Maynard-Smith, major evolutionary transitions of function and structure
must occur gradually, and smoothly, through functional intermediates states. However,
the nature of such transitions and intermediates remains largely unknown. To explore this
process, we have used laboratory evolution to generate a complete trajectory: starting
from a promiscuous aryl esterase activity (kcat/KM = 1.4×102), 105 fold less efficient
than the native activity of a phosphotriesterase, incremental sequence changes gradually
produced a smooth ‘functional switch’, involving a 4×108-fold reversal in the relative
catalytic efficiencies, generating an efficient aryl esterase (kcat/KM = 5 x 106). Structural
analysis has been used to investigate the structure-function relationship, revealing the
‘smoothness’ of the transition is based upon the ability of the protein to adopt a range of
conformations with different catalytic properties. In this sense, evolution of new function
can be viewed as a gradual shift in the conformational equilibrium of an enzyme, rather
than a series of discrete changes.
Axe
– IAB Seminar Room
– IBS Seminar Room
hosted by P. Masson (IBS)
– IBS seminar room
Bacterial viruses are macromolecular machines whose assembly and activation are highly regulated within the host bacterium. Upon infection bacteriophages bind a specific receptor and transfer their genome into the bacterium. Viral genome and proteins are synthesized within the host cytoplasm leading to the formation of new viral particles that are released by lysis of the infected bacteria. Despite diversification in detail, the assembly and maturation of bacteriophages follows the same basic pathways. Common features for dsDNA bacteriophages include: (i) assembly of an icosahedral procapsid from several hundred of copies of a capsid protein (ii) integration of the portal at one vertex of the capsid. This dodecameric protein forms a channel required for packaging and release of the DNA and for tail attachment (iii) Packaging of the phage DNA into the capsid driven by a molecular motor, the terminase (iv) Attachment of the phage tail - assembled via a separate pathway - to the portal.
The Syphoviridae coliphage T5 shows several original features that make it an interesting model to investigate the mechanisms of genome ejection, capsid assembly, and DNA packaging. It differs from other members of this family by the large size of its genome (121 kbp) and of its icosahedral T=13 capsid (90 nm). We have been deciphering the early events of the assembly and maturation pathways of its capsid from a combination of genetics, biochemical and structural data (cryo-EM/image reconstruction and SAXS). I will present recent data obtained by in vitro and in vivo approaches that show how bacteriophage T5 will contribute to understand the process of capsid assembly.
– CIBB seminar Room
A wide variety of strategies, using a range of methods, exist to carry out quantitative proteomic analyses. The nature of the biological material, and the type of question asked, determine the choice of one method over another. Two types of complementary strategies can be distinguished: large-scale proteomics studies which may be with or without a priori, and quantitative studies targeted towards proteins of interest.
Large-scale studies are, by their essence naïve; they can, for example, be implemented for the analysis of the dynamics of a biological system as part of a kinetic study, or to determine the consequences of a mutation. This type of approach allows the discovery, with no preconceptions, of molecular actors involved in the biological mechanisms studied. In the clinical context, the same naïve approaches can be used to compare biological samples from healthy control patients to samples from patients suffering from a particular pathology; they will lead to the discovery of candidate biomarkers for the pathology in question.
As a second step, it is necessary to refine the knowledge derived from large-scale approaches by carrying out new analyses targeting the proteins of interest revealed by the naïve approach using methods which allow better quality data to be acquired. This can be done by using SRM (“Selected Reaction Monitoring†) mass spectrometry combined to adequate internal isotopically labeled standards.
My talk will present different quantitative analytical strategies that are currently being used in the EDyP Lab, especially in the context of the discovery and evaluation of bladder cancer biomarkers.
Room 216 Building 45, Lab. de Spectro. Physique, Campus,
contact: jocelyn.etienne@ujf-grenoble.fr
– Cermav, Conference room, 601 rue de la chimie, campus
Contact: Nishiyama@cermav.cnrs.fr
– ESRF Auditorium, Central Building
We have found a way to target tumors based on their elevated level of extracellular acidity. Acidosis is a hallmark of tumor development both at very early and at advanced stages. However, the acidic extracellular environment in tumors has not been properly explored yet probably due to a lack of compounds that dramatically change their properties in the range of pH 6.0-7.5. Recently we designed the pH Low Insertion Peptide (pHLIP), which acts as a bionanosyringe, it inserts in cellular membrane and forms transmembrane helix at acidic extracellular pH (6.0-6.5) but not at normal pH. Our data demonstrated that the fluorescently labeled pHLIP was accumulated in tumors established in mice. pHLIP can find cancer cells and insert itself in their membrane. No insertion occurs in normal cells (pH 7.4). pHLIP possesses dual delivery capabilities: it can inject and release cargo molecules into the cytoplasm and/or it can tether cargo molecules to the cell surface. In the first scenario, a cargo molecule is attached to the pHLIP C-terminus via a cleavable S-S bond while in the second it is conjugated to the N-terminus via a non-cleavable bond. Among molecules tethered for the surface of cancer cells in vivo are fluorescent dyes, PET and SPECT imaging agents. Among cell-impermeable molecules translocated across a cell membrane are cyclic peptides, toxin – phalloidin and PNAs. Our technology opens the new opportunity to target cancer tumors with high selectivity and decreased side effects.
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE
ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Requests made by e-mail will be confirmed. If you do not receive a
confirmation e-mail, please contact us by phone.
Hosted by Narayanan Theyencheri (ESRF)
– CIBB Seminar Room
We are studying the molecular events that occur when a peptide inserts across a membrane or exits from it. Using pH jumps to trigger insertion/exit of the pHLIP (pH Low Insertion Peptide) to enable kinetic analysis, we show that insertion occurs in several steps, with rapid (0.1 sec) interfacial helix formation followed by a much slower (100 sec) insertion pathway to form a transmembrane helix. The reverse process of unfolding and peptide exit from the bilayer core, which can be induced by a rapid pH jump from acidic to basic, proceeds much faster than folding/insertion and through different intermediate states. In the exit pathway, the helix-coil transition is initiated while the polypeptide is still inside the membrane. We also designed two pHLIP-variants where Asp and Glu residues were removed from the C-terminus, which inserts across the membrane. The variants preserve the same pH-dependent properties of pHLIP peptide interaction with the membrane, but insertion occurs 10-100 times faster than in the case of the parent pHLIP peptide. A kinetic model of peptide-membrane insertion/folding and exit/unfolding will be discussed.
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE
ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Requests made by e-mail will be confirmed. If you do not receive a
confirmation e-mail, please contact us by phone.
Hosted by Narayanan Theyencheri (ESRF)
CEA Grenoble, Amphithéâtre Daniel Dautreppe,
– please contact odile.rossignol@cea.fr for an entry badge
– IBS seminar Room
Les protéines fluorescentes présentent des caractéristiques photophysiques (rendement
quantique, durées de vie de fluorescence, sensibilité au pH…) variées pour un même
chromophore et des changements structuraux limités. La compréhension à l’échelle
moléculaire des mécanismes sous-jacents peut se nourrir efficacement de la modélisation
de ces systèmes. Dans ce séminaire, l’étude de la dynamique du chromophore à l’état
excité dans la protéine GFP ou certains mutants sera analysée grâce au développement
d’une approche théorique couvrant plusieurs échelles de temps. Il apparaît qu’un dialogue
théorie-expérience est indispensable pour optimiser les modes d’exploration des surfaces
à la recherche du ou des ‘chemins de réaction’.
– IBS seminar Room
Le rôle de C1q dans l’immunité est aujourd’hui revisité par le décryptage en cours des
mécanismes de l’élimination des cellules du soi altéré. Secrété par les macrophages et
les cellules dendritiques immatures, C1q sert de harpon au phagocyte pour la pêche aux
cellules à éliminer tout en modulant la réponse immune adaptée. Le point sera fait sur
ses ligands avérés ou supposés à la surface des deux cellules en présence, le phagocyte
et la cellule cible. Mauvaise nouvelle: les pathogènes savent probablement cela depuis
longtemps et l’utilisent aujourd’hui pour se mettre à couvert, ou pire!
Axe
– EMBL Seminar Room,
Host: Eva Maria Geenen
– EMBL seminar room
Hosted by Michael Lipp (EMBL)
– ESRF Central Building room 500 - 501
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Requests made by e-mail will be confirmed. If you do not receive a confirmation e-mail, please contact us by phone.
– IBS seminar Room
hosted by M. Blackledge (IBS)
– EMBL Seminar Room
Host: Imre Berger
– EMBL Seminar Room,
Host: Christiane Schaffitzel
РSalle de conf̩rences, Grenoble Institut des Neurosciences (GIN)
A complex molecular assembly accounts for receptor accumulation at synapses and “synaptic plasticity†derives partly from modifications of postsynaptic receptor number resulting from receptor trafficking. New concepts now emerge from imaging of receptor movements at the single molecule level.
Inhibitory glycine or GABA receptors, and the excitatory AMPA and NMDA glutamate receptors are mobile in synapses, switch between extrasynaptic and synaptic localizations by lateral diffusion and can be exchanged between synapses through lateral diffusion in the plane of the extrasynaptic plasma membrane. This dynamic behavior can be tuned by the cytoskeleton or by the synaptic activity. This diffusive behavior, provides a new framework for the understanding of synaptic strength regulations.
I will present recent data on the regulation of the diffusive properties of inhibitory receptors which provide new mechanisms underlying the modifications of the excitation–inhibition balance during the so-called plasticity within neuronal networks. I will also show how mGluR diffusion is affected by a-beta oligomeres and how this can be at the origin of defects seen in Alzheimer disease.
– Contact: claude.feuerstein@ujf-grenoble.fr
– EMBL Seminar Room
Host: Imre Berger
– IBS seminar room
TLR4 and MD-2 form a heterodimer that recognizes LPS from Gram negative bacteria. Eritoran is
a candidate anti-sepsis drug that antagonizes LPS activity by binding to the TLR4-MD-2 complex.
We determined the crystal structures of TLR4-MD-2 in complex with Eritoran and LPS. TLR4 is
an atypical member of the LRR family and is composed of N-terminal, central and C-terminal
domains. The b sheet of the central domain shows unusually small radii and large twist angles.
MD-2 binds to the concave surface of the N-terminal and central domains. Agonistic LPS induced
the formation of an “m†-shaped receptor multimer composed of two copies of the TLR4-MD-2-LPS
complex arranged in a symmetrical fashion. LPS interacts with a large hydrophobic pocket in MD-2
and directly bridges the two components of the multimer. Five of the six lipid chains of LPS are
buried deep inside the pocket and the remaining chain is exposed to the surface of MD-2, forming
a hydrophobic interaction with the conserved phenylalanines of TLR4. The F126 loop of MD-2
undergoes localized structural change and supports this core hydrophobic interface by making
hydrophilic interactions with TLR4. Eritoran binds to the LPS pocket in MD-2 and blocks LPS binding
and TLR4-MD-2 heterotetramerization. Structural comparison of the TLR4-MD-2-LPS complex with
the TLR4-MD-2-Eritoran complex indicates that two additional lipid chains in LPS displace the
phosphorylated glucosamine backbone towards the solvent area by 5 angstrom. This structural
shift allows phosphate groups of LPS to contribute to receptor multimerization by forming ionic
interactions with a cluster of positively charged residues in TLR4 and MD-2. The TLR4-MD-2-LPS
structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by
the TLR family, which is essential for defense against diverse microbial infection. We propose that
formation of the TLR dimer brings the intracellular TIR domains close to each other to promote
dimerization and initiate signaling.
Host: C. Petosa
– IBS seminar Room
As formalized by Maynard-Smith, major evolutionary transitions of function and structure
must occur gradually, and smoothly, through functional intermediates states. However,
the nature of such transitions and intermediates remains largely unknown. To explore this
process, we have used laboratory evolution to generate a complete trajectory: starting
from a promiscuous aryl esterase activity (kcat/KM = 1.4×102), 105 fold less efficient
than the native activity of a phosphotriesterase, incremental sequence changes gradually
produced a smooth ‘functional switch’, involving a 4×108-fold reversal in the relative
catalytic efficiencies, generating an efficient aryl esterase (kcat/KM = 5 x 106). Structural
analysis has been used to investigate the structure-function relationship, revealing the
‘smoothness’ of the transition is based upon the ability of the protein to adopt a range of
conformations with different catalytic properties. In this sense, evolution of new function
can be viewed as a gradual shift in the conformational equilibrium of an enzyme, rather
than a series of discrete changes.
Axe
– IBS seminar room
Archaea, prokaryotes representing the third domain of life, often thrive under conditions
approaching the physical limits of life (high temperature and salinity), which continuously
attack the integrity of the genetic material. To understand how these fascinating organisms
efficiently duplicate and repair their chromosomes under extreme conditions, we have
been working on the identification and characterization of protein complexes required
for genome maintenance in hyperthermophilic and halophilic archaea. This presentation
will summarize how our work has led to the discovery of a novel family of DNA metabolic
enzymes and DNA repair endonucleases. Special attention will be given to the structural
(crystallography, SAXS) and functional characterization of these previously uncharacterized
enzymes. Moreover, in a second part of my talk, I will discuss how our work has led to the
unexpected discovery of a new drug target and provided the structural basis for rational
design of anti-microbial compounds
host: Bruno Franzetti (IBS)
– Room 158, 1st floor, ILL4.
Chagas disease is caused by a parasite (Trypanosoma cruzi). It affects 18 million people in the American continent and there is no cure for it. One possible strategy to combat parasitic diseases is the search for molecules that perturb the function of enzymes. In turn, the target enzyme might be exclusive of the parasite or exist in both, the parasite and the host. In the later case, the molecule that is sought must be selective for the enzyme of the parasite, leaving intact that of the human host. We have followed this approach, choosing as the target protein Triosephosphate Isomerase (TIM). TIM is a homodimer, each subunit having 250 amino acid residues and folding into a (b/a)8 domain. Although the catalytic residues are self-contained in each monomer, only dimers are active. TIM catalyzes the fifth step of glycolysis, ensuring the net production of ATP in the conversion of glucose to pyruvate and, hence, it is essential for maintaining life under anaerobic conditions. Inhibiting the TIM of Trypanosoma cruzi (TcTIM), leaving functional the TIM of human (hTIM), would produce the elimination of the parasite infecting the human. We have found several molecules (having in common the benzothiazol chemical group) that able to inhibit TcTIM with a high level of selectivity, i.e. they barely inhibit hTIM. Using calorimetric and biochemical methods (and in one case, crystallographic information), we have characterized the action of the inhibitors. A salient result is that the inhibitors are more effective at low than at high protein concentrations indicating that they perturb the association between the two TcTIM monomers. This is consistent with the fact that the interface of TcTIM (an area of about 1400 Ã…2) that might be binding the inhibitor and its equivalent region in hTIM differ in amino acid composition and hydrophobic packing. Our working hypothesis is then that the inhibitors displace the dimer-monomer equilibrium towards inactive monomers, by binding into the dimer interface. To design better inhibitors, it would be very useful to characterize the dimer to monomer dissociation constants TcTIM and hTIM. However, this is a difficult task since TIM activity essays indicate that TIM dissociation occurs at very low concentrations (10-7-10-8 M), precluding the use of techniques such as fluorescence, circular dichroism or highly-sensitive calorimetry. As an alternative, assuming that TIM dimers might dissociate at the liquid/air interface, we have measured the dynamic surface tensions of TIMs at several concentrations.
PhD Defence
– CEA Amphi Dautreppe
Рcontactez Odile Rossignol (t̩l. 04.38.78.45.63 - Email: odile.rossignol@cea.fr).
Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– CEA Room C3/104
Please contact Odile Rossignol for a site access (odile.rossignol@cea.fr, 04 38 78 45 63)
– IBS seminar room
HDR defence: The short is: “a lot†. It was transient absorption spectroscopy on geminate recombination
in myoglobin that led Hans Frauenfelder to constructing his picture of protein’s hierarchical
energy landscape. And even before that (in 1973), Joseph Lakowicz and Gregorio Weber at
UIUC used quenching of tryptophan fluorescence by oxygen diffusing to solvent-inaccessible
protein regions to conclude that “proteins, in general, undergo rapid structural fluctuations
on the nanosecond time scale “ .
The not-so-short answer is that the present HDR thesis is written at a point where, after a
decade of applying transient absorption spectroscopy to understand light induced electron
transfer in a variety of enzymes, I am about to change the angle of attack and ask how
these techniques and enzymes could be of help to solve some problems that are addressed
in the IBS environment, namely protein dynamics, both structural and functional.
It is for this reason that the answer will have to be delayed to the third and final part, “future†,
that deals with the perspectives. Meanwhile, the first part, “past†, is dedicated to showing
on the example of the “paradigm†enzyme –DNA photolyase-, what transient absorption
spectroscopy is capable of and the middle part, “present†dresses a very short review into
the literature on protein dynamics. In the final section, I will delineate ways how optical
spectroscopy could interact with projects existing or emerging in the protein dynamics
community at IBS and thus contribute elements of an answer to the title question.
Axe
– room 337, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
Hosted by Sean McSweeney
РWhere: Institut Jean Roget, Salle de Conf̩rence (5th Floor),
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
– IBS seminar room
– IBS seminar room
– IBS seminar room
– IBS seminar room
The pneumococcus can colonize asymptomatically its host but bacterial
carriage is believed to be a prerequisite and precede the development of
invasive infections. Up to 70% of children attending daycare centers,
are carrying this potentially devatasting pathogen in their
nasopharynx. However, both the microbial and host factors that influence
the establishment of asymptomatic carriage and/or facilitate invasive
infections are not clearly defined. It is, therefore, imperative to
increase our understanding of both host responses against pneumococci
and immune evasion mechanisms developed by the pneumococcus. These
knowledge are fundamental to improve diagnostics and foremost treatment
of infectious diseases, including development of new preventive and
therapeutic strategies. The data that I will present will address these
aspects with a focus on the role of the Toll-like receptors in
pneumococcal infections, the role of the CXC chemokines as mucosal
antibiotics and the strategies of complement evasion by the pneumococcus.
– room 337, Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Isabelle Combe tel +33 (0)438 88-19-92.
hosted by S. McSweeney
– 14:00 ILL Chadwick Amphitheatre
NB:
The policy of ILL for delivering badges should change in January 2011. In order to prevent any problems at the site gates, if you plan to attend the seminar, PLEASE fill up the form for a badge request and send it back to Elena Colas (ecolas@embl.fr) before the 10th January 2011, 12:00
Hosted by Patricia Renesto (UVHCI)
Les séminaires ont lieu à 11h. dans la salle de conférence de l’Institut Albert Bonniot, Rond Point de La Chatourne, 38700 La Tronche.
http://www-iab.ujf-grenoble.fr
Les séminaires ont lieu à 11h. dans la salle de conférence de l’Institut Albert Bonniot, Rond Point de La Chatourne, 38700 La Tronche.
– room 500 - 501, ESRF Central Building
– Abstract
– IBS seminar room
host: M. Blackledge (IBS)
– ILL Chadwick Amphitheatre
Webpage of stephen West
host: Simone Pellegrino (ESRF)
– CEA, room C3-104.
Functional genomics approaches are indispensable tools in the drug discovery arena and, with the malaria parasite Plasmodium genus having the most species sequenced of any eukaryotic organism so far, the Plasmodia could provide unique opportunities for the study of intracellular eukaryotic pathogens. The application of functional genomics to post-genomics research of Plasmodia is providing remarkable fingerprints of specific drug actions in the parasite and thus provide information on mode of action of novel antimalarials. As such, evidence of the antimalarial properties of herbicide-derived compounds will be presented.
for a site access, contact odile.rossignol@cea.fr (04.38.78.45.63)
– IBS seminar room
host: J. Boisbouvier
– IBS seminar room
Hirofumi Shimizu is a visting scientist at the ESRF for one year. He is working on innovative ways to study the dynamics of membrane proteins, transporters and ion channels. He will present his current work on the study of K channels using attached gold nanocrystal and irradiation with white X-rays to track conformational changes induced by a modulator in real time.
Ref: Shimizu H, Iwamoto M, Konno T, Nihei A, Sasaki YC, Oiki S (2008) Global twisting motion of single molecular KcsA potassium channel upon Gating. Cell 132: 67-78
hosted by Michel Vivaudou (IBS)
РInstitut Jean Roget, Salle de Conf̩rence du 5̬me Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Pour y accéder: Prenez l’ascenseur sud.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
Recent studies indicate that bacterial gene expression is coordinated by a global regulatory network, involving
DNA topoisomerases, chromatin proteins (mainly H-NS and Fis) and the RNA polymerase with associated
factors. The bacterial genetic response to a challenge, including the exposure to drugs or changes in the
environmental conditions, thus depends on how this network is poised. Dickeya dadantii (formely Erwinia
chrysanthemi) is an enterobacteria responsible for the soft rot disease of many plants of agricultural importance
such as potato, carrot, chicory, African violet, etc… Its pathogenicity is characterized by a rapid necrosis of
parenchymatous tissues and a broad host specificity. Soft rot symptoms are mainly associated with the
synthesis of extracellular degradative enzymes, mostly pectate lyases (Pels), that will destroy the cell wall.
However, an efficient colonization of the plant requires additional factors such as production of
exopolysaccharides, iron assimilation and proteins able to fight the plant defense reactions. I will show that the
transcription of the D. dadantii virulence genes is modulated by a complex regulatory network involving various
regulators, the activity of which is modulated by different stimuli such as pectic compounds (KdgR), growth
phase (Fis), catabolic repression (CRP), temperature and nutritional starvation (H-NS and Fis). I will also show
that the expression of the virulence genes is modulated by changes in the DNA topology and that H-NS and Fis
adjust the global structural modifications of the chromatin at the virulence gene promoters in order to optimize
their expression. A dynamic model of the regulatory network controlling plant infection will be presented.
РInstitut Jean Roget, Salle de Conf̩rence du 5̬me Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Pour y accéder: Prenez l’ascenseur sud.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
Malaria pathology is caused exclusively by Plasmodium blood stages and is preceded by a clinically silent
parasite expansion phase in the liver. This pre-erythrocytic phase ranges from sporozoite delivery via infected
mosquitoes to merozoite egress out of an infected hepatocyte. The identification of parasite-encoded molecules
that drive this developmental program offers opportunities for novel malaria intervention strategies. Using
experimental genetics we analyze the cellular roles of sporozoite- and liver stage- specific proteins. These
studies led to the identification of key molecules for parasite motility and intracellular growth. In experimental
animal models, lasting sterilizing immunity against re-infection can be elicited with arrested Plasmodium liver
stages. I will discuss our recent findings on Plasmodium sporozoite and liver stage biology.
Our group: Our laboratory employs experimental genetics to study Plasmodium gene functions. We want to
contribute to the understanding of the molecular mechanisms that drive Plasmodium life cycle progression,
including parasite motility, invasion and egress. Some of the knockout strains turn out to be useful tools to study
parasite/host interactions and protective immune responses. We hope to eventually translate our findings to the
human pathogens and engage in joint projects with teams working in malaria-endemic areas.
– CEA Amphi Dautreppe
Рcontactez Odile Rossignol (t̩l. 04.38.78.45.63 - Email: odile.rossignol@cea.fr).
Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– CEA Amphi Dautreppe
Рcontactez Odile Rossignol (t̩l. 04.38.78.45.63 - Email: odile.rossignol@cea.fr).
Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS seminar room
Pseudomonas aeruginosa is the third most common cause of nosocomial infections and
causes chronic infection of patients with cystic fibrosis (CF), leading to a reduced life
expectancy. Its pathogenicity relies on a type III secretion system (T3SS) which enables
the bacterium to inject toxins directly into the cytoplasm of eukaryotic cells. ExoU is
one of the major toxins injected by the T3SS. In the bacterial cytoplasm, ExoU forms a
stable complex with its chaperone SpcU. After secretion, the toxin has been shown to
associate with the plasma membrane of the target cell, where it acts as a phospholipase.
An ubiquitinylated form of ExoU has been identified, but the significance of this modification
remains to be determined.
We have purified a truncated form of ExoU stabilised by its chaperone SpcU, and obtained
crystals of the complex that diffract at 4 A. We also developed an in vivo system of detection
of the ubiquitinylated form of ExoU, which will enable us to further explore the outcome
of ExoU in the eukaryotic cell. Ubiquitinylation of a bacterial protein is a remarkable
adaptation to life from another kingdom, and the deciphering of this phenomenon will
offer new insights into the mechanisms of bacterial pathogenicity.
– EMBL seminar room
– IBS seminar room
Host: E. Pebay-Peyroula (IBS)
– IBS seminar room
– room 03-1-14, Experimental Hall
Visitors from off-site please contact Isabelle Combe Ph +33 (0)438 88-19-92 to arrange for a gate pass.
Requests made by e-mail will be confirmed. If you do not receive a confirmation e-mail, please contact us by phone.
– ILL Chadwick Amphitheatre
Faculté de Médecine Pharmacie, amphi Boucherle, La Tronche, (contact: zohra.termache@cea.fr)
– CIBB Seminar Room
It is becoming increasingly clear that protein structure does not, in and of itself, provide all the necessary information to understand protein function. Dynamics and disorder contribute significantly to the directed activities of many, if not all, proteins. Proteins in solution undergo structural fluctuations that generate an ensemble of structures populating low energy pathways that correspond to functionally important conformational transitions. Study of those fluctuations provides insight into the form of these transitions and the nature of the dynamic motions of the protein. In this talk I will describe our use of neutron spin echo spectroscopy to study the dynamics of hemoglobin and myoglobin. Comparison of the behavior of these two proteins makes possible the identification of relaxations that correspond to the relative motions of subunits - motions that occur in hemoglobin but not myoglobin. The molecular basis of function in these two proteins was established 40 years ago, but recently has come under renewed scrutiny. Our observations provide new insights into this intriguing controversy.
External visitors may ask for a site access to Karine Sultan (sultan@ill.fr).
hosted by College 8
– ESRF Auditorium - Central Building
In this talk, Prof. Hong Ding will give an overview introduction of synchrotron development in China, mainly focusing on future plan of the new 3.5-GeV Shanghai Synchrotron Radiation Facility and the proposed 5-GeV Beijing Advanced Synchrotron.
For a site access request, please contact romero@esrf.fr
– Seminar Room, 5th floor.
The persistence of the human malaria parasite Plasmodium falciparum during blood stage proliferation in its
host depends on the successive expression of variant molecules at the surface of infected erythrocytes. This
variation is mediated by the differential control of a family of surface molecules termed PfEMP1 encoded by
approximately 60 var genes. Each individual parasite expresses a single var gene at a time, maintaining all
other members of the family in a transcriptionally silent state. PfEMP1/var enables parasitized erythrocytes to
adhere within the microvasculature, resulting in severe disease. I will highlight key regulatory mechanisms
critical for monoallelic expression of var genes. Antigenic variation is orchestrated by epigenetic factors
including monoallelic var transcription at separate spatial domains at the nuclear periphery, differential histone
marks on otherwise identical var genes, and var silencing mediated by telomeric heterochromatin
– Seminar room, 5th floor
– Seminar room, 5th floor
– Seminar room, 5th floor
– CEA Amphitheatre DAUTREPPE
– for a site access, contact Odile Rossignol (04.38.78.45.63 - Email: odile.rossignol@cea.fr
– CEA Amphitheatre DAUTREPPE,
– for a site access, contact Odile Rossignol (04.38.78.45.63 - Email: odile.rossignol@cea.fr)
– ESRF Auditorium
– from 13:30 to 17:00
– Please Download the program
– Peer Bork (EMBL, Heidelberg)
– Chris Tyler-Smith (Wellcome Trust Sanger Institute, Hinxton)
– Jean Weissenbach (Genopole, Paris)
– IBS seminar room
– IBS seminar room
– IBS seminar room
Structural biology is a very successful sub-field of the life-sciences. Technical innovations,
including constant improvements surrounding the use of synchrotron radiation, have
contributed to an extended acceleration in the rate at which new structures are determined.
Nevertheless, all enzymes undergo conformational changes during their reaction cycles
and an X-ray structure of a resting conformation alone describes only the starting point
for the reaction. Time-resolved structural studies of protein reaction dynamics aim to
elucidate the conformational changes occurring in proteins and thereby elucidate the
chemical details of their reaction mechanism.
In this presentation I will describe two different approaches to studying the structural
dynamics of membrane proteins. I will first present structural results from time-resolved
Laue diffraction studies of a photosynthetic reaction centre using 3D crystals. Thereafter I
will describe the method of time-resolved wide angle X-ray scattering applied to the study
of detergent solubilised bacteriorhodpsin in solution. I argue that this latter method, in
particular, offers a promising approach to study, at low-resolution, the structural dynamics
of a broad range of biological systems using synchrotron radiation. Finally I touch on the
implications of developing X-ray free electron lasers on the field of time-resolved structural
biology.
– IBS seminar room
Biological macromolecules are, by essence, dynamical systems. While the importance
of this flexibility is nowadays well established, the accurate characterization of the
conformational disorder of these systems remains an important challenge. Nuclear
magnetic resonance spectroscopy is a unique tool to probe these motions at atomic level,
through the analysis of spin relaxation or residual dipolar couplings. The latter allows all
motions occurring at timescales faster than the millisecond to be investigated, including
physiologically important timescales. The information presents in those couplings is
interpreted here using mainly analytical approaches in order to quantify the amounts
of dynamics present in folded protein, to determine the direction of those motions and
to obtain structural information within this conformational disorder. These analytical
approaches are complemented by numerical methods, that allowed the observation of
phenomena from a different point of view or the investigation of other systems such
as intrinsically disordered proteins. All of these studies demonstrate an important
complementarity between structural order and conformational disorder.
– CIBB seminar room.
– EMBL seminar room
– CIBB seminar room
– IBS seminar room
– Institut Albert Bonniot, Seminar room, Dom. de la Merci, la Tronche, (contact: stephanie.renaud@ujf-grenoble.fr)
– Salle de conférence, bât. E – André Rassat, 470 rue de la Chimie, Campus,
(contact:pascale.maldivi@cea.fr)
Where: Institut Jean Roget, Salle de Conférence du 5ème Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
Where: Institut Jean Roget, Salle de Conférence du 5ème Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
Where: Salle de conférence, lnstitut de Biologie et de Pathologie,
Site Nord du CHU de Grenoble.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
– Neurosciences Institut, Grenoble
– contact: moutinm@ujf-grenoble.fr
– IBS seminar room
– IBS seminar room
– IBS seminar room
– IBS seminar room
– IBS seminar room
– CNRS Amphitheatre
– Afin de limiter votre attente si vous venez de l’extérieur du CEA, contactez Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr ; une autorisation d’entrée sera établie avant votre arrivée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. Les auditeurs étrangers (hors CEE) sont invités à demander cette autorisation d’entrée au moins une semaine avant la date du séminaire. N’oubliez pas de vous munir d’une pièce d’identité.
– EMBL seminar room
CEA Grenoble - conference room C5-421A
PLEASE REQUEST A SITE ACCESS in advance and Contact: Sabine HEDIGER - 04 38 78 68 12
– CIBB seminar room
Disruption of cellular membranes is a very efficient way to alter cellular function and pore-forming toxins are well known as important bacterial virulence factors. Actinoporins are effective pore-forming toxins produced by sea anemones. They exclusively form pores in membranes that contain sphingomyelin. Actinoporins are an important example of so-called a-helical pore-forming toxins, since the final conductive pathway is formed by amphipatic a-helices. The pore formation is a multistep process that involves recognition of the membrane sphingomyelin, firm binding to the membrane accompanied with the transfer of the N-terminal region to the lipid-water interface and final pore formation after oligomerization of several monomers. We have recently shown that equinatoxin II, the most studied representative of actinoporins, specifically binds SM, but not other lipids, and described molecular mechanism of SM recognition. Ability of actinoporins to form transmembrane pores and selectively recognise important membrane lipids was exploited in some novel biomedical applications. Further studies on the oligomerization mechanism are needed to fully elucidate the pore formation at the molecular level.
External visitors may ask for a site access to Karine Sultan (sultan@ill.fr).
– Amphitheatre Boucherle, Batiment Jean Roget, Faculte de Medecine et Pharmacie (la Tronche)
– IBS seminar room
РAmphith̢̩tre du LPSC (53 rue des Martyrs, Grenoble)
Sur le très long terme, à l’échelle du milliard d’années, le climat de notre planète a été influencé par la lente augmentation de l’intensité lumineuse du soleil d’environ 30% depuis la naissance de la Terre. Et cependant ce que l’on sait de l’évolution des températures est tout sauf un réchauffement monotone à cette échelle de temps. Les forçages radiatifs « externes » (par exemple les variations de l’orbite de la Terre, la configuration des continents) et les variations de la composition atmosphérique (dues au volcanisme, aux gaz à effet de serre, aux aérosols…), partiellement issues des effets rétroactifs du système Terre, ont largement modulé la courbe de température de la planète et son évolution climatique. Et puis au cours des derniers siècles sont clairement apparues les perturbations anthropiques du bilan radiatif de la Terre (gaz à effet de serre, aérosols,…) , au point que certains définissent cette période comme une nouvelle ère géologique : « l’Anthropocène ».
L’objet de la conférence est de focaliser sur la période récente, la perturbation anthropique du cycle du carbone et ses effets sur le climat. On présentera l’état des connaissances du budget de carbone et de sa dynamique entre les différents réservoirs (océan, continent, atmosphère). Que sait-on des émissions anthropiques en CO2 et CH4 (énergies fossiles, pratiques agricoles, déforestation), de leur évolution temporelle, de leur distribution géographique, du devenir de ces émissions en terme de redistribution entre l’atmosphère et les puits océaniques et continentaux ?
L’effet climatique de la perturbation anthropique en gaz à effet de serre (CO2 , CH4 , N2 O, CFCs) peut être évalué à partir de modèles et comparé aux effets provenant des autres forçages radiatifs. Nous décrirons le type de modèles utilisés pour les projections climatiques et les stratégies d’évaluation de ces modèles. Nous insisterons en particulier sur la classe émergente des « Earth System Models » qui tentent de prendre en compte et reproduire les rétroactions entre le climat et le cycle de carbone.
– EMBL seminar room
– CIBB seminar room
The molecular chaperone Hsp90, assisted by a large number of
cochaperones, forms highly dynamic complexes with some 200 client proteins,
many of which are signaling molecules controlling cell homeostasis, proliferation,
differentiation and cell death. Among these clients are key regulators involved in all
six hallmarks of tumorigenesis explaining why Hsp90 became in recent years a
prime target for anti-cancer drug development.
We are interested in the molecular mechanism of the Hsp90 machinery focussing
on allosteric intra- and intermolecular regulation. To elucidate the mode of action of
this protein we use biochemical and biophysical methods and analyse mutant
proteins. In addition, we study the conformational dynamics of Hsp90 and its
cochaperones using amide hydrogen exchange combined with high-resolution
mass spectrometry and fluorescence spectroscopy. With these methods we are
able to resolve conformational changes in individual structural elements and define
allosteric pathways within Hsp90.
– EMBL seminar room
– EMBL seminar room
– CIBB seminar room
Water treatment is a serious challenge in both developed and developing countries. Aluminium salts, iron salts and synthetic polymers are the commonly used coagulants in the treatment. The cost, health issues and environmental side effects of these compounds are their main disadvantages. Therefore, it is imperative to find alternatives which are cheaper, more environmentally friendly and have minimal health concerns. The protein extract from Moringa oleifera (MO) seeds is advocated as one such alternative. However, the nature and mechanism of water treatment is not well understood.
This presentation is a review of the results of the studies we have done so far to address the fundamental colloidal questions about the protein from MO seeds. Lack of such information or data compromises the interpretation of biophysical parameters and its use in water treatment. A particular extraction and purification protocol reported in literature which results in the production of a coagulant protein with molecular weight of about 7 kDa and isoelectric pH between 10 and 11 has been used. A number of techniques have been used to study the properties of this protein especially in aqueous solution and these include: surface tension1,2, UV-Vis spectroscopy3, densitometry3, fluorescence1,4,5, fourier transform infrared5, circular dichroism (CD)5, capillary viscometry6, amino acid composition and elemental analysis7, neutron reflection (NR)7, zeta potential8, turbidity8 and dynamic light scattering (DLS)8. The techniques have been able to elucidate structure (primary, secondary and tertiary), conformational states and physiochemical properties as function of microenvironment (i.e. pH, ionic strength and added surfactant). The adsorption of the protein on silicon oxide and the effects of an anionic surfactant sodium dodecyl sulphate (SDS) were studied using NR data measured at ILL Grenoble (France) to determine the structure and composition of interfacial layers at the solid/solution interface. SDS was used as it is considered as a proxy for natural surfactants in ground water. NR data has shown shown that the purified protein binds in a dense layer to silica even at low concentrations. SDS co-adsorbs and does not significantly remove the adsorbed protein. The strong adsorption of protein, even in the presence of other surfactants, in combination with the tendency for the protein to associate suggests a mechanism for destabilizing particulate dispersions to provide filterable. Zeta potential provided the charge characteristics of the protein and identified points of charge reversal whereas turbidity and dynamic light scattering (DLS) measurements were used to characterise the microstructure and size of protein-surfactant complexes. Zeta potential, turbidity and DLS measurements were made at Uppsala University (Sweden).
– IBS seminar room
– IBS seminar room
– IBS seminar room
– IBS seminar room
РAmphith̢̩tre Boucherle, Fac de M̩decine, La Tronche
– EMBL seminar room
– EMBL seminar room
– Room 500 - 501, ESRF Central Building
Visitors from off-site please contact Claudine Romero tel +33 (0)476 88-20-27 to arrange for a gate pass.
– EMBL Seminar Room.
– CIBB seminar room
– Amphitheatre Dautreppe
Afin de limiter votre attente si vous venez de l’extérieur du CEA, contactez Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr ; une autorisation d’entrée sera établie avant votre arrivée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. Les auditeurs étrangers (hors CEE) sont invités à demander cette autorisation d’entrée au moins une semaine avant la date du séminaire. N’oubliez pas de vous munir d’une pièce d’identité.
– CEA Amphitheatre Dautreppe
– Afin de limiter votre attente si vous venez de l’extérieur du CEA, contactez Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr ; une autorisation d’entrée sera établie avant votre arrivée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. Les auditeurs étrangers (hors CEE) sont invités à demander cette autorisation d’entrée au moins une semaine avant la date du séminaire. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS seminar room
– CIBB seminar room
Fluorescent proteins and chromoproteins share a same fold that consists of an 11 strand beta-barrel. The chromophore, which is responsible for the optical properties of the protein, is located in the center the beta barrel. The aim of this study is to understand structural and optical properties driven by the interactions between the chromophore and protein matrix.
Enhanced consensus fluorescent protein (eCGP123 is an extremely thermostable green fluorescent protein that exhibits useful reversible photo switching properties. eCGP123 was derived by the application of both a consensus engineering approach and a recursive evolutionary process. We introduced mutations to the chromophore and the surrounding residues. Thus, we have been able to change eCGP123 from a bright fluorescent protein (QY=0.69) to Phanta, a virtually non-fluorescent (QY=0.0087). Here we present, the crystals structures and the spectral properties of wild type eCGP123 and its mutants.
The same approach was used to study the properties of Rtms1 and Rtms5, two chromoproteins isolated from the coral Montipora efflorescens. Interestingly, while both are virtually non fluorescent (QY = 0.001 and 0.007 respectively), Rtms1 can be photo activated. Variant of Rtms5 and Rtms1 were generated to understand the chemistry of chromophore formation. The crystals structures of Rtms1, Rtms5 and mutants also will be presented.
– Amphi. du LPSC, avenue des Martyrs, Grenoble,
For additional information, please contact mariane@lpsc.in2p3.fr.
– IBS seminar room
– IBS seminar room
– IBS seminar room
– Building: C3, room: 104 (iRTSV – CEA/Grenoble)
– Secreted proteins are an important medium by which bacteria
interface with their environment. As such, these organisms
have evolved many independent pathways for the export of
proteins, each specializing in the type of protein transported
or the manner by which a substrate protein is delivered to its
target.
The type VI secretion system has emerged as a functionally
versatile pathway for protein export from Gram-negative
bacteria. In this presentation, results implicating this system
in the antagonistic interactions between bacterial cells will be
presented.
For a site access, please contact in advance odile.rossignol@cea.fr
If you wish to meet the invited speaker, please contact Sylvie.elsen@cea.fr
– ILL Chadwick Amphitheatre
invited by Ramesh Pillai (EMBL)
– EMBL seminar room
РSalle de conf̩rences, Grenoble Institut des Neurosciences (GIN)
CNS myelination of axons by oligodendrocytes requires timely and spatially controlled transport of myelin membrane components adapted to axonal specifications. Furthermore, the integrity of myelinated axons depends on glial-derived support that remains unresolved in its molecular nature. We are studying myelin membrane trafficking pathways and their control by axon-glia interaction. The major myelin membrane protein PLP is enriched in late endosomal compartments with the appearance of multivesicular bodies (MVB) and surface transport of PLP is controlled by the endosomal R-SNAREs VAMP3/cellubrevin and VAMP7/TI-VAMP. MVB fusion with the oligodendroglial plasma membrane results in secretion of intraluminal vesicels into the extracellular space, then termed exosomes. These exosomes contain PLP in addition to a typical pattern of exosomal proteins as well as mRNA and microRNA. Intriguingly, oligodendroglial exosome release is stimulated by the neurotransmitter glutamate, indicating that neuronal electrical activity controls glial exosome release. We further analyzed the putative transfer of oligodendroglial exosomes to other neural cells and found them specifically internalized by microglial cells and cortical neurons. Neuronal exosome uptake appears to be mediated by clathrin-dependent endocytosis. Furthermore, preliminary experiments demonstrate that neurons exposed to exosomes exhibit distinct modifications of the neuronal metabolism. In addition to neuroimmunological implications, oligodendroglial exosome secretion thus appears to represent a mechanism of bidirectional communication between neurons and oligodendrocytes and may contribute to the neurotrophic function of myelinating glial cells.
– EMBL seminar room.
Water is synonymous with life, and accordingly, biological macromolecules such as proteins have evolved to utilise the ensemble of forces that arise in an aqueous environment. Such forces help to drive protein folding and modulate dynamical behaviour, which in turn facilitate biological function. Although some proteins can retain some enzymatic activity when extracted into anhydrous solvents1, we have demonstrated that completely solvent-free (molten) functional protein liquids can be produced by modifying the surface of a protein with a polymer surfactant. The electrostatically-grafted surfactant molecules act to extend the range of the intermolecular interactions, which allows the protein molecules to access an anhydrous liquid phase that is amenable to protein folding and function. This was exemplified by producing a room-temperature solvent-free myoglobin liquid, where circular dichroism (CD) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra revealed significant levels of secondary structure, and diffuse reflectance UV-visible spectroscopy (DR-UV-vis) showed a 6-coordinate geometry for the haem prosthetic group.2 Moreover, protein function was demonstrated through gas-binding experiments in which reversible oxygen binding was observed with a binding affinity equivalent to the native haem protein under physiological conditions. We then extended the methodology to include a solvent-free protein liquid based on an equine ferritin–surfactant construct. Significantly, the spheroidal nano-constructs undergo anisotropic ordering during melting at 30°C to produce a viscoelastic protein liquid that exhibits thermotropic liquid-crystalline behaviour, and which subsequently transforms to a Newtonian fluid at temperatures above 40°C.3
These findings present a significant challenge to existing theories on the role of water molecules in determining protein structure and function, and the robustness of this facile approach for achieving protein fluidity indicates that it could readily be developed for a wide range of biologically derived nanostructures.
References
1. Clark, D. S. Characteristics of nearly dry enzymes in organic solvents: implications for biocatalysis in the absence of water. Philos. Trans. R. Soc. London Ser. B 2004, 359, 1299-1307.
2. Perriman, A. W.; Brogan, A. P. S.; Colfen, H.; Tsoureas, N.; Owen, G. R.; Mann, S., Reversible dioxygen binding in solvent-free liquid myoglobin. Nature Chemistry 2010, 2 (8), 622-626.
3. Perriman, A. W.; Colfen, H.; Hughes, R. W.; Barrie, C. L.; Mann, S., Solvent-Free Protein Liquids and Liquid Crystals. Angewandte Chemie-International Edition 2009, 48 (34), 6242-6246.
– Room: C3-104 (CEA)
– Afin de limiter votre attente si vous venez de l’extérieur du CEA, contactez Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr ; une autorisation d’entrée sera établie avant votre arrivée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. Les auditeurs étrangers (hors CEE) sont invités à demander cette autorisation d’entrée au moins une semaine avant la date du séminaire. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS seminar room
b-lactam antibiotics remained the most widely used family of drugs against severe infections due to
their low toxicity, excellent bioavailability, and broad-spectrum bactericidal activity. The latter property is
accounted for by the conservation of the target, the active-site serine D,D-transpeptidases, that catalyze
the final step of peptidoglycan polymerization in the stress-bearing bacterial cell wall. The discovery of
hundreds of b-lactams and of b-lactamase inhibitors has made it possible to partially compensate for the
erosion of antibacterial activity due to the emergence of various mechanisms of resistance. In Gramnegative
bacteria, these mechanisms mostly involve the production of b-lactamases, often associated with
decreased outer membrane permeability and drug efflux. In Gram-positive bacteria modification of the
D,D-transpeptidases is the clinically relevant mechanism in important pathogens such as Staphylococcus
aureus, Streptococcus pneumoniae, and the enterococci. Peptidoglycan was previously thought to
be exclusively cross-linked by active-site serine D,D-transpeptidases. However, we have shown that
unrelated active-site cysteine L,D-transpeptidases are predominantly responsible for peptidoglycan crosslinking
in Mycobacterium tuberculosis. An enzyme of the L,D-transpeptidase family can also by-pass the
classical D,D-transpeptidases in mutants of Enterococcus faecium and confer high level cross-resistance
to glycopeptide antibiotics and to all b-lactams, except molecules of the carbapenem class. A combination
of fluorescence kinetics and mass spectrometry analyses showed that irreversible inactivation of L,Dtranspeptidases
by carbapenems result from formation of a non-covalent complex followed by acylation
of the catalytic cysteine residue. The binding step was found to be kinetically limiting at the minimal drug
concentration required for bacterial growth inhibition. The non-covalent complex is committed to enzyme
inactivation since the rate of dissociation is much smaller than the rate of acylation. By exploring the
role of amino acid substitutions in the emergence of carbapenem resistance, we have identified kinetic
parameters predictive of the antibacterial activity of the drug. These approaches could therefore be
applied to the determination of structure-activity relationships in the development of new antibacterial
agents targeting the L,D-transpeptidases, in particular the enzymes from extensively resistant clinical
isolates of M. tuberculosis, which are associated with mortality rates as high as 50% due to the lack of
activity of currently available drugs.
– ILL Chadwick Amphitheatre
Abstract: The crystal structure of the yeast 80S ribosome determined at 4.15 Ã… resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our crystals capture the ribosome in the ratcheted state which is essential for translocation of mRNA and tRNA and where the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting, and their implications to mRNA and tRNA translocation. Structural rearrangements of the ribosome in the tRNA binding step have been studied on bacterial ribosome model. Discrimination of tRNA on the ribosome occurs in two consecutive steps: initial selection and proofreading. We propose a proofreading mechanism based on comparison of crystal structures of the 70S ribosome with an empty A site or the A site occupied by cognate or non-cognate tRNA. We have shown involvement of tales of ribosomal proteins in stabilization of correct tRNA on the ribosome. We suggest that proofreading begins with stabilization of tRNA anticodon loop with involvement of magnesium ions, following by stabilization of elbow region and accommodation of the acceptor end in the peptidyl transferase center.
– IBS seminar room
Lactic acid bacteria (LAB) are a phylogenetically diverse group, comprising starter
bacteria for food fermentations and also opportunist pathogens. A little known attribute
of numerous LAB is that they are genetically equipped for aerobic respiration metabolism
when provided with exogenous sources of heme (and menaquinones for some species).
Respiration metabolism is energetically favorable and leads to decreased oxidative and
acid stress during growth of some LAB, and consequently, dramatically improved growth
and survival. Respiration metabolism has industrial applications for the preparation of dairy
starter cultures, and we suspect that it is part of the natural lifestyle of numerous LAB.
The intracellular heme interactants and factors of heme homeostasis in two LAB models,
Lactococcus lactis and Streptococcus agalactiae, will be presented
– CERMAV Seminar Room: salle Chartreuse
Here we describe the enzymology and metabolic pathways underpinning the design of chemical tools that can be used to probe intracellular O-glycosylation. We discuss the use of some of these tools in the cellular setting, as well as in vivo, and touch on the general utility of these probes to study intracellular O-glycosylation.
Contact: A. VARROT (varrot@cermav.cnrs.fr)
– EMBL seminar room
– Auditorium, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Lynda Graham tel +33 (0)476 88-21-92.
– IBS seminar room
In spite the robustness and perfection of their mechanism of action, proteins posses a
remarkable ability to rapidly change and adopt new functions. I will describe experimental
work aimed at reproducing the evolution of new proteins in the laboratory, and unraveling
their traits of evolvability. I will show structural work aimed at better understanding the
mechanisms by which proteins change. Specifically, I will describe how the functional
promiscuity of proteins, their conformational plasticity, and their modularity of fold,
accelerate their evolution.
– IBS seminar room
Par Dorit Hanein – Sanford Burnham Medical Research Institute La Jolla, CA
Room at the entry site of the CEA
by
– Pr. J. CHOU (Harvard medical School, Boston), expert in structural studies of membrane proteins in solution,
– Pr. M. KAINSHO (Tokyo Metropolitan University), One of the pioneer in the field of Cell-free expression and isotopic labelling of protein
– and Pr. S. VAN DOREN (University of Missouri , Columbia) , specialist in the studies of protein-protein interaction involved in arthrosclerosis and Cancer diseases.
Hosted by J. Boisbouvier & B. Brutscher. (IBS/NMR)
IBS Seminar room
– CEA - Salle C5-421A, INAC/SCIB,
Contact: Jean-Luc Ravanat : 04.38.78.47.97
– CTRM Control Room
– CIBB seminar
Conférence d’Intérêt Général
– Amphitheatre du LPSC, avenue des Martyrs, Grenoble,
– Contact: mariane@lpsc.in2p3.fr
– IBS seminar room
Membrane co-transport proteins that utilize a 5-helix inverted repeat motif have recently
emerged as one of the largest structural classes of secondary active transporters. I
will discuss a comprehensive study of the Sodium-Galactose Transporter from Vibrio
parahaemolyticus (vSGLT) consisting of multiple structures, molecular dynamics simulations
and biochemical characterization. Our data show that sodium exit causes a reorientation
of transmembrane helix 1 (TM1) opening an inner gate required for substrate exit. This
cascade of events, initiated by sodium release, ensures proper timing of ion and substrate
release. Once set in motion, these molecular changes weaken substrate binding to the
transporter and allow galactose to readily enter the intracellular space. These events
appear to be constant in the other sodium dependent 5-helix inverted repeat members.
– IBS seminar room
– IBS seminar room
Depending on the glycan structure, proteoglycans (PGs) can act as (co-)receptors for growth
factors and chemokines thereby contributing to cell recruitment, proliferation and fibrosis. Chronic
transplant dysfunction (CTD) is characterized by extensive tissue remodeling and an interstitial
infiltrate. We hypothesized that alterations in expressions of PGs and their ligands orchestrate
tissue remodeling in CTD. Therefore, we studied proteoglycan and growth factor expression in a rat
renal transplantation model. In contrast to non-transplanted and isografted kidneys, allografted
kidneys developed severe CTD evidenced by routine histology. Laser dissection microscopy of
glomeruli and tubulo-interstitium separately followed by low density qPCR revealed uniform
upregulation for TGF-β1, Collagen I and IV confirming fibrosis in CTD kidneys. However, we found
spatial differences in PGs expression and ligand binding properties. In affected glomeruli of CTD
kidneys we found a 4 fold induction of the matrix heparan sulfate (HS)PG perlecan along with
massive accumulation of FGF2. The functional significance of these findings is evidenced by in vitro
experiments with rat mesangial cells showing that FGF2-induced proliferation (2-3 fold increase)
is sulfation dependent and can be inhibited by exogenous HS. Tubulo-interstitial remodeling in
the allografts was characterized by a 5 fold induction of the cell surface HSPG syndecan-1 and
associated with co-localization of HB-EGF and phospho-EGFR. Profiling the HS polysaccharide side
chains of renal HSPGs reveals conversion of a quiescent HS phenotype in control and isografted
kidneys towards a more pro-remodeling HS phenotype in the allografts. These data indicate that
HSPGs such as perlecan and syndecan-1 serve as docking platforms for growth factors in the
various renal compartments during CTD. We speculate that heparin-like glycomimetica could serve
as a promising intervention modality to retard development of CTD.
– IBS seminar room
– IBS seminar room
Biofilms are sessile communities of bacteria that adhere to biotic and abiotic surfaces. The
formation of bacterial biofilms requires an extracellular matrix to facilitate adherence of
bacteria to the surface they colonize. A wide variety of medically important biofilm-forming
bacterial strains, including S. epidermidis, S. aureus, E. coli, B. pertussis, and Y. pestis
generate the same β(1-6)-N-acetylglucosamine (PNAG) homopolymer as a key biofilm
matrix exopolysaccharide. In these bacterial strains PNAG undergoes partial enzymatic
de-N-acetylation, which is essential for polysaccharide export and surface attachment. In
vivo studies have implied that the enzyme responsible for carrying out de-N-acetylation in
E. coli is PgaB, an enzyme which has sequence homologues in gram-negative species that
form PNAG-dependent biofilms. This seminar will discuss the synthesis, properties and
functionalization of PNAG. The enzymatic activity, metal dependence, structure and initial
results of inhibitor development against PgaB will also be discussed.
Hôte
– IBS seminar room
Structurally disordered proteins (IDPs) can be classified into six functional categories [1]. Based mainly on bioinformatic analysis, we have suggested a couple of years ago that disordered regions of traditional chaperones or even fully disordered proteins can have potent chaperone activity, probably by an “entropy transfer†mechanism [2]. To carry out detailed structure-function analysis of this phenomenon, we studied two dehydrins of A. thaliana, ERD10 and 14, and show that they are potent chaperones. To address the structural background of this effect, we carried out full NMR resonance assignment of the 185 amino acid-long ERD14. Secondary chemical shift and relaxation data show that this IDP is not fully disordered, but have five short regions of somewhat restricted flexibility. In-cell NMR of ERD14 overexpressed in E. coli shows that three of these regions (conserved K-segments) undergo further ordering. Overexpressed ERD14 provides significant protection to cells against stress conditions elicited by various means (unpublished observations). These observations on IDP function are also put in the general context of the evolution of IDP function, by showing that certain IDP functions do not require long evolution refinement, but may suddenly arise in the cell. Two further such mechanisms will be discussed, chromosomal translocations in cancer [3] and the shift in the translation frame caused by alternative splicing [4]. All these results suggest that structural disorder enables IDPs to exist and function in the cell without the involvement of a lengthy evolutionary selection procedure. The evolutionary, functional and pathological implications of this observation will be discussed in detail.
tompa@enzim.hu
http://tompa.enzim.hu
– IBS seminar room
Lipoprotein particles are naturally occurring nanostructures in the blood stream entrusted
with the task of delivering cholesterol and energy-rich fat to and from tissues and cells. As
major lipid transporters, lipoproteins are also involved in the progression of cardiovascular
diseases such as atherosclerosis or stroke, which are among the most prevalent causes
of death in developed countries. Among pro-atherogenic lipoprotein classes are low
density lipoproteins (LDL), which are about 20 nm in size consisting of an apolar core
filled with triglycerides and cholesterylesters surrounded by a phospholipid monolayer,
free cholesterol and one single molecule of apolipoprotein B100 (apoB100). ApoB100 is
amongst the largest amphiphilic glycoproteins known and its structure is an important
determinant for cellular uptake.
A range of biophysical techniques have been applied to obtain structural information on
apoB00/LDL, and only the combination of all results has lead to our current understanding
of lipoprotein structure. Unfortunately, molecular structure determinations, in particular by
X-ray crystallography or e.m. reconstruction, are hampered by the intrinsic conformational
flexibility, dynamics and variablity of both, apoB100 and LDL particles.
In this talk I will present recent advances in structural studies on LDL and apoB100.
Prevailing conceptions of the molecular assembly of LDL will be shown, and finally, how the
synergy of complementary biochemical, biophysical and molecular simulation approaches
has lead to the current structural model of LDL.
– IBS seminar room
In the last decade there has been an increasing amount of experimental and computational evidence pointing out that eukaryotic genomes code for a high proportion of intrinsically disordered proteins (IDPs). IDPs are ubiquitary functional proteins that lack stable II and III structures under physiological conditions in the absence of a partner and that rather exist as conformational ensembles. IDPs are often involved in biological processes implying manifold protein-protein interactions, such as cellular regulation, transcription and signal transduction.
In the course of the structural and functional characterization of the measles virus replicative complex, we discovered that the nucleoprotein (N) and the phosphoprotein (P) contain long disordered regions possessing sequence and biochemical features that typify IDPs. Subsequently, we have extended these results to the N and P proteins from other paramyxoviruses. My talk will focus on the identification and characterization of disordered regions of the N and P proteins, as well as onto the interactions that they establish with their partners. Finally, I will discuss the functional implications of disorder within the replicative complex of these viruses.
– Ecole de Management de Grenoble
http://www.grenoble-em.com/242-acces-1.aspx
– Salle de conférence de l’Institut Albert Bonniot,
Rond Point de La Chantourne, 38700 La Tronche (arrêt de tram Grand Sablon, ligne B).
Les microtubules représentent un élément majeur du cytosquelette eucaryote et jouent
un rôle central dans la division, la motilité et la morphogenèse cellulaires. Ils sont
particulièrement abondants dans les neurones, où ils participent à la polarisation et Ã
l’activité de ces cellules. Les microtubules assurent leurs fonctions grâce à leurs
propriétés structurales et dynamiques qui sont contrôlées dans la cellule par de
nombreuses protéines appelées MAPs (Microtubule Associated Proteins). Notre projet
principal est l’étude des bases moléculaires de la régulation des microtubules par les
MAPs impliquées dans la différentiation neuronale. Nous nous proposons d’analyser les
propriétés dynamiques et l’arrangement spatial des microtubules à l’aide de techniques
d’imagerie photonique dans des systèmes simples reconstitués à partir de composants
purifiés, ainsi que dans des modèles de différentiation cellulaire. En parallèle, des
méthodes de cryo-microscopie et cryo-tomographie électronique seront utilisées afin
d’obtenir des reconstructions tridimensionnelles de complexes macromoléculaires en
solution et dans leur environnement cellulaire natif. Nous visualiserons ainsi comment
les MAPs étudiées interagissent avec les microtubules et affectent la structure de ces
polymères. Cette approche corrélant microscopie optique et microscopie électronique,
et appliquée à des systèmes de complexité croissante, devrait permettre de comprendre
à un niveau moléculaire l’organisation du cytosquelette par un réseau de MAPs au
cours de la différentiation neuronale.
– EMBL seminar room
– EMBL seminar room
– IBS seminar room
Amphipols (APols) are short amphipathic poly¬mers designed to substitute to detergents for hand¬ling membrane proteins (MPs) in aqueous solutions. Upon trapping a MP with APols, a non-covalent but stable complex forms, which is hydrosoluble and in which the protein is, in general, much more stable than in deter¬gent solution. In MP/APol complexes, the surfactant adsorbs onto the hydrophobic trans¬mem¬brane sur¬fa¬ce of the protein, leaving extramembrane surfaces free to interact with water-soluble ligands (cartoon). Functional per¬turbations appear to be rare.
One of the first APols to be designed, called A8-35, has been exten¬sively stu¬died, as well as the com¬¬plexes it makes with a number of MPs. A8-35 consists of a relatively short polyacrylate chain, part of the carboxylates of which have been randomly grafted with octylamine and isopropylamine, making it amphipathic. APols with a dif¬¬ferent chemical structure, such as non-ionic APols, are currently being deve¬lop¬ed. Over the years, variously labeled and functionalized versions of A8 35 have been synthesized and validated. Those include deuterated A8 35, particularly useful for neutron scattering and NMR stu¬dies, fluo¬rescent APols, whose distribution can be easily followed during fractionation experi¬ments and which can be used to carry out FRET studies, and biotinylated A8 35, which can mediate the attachment of MPs onto solid supports such as chips or beads.
The applications of APols that have been validated to date include stabilizing fragile MPs and MP complexes, solution NMR studies, electron microscopy, diagnostics and ligand binding studies, folding MPs from a denatured sta¬te, and MP cell-free synthesis. Various other applications, e. g. in proteomics, are being developed. An overview will be presented of those applications that appear most ready to be usefully exploited by the membrane protein community. The applications and implications of APol-assisted MP folding will be discussed.
– IBS seminar room
– EMBL seminar room
– EMBL seminar room
> p53 is a multi-domain protein central to a complex network of signaling pathways that organize the cellular response to stress. During the cellular response to stress, p53 can activate more than 100 genes in the DNA repair, cell arrest, senescence and apoptotic pathways. In the nucleus of normal cells, p53 binds to its responsive DNA elements and acts as a transcription factor. p53 has been broadly studied because is the protein most commonly mutated in cancerous cells with about 50% of human tumors having a mutation on the p53 gene. Nonetheless, a gap exists in our knowledge of p53 structure because we do not understand how p53 domains interact with each other to explain p53’s diverse functions and regulations. In our work, using electron microscopy and X-ray crystallography we are aiming to understand the structure of full-length p53 and how its activity its regulated by its binding partners.
>
– EMBL seminar room
– EMBL seminar room
– EMBL seminar room
– CEA - room C3-104
please contact odile.rossignol@cea.fr for a site entry
– EMBL seminar room
– IBS seminar room
– CIBB seminar room
The ins and outs of NS1 nonstructural lipoprotein secretion during dengue virus infections
Dengue virus (DENV) is the major vector-borne viral disease of the tropics, leading to over half a million hospitalization per year and tens of thousand deaths. DENV infection is characterized in its most severe form by signs of hemorrhage and plasma leakage, to which a risk of fatal hypovolemic shock is associated. DENV encodes a nonstructural glycoprotein NS1 that associates with intracellular membranes and the cell surface. NS1 is eventually secreted as a soluble hexamer from DENV-infected cells and circulates in the bloodstream of infected patients, representing a potent diagnostic marker of acute DENV infections. Extracellular NS1 has been shown to modulate the complement system and to enhance DENV infection, yet its structure and function remained essentially unknown. By combining cryoelectron microscopy analysis with a characterization of NS1 amphipathic properties, we show that the secreted NS1 hexamer forms a lipoprotein particle with an open-barrel protein shell and a prominent central channel rich in lipids. Biochemical and NMR analyses of the NS1 lipid cargo reveal the presence of triglycerides, bound at an equimolar ratio to the NS1 protomer, as well as cholesteryl esters and phospholipids, a composition evocative of the plasma lipoproteins involved in vascular homeostasis. This study suggests that DENV NS1, by mimicking or hijacking lipid metabolic pathways, contributes to endothelium dysfunction, a cardinal feature of severe dengue disease. These findings open promising alternative therapeutic avenues to fight dengue disease, such as interfering with NS1 secretion or targeting its hydrophobic channel.
– IBS seminar room.
Following engagement of the cell surface CD95 (Fas/APO-1) programmed cell
death receptor by its ligand, the apoptotic signalling pathway depends on an initial
interaction between the the C-terminal death domain of the receptor and the adaptor
protein FADD, followed by the recruitment and activation of procaspase-8/10 into
the death-inducing signalling complex (DISC). The composition, structure and
mechanism of formation for the DISC has been the subject of extensive investigation.
I will describe our contributions to this endeavour using, amongst other techniques,
methyl-TROSY NMR spectroscopy. I will also discuss more broadly the potential for
structural plasticity of the CD95 death domain implied by results from cell biology
and biochemical experiments.
– IBS seminar room.
La dengue, décrite comme une « grippe tropicale » depuis le XVIIIe siècle, est une maladie
virale transmise à l’homme par des moustiques du genre Aedes. Les formes graves de la
maladie sont la dengue hémorragique et la dengue avec syndrome de choc qui peuvent
s’avérer mortelles. L’incidence de la dengue progresse actuellement de manière très
importante au niveau mondial. L’OMS estime à 50 millions le nombre de cas annuels, dont
500 000 cas de dengue hémorragique qui, faute de traitement, peuvent être mortels dans
20% des cas. Il n’existe pas encore de vaccin contre la dengue.
Le virus de la dengue appartient au genre flavivirus qui sont des virus à ARN, de capside
en forme d’icosaèdre, dont l’enveloppe mesure de 40 à 50nm de diamètre. Cette enveloppe
est formée par une protéine de membrane, et par près d’une centaine de dimères d’une
protéine d’enveloppe, la protéine E, qui contient le peptide fusion et qui n’est fonctionnelle
que sous une forme trimérique. La fusion du virus est une étape fondamentale pour qu’il
puisse pénétrer dans une cellule.
Le trimère de la protéine E a été étudié par des techniques de simulation moléculaire
sous diverses conditions de force ionique en pH acide. Les premiers résultats d’études du
trimère, obtenus au long de simulations de 350 ns, montrent que la reconstruction de la
protéine à partir des données de cryo-microscopie électronique est stable. On a aussi pu
identifier une poche dans la région du point de rencontre des trois monomères, poche qui
semble être un excellent candidat comme cible dans la recherche d’inhibiteurs de l’activité
de cette protéine clef.
– IBS seminar room
The amylome is the universe of proteins that are capable of forming
amyloid-like fibrils. The factors that enable a protein to belong
to the amylome will be discussed, including sequence complementarity,
structural flexibility, and the features of proteins
that make them self-chaperones. The structure-based design of
amyloid blockers will be described, along with structures of small
molecules bound to fibers. The nature of some classes of small
amyloid oligomers will be discussed.
We have determined at 1.1 A resolution the structure of the ruthenium complex lambda-[Ru(TAP)2(dppz)]2+ bound to the DNA oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. In the absence of the ruthenium complex, crystals of the stacked-X Holliday junction would be formed. In the presence of the ruthenium complex, both intercalation and semi-intercalation are observed, thus non-covalently linking two duplexes and creating a kink in the duplex at the semi-intercalation site.
This is the first crystal structure determination of any of the ruthenium ‘light-switch’ complexes, more than twenty five years after the ‘light-switch’ phenomenon was first recorded. The crystallisation is completely enantiomerically specific.
The talk will include a description of three crystal forms, showing three different degrees of bending, together with differing arrangements of the terminal AT basepair.
External visitors may ask for a site access to Karine Sultan (sultan@ill.fr).
Accueil CEA Grenoble
please contact odile.rossignol@cea.fr
CEA Grenoble, Salle C5-421A, (contact thierry.douki@cea.fr)
– CIBB seminar room
– EMBL seminar room
– IBS seminar room
Streptococcus pneumoniae is a common nasopharyngeal commensal, but is also able to
cause severe infections such as pneumonia, septicaemia and meningits and is responsible
for nearly a million deaths in infants worldwide each year. S. pneumoniae is surrounded by
a polysaccharide layer called the capsule which is vital for virulence.
The capsule seems to inhibit the ability of S. pneumoniae to interact
with host epithelium and form biofilms, so perhaps prevent it from
colonising the nasopharynx. This raises the question of why has S.
pneumoniae evolved a capsule if it does not assist colonisation? I
will discuss the properties of the S. pneumoniae capsule that may
benefit nasopharyngeal colonisation, and how these effects also
allow the bacteria to cause invasive infections.
– IBS seminar room
Regarding to the evolution of biological molecules, M. Eigen mentioned that the evolution
might start from random events and the instructions for evolution required information.
However, this specific information should originate from unique chemical structures. How
the nature selection related to the chemical selection? In this lecture, we will discuss our
research results related to the following questions:
Why did nature choose a-amino acids?
Why did nature choose ribose?
How Amino acids “talk with†nucleosides?
We have proposed a model for the co-evolution of protein, nucleic acid and membrane.
– Biography: Professor Yu-Fen Zhao is a Professor of Chemistry in the Universities of Tsinghua, Xiamen and
Zhengzhou and a member of the Chinese Academy of Sciences. She was educated in Taiwan and did her
doctoral and postdoctoral work at SUNY Stony Brook and NYU in the USA. Her research is in the area of bioorganic
chemistry, especially the chemistry of phosphorus.
– IBS seminar room
Electron microscopy and X-ray crystallography provide unique insight into the architecture
of cells, molecular assemblies and (macro)molecules. Ultimately, both methods are
limited by radiation damage. Compared to synchrotron sources, free-electron lasers (FEL)
provide orders of magnitude brighter and shorter X-ray pulses that have been proposed to
yield diffraction patterns of biological samples before the onset of significant radiation damage
(“diffraction before destruction†). Recently, the Linac Coherent Light Source (LCLS)
has become accessible to users, accessing the hard X-ray regime, thereby allowing Ã…ngstrom-
resolution studies with femtosecond time resolution. This enables a plethora of new
experiments, including femtochemistry and the structural analysis of complex materials,
warm dense matter, and biological samples. The latter include single particles such as
viruses and nanocrytals. Recent results will be described that were obtained by a collaboration
consisting of the Max Planck Advanced Study Group at CFEL, CFEL DESY, Arizona
State University, SLAC National Laboratory, Uppsala University, LLNL, and University of
Wisconsin-Milwaukee. The LCLS is operated by Stanford University on behalf of the U.S.
Department of Energy, Office of Basic Energy Sciences.
– IBS seminar room
– IBS seminar room
Utilization of membrane proteins in chemical sensors presents a wide range of opportunities
for the design of analyte specific chemical and biological sensing platforms. Functional
inclusion of membrane proteins in sensors requires the incorporation of a lipid membrane
with sufficient lifetime to facilitate sensor utilization. Unfortunately, most natural lipids lack
the requisite stability to meet these requirements. We have developed a series of highlystable
polymer lipid membranes that support the activity of ion channels and membrane
receptors for spectroscopic and electrophysiological analysis. Membrane lifetimes in excess
of one month that support transmembrane protein activity for up to one week have been
prepared. In this seminar, we will explore the preparation, characterization and potential
applications of highly stable lipid membranes.
– ESRF Auditorium
Abstract : http://www.esrf.fr/events/Seminars/di-jing-huang22july2011
– room 500 - 501, ESRF Central Building
The Partnership for Soft Condensed Matter (PSCM) was recently established [1] with the goal of
combining cutting-edge experiments performed at new state-of-the-art nuclear-reactor and synchrotron
beamlines with the on-site availability of sample preparation facilities, complementary sample
characterization techniques, and specialized sample environments. Such an approach is particularly wellsuited
due to the rapidly growing interest for out-of-equilibrium and transient states found in novel
complex fluids and meso-scale soft and composite materials. The latter often need to be prepared and
characterized just prior to neutron/x-ray experiments. In addition, a meaningful interpretation of the
detailed atomic/molecular scale information provided by neutron/x-ray probes can often be reached only
in combination with supportive data from complementary techniques such as light scattering, tensiometry,
rheology, microscopy, ellipsometry, calorimetry, etc.
Recent examples of in-house and user-driven x-ray studies of soft and hard surfaces and interfaces
[2-8] will be used to illustrate the multiple ways in which the PSCM can favor and strengthen synergistic
interactions among the on-campus members and the external representatives of the European Soft-Matter
community, thus leading to enhanced quality and scope of the user support services. This will enable the
implementation of new ambitious research collaborations with world-leading Soft-Matter groups. The
success of these collaborations will depend on the ability of the PSCM to draw on the vast human and
technical resources of the EPN Campus, and to manage concerted research efforts reaching beyond what
is usually available to individual University Labs and Industrial R&D Units. The PSCM will thus succeed
in attracting to the field new brilliant young researchers, and in providing a center where new cuttingedge
Soft-Matter Science can nucleate and grow.
The PSCM will allow expanding and deepening the ongoing investigations of the fundamental
physical and chemical phenomena that govern the bulk and interfacial structure and dynamics of soft
materials, comprising micro- and nano-particles, polymers and hierarchical multi-length-scale structures,
synthetic and natural macromolecules, and combinations thereof.
In parallel to fostering fundamental science, the PSCM will also promote applied and industrial
research programs aimed at developing the next generation of smart multi-functional nanomaterials and
self-assembled multi-component nano-devices of interest for example to the information-technology,
health, and energy sectors, thus leading the path towards the green, sustainable, and knowledge-based
economy of the future.
In this talk, a few examples of my recent research activities will be shortly presented as a means to
introduce and discuss the strategy needed to achieve the overall PSCM goals outlined above.
– room 500 - 501, Central Building
– Abstract: http://www.esrf.fr/events/Seminars/estelle-mossou26july2011
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Eva Jahn-Feppon tel +33 (0)476 88-26-19.
– CIBB seminar room
Australia is usually known for its vast size and limited population. However, over the
past five years, Australian researchers in the biological sciences have successfully
embraced both small-angle neutron and X-ray scattering as complementary tools to
probe the structures of a number of bio-macromolecular systems. Laboratory-based
X-ray sources are being installed every year; new SAXS facilities are being
developed at the Australian Synchrotron; biodeutration facilities are up and running;
and the QUOKKA-SANS beamline is beginning to yield results. Using cardiac
myosin binding protein-C (cMyBP-C) as an example, I will illustrate how a
deceptively simple set of SAXS and SANS experiments have formed the basis of an
entire research program that has stimulated some quite vigorous debate amongst the
muscle-research community. Cardiac myosin binding protein-C is an accessory
protein of muscle sarcomeres that plays a key role in maintaining regular heart
function. The protein performs this maintenance through its regulation of a complex
series of interactions between myosin and actin – some of which are fascinatingly
timed to the cardiac cycle. SAXS and SANS investigations – that encompass gene
design to protein isolation and data analysis – have revealed the global domain
architecture of cardiac myosin binding protein-C and have shown that it interacts with
actin to modulate contractile events. These results have been reinforced by several
notable and rather more recent electron microscopy investigations. Indeed, and
perhaps against expectations, both SAXS and SANS continue to reveal far more than
they ought to…
– IBS seminar room
– IBS seminar room
– IBS seminar room
For decades, electron microscopy (EM) has been the method of choice to study intracellular
structures. Yet, traditional EM has numerous shortcomings, which have gradually restricted
it’s use in cell biology. Recently, numerous approaches were developed to overcome EM
weaknesses. Are we getting there yet ? I’ll use projects i have been working on to illustrate
the ins and outs of electron microscopy in cell biology and where i believe it is going.
– IBS seminar room
– IBS seminar room
– EMBL seminar room
– CIBB seminar room.
Visitors from off-site please contact Claudine Romero tel +33 (0)476 88-20-27 to arrange for a gate pass.
– Auditorium - ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
– in room 337, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
– room 500 - 501, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
– Salle d’accueil CEA.
To request a badge, please contact Odile Rossignol (04 38 78 45 63, odile.rossignol@ces.fr) with the following data
– date/city/country of birth
– Nationality.
– Salle d’accueil CEA.
To request a badge, please contact Odile Rossignol (04 38 78 45 63, odile.rossignol@cea.fr) with the following data
– date/city/country of birth
– Nationality.
– Amphitheatre DAUTREPPE - CEA.
To request a badge, please contact Odile Rossignol (04 38 78 45 63, odile.rossignol@ces.fr) with the following data
– date/city/country of birth
– Nationality.
– in room 407, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
– in room 500 - 501, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
– in room 337, ESRF Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Claudine Romero tel +33 (0)476 88-20-27.
РInstitut Jean Roget, Salle de Conf̩rence du 5̬me Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
РLieu: Institut Jean Roget, Salle de Conf̩rence du 5̬me Etage,
Faculté de Médecine-Pharmacie, Domaine de la Merci, La Tronche.
Contact: Cordelia.Bisanz@ujf-grenoble.fr, Tel : 04 76 63 74 74
– EMBL seminar room
– ESRF Auditorium
Onkar Singh has spent 25 years in pharma, he started off working on large scale protein folding and then moved into macromolecular crystallography slowly as MX became an integral part of the drug discovery. GSK were probably one of the first companies in the UK to start using x-ray crystallography routinely. He has worked on many key target classes (taken from initial biology to many complexed structures) kinases, viral and mammalian proteases, flu neuraminidase, viral RNA polymerases, bacterial DNA gyrase etc a long list of drug targets including some membrane protein targets.
The membrane proteins he has worked on are essentially membrane associated with the hydrophobic regions deleted but still require understanding of detergent requirements. Has has also worked with ion channels and GPCRs.
In Pharma the key aim is to develop reproducible crystal systems to determine not one but 100s of complexed structures.
– IBS seminar room
– ILL Chadwick Amphitheatre.
Small-angle X-ray and neutron scattering with contrast variation have made important contributions in advancing our understanding muscle regulatory protein structures in the context of the dynamic molecular processes governing muscle action (1). The contributions of the scattering investigations have depended upon the results of key crystallographic, NMR and electron microscopy results that have provided detailed structural information that has aided in the interpretation of the scattering data. This talk will cover the advances made using small-angle scattering techniques, in combination with the results from these complementary techniques, in probing the structures of troponin and myosin binding protein C (MyBP-C). A focus of these studies has been to elucidate isoform and species differences between these muscle proteins and the relationship between structural and functional differences. In the case of MyBP-C, neutron scattering with contrast variation (2) has played a critical role in shifting the view of the community from a ‘myosin-centric’ model of MyBP-C function toward one involving a model of regulation involving specific actin interactions. Significant data are accumulating indicating that cMyBP-C may act to modulate the primary calcium signals from troponin, and our most recent electron microscopy and NMR studies have added important details to this emerging picture (3, 4). Our scattering studies also have revealed important structural differences between human and mouse cardiac MyBP-C that have significant potential functional implications. Interest in MyBP-C and its biological role has grown due to linkages between mutations in the cardiac isoform and serious heart disease.
References
1. Y. Lu, C. M. Jeffries, and J. Trewhella, Probing the Structures of Muscle Regulatory Proteins using Small-Angle Solution Scattering, Biopolymers 95, 505-516 (2011)
2. A. E. Whitten, C. M. Jeffries, S. P. Harris, J. Trewhella, Cardiac Myosin Binding Protein-C Decorates F-actin: Implications for Cardiac Function, Proc. Natl Acad. Sci. U.S.A. 105, 18360-18365 (2008)
3. Orlova, A., Galkin, V. Jeffries, C. M., Egelman, E. H. and Trewhella, J. “The N-terminal Domains of Myosin Binding Protein C Can Bind Polymorphically to F-Actin†J. Mol. Biol. 412, 379-386 (2011)
4. Lu, Y., Kwan, A., Trewhella, J., Jeffries, C. M. “The C0C1 Fragment of Human Cardiac Myosin-Binding Protein C has Common Binding Determinants for Actin and Myosin,†J. Mol. Biol. accepted (2011.)
– EMBL Seminar Room.
– IBS seminar room
– IBS seminar room
The Grenoble Institute of Research for Cancer (GIRC) is an “Institut Hors Murs†. It aims to gather all the structures involved in research and care for cancer on the three main locations Grenoble site: Heath site (CHU, Medical School), Campus Site, and Polygone site (CEA, IBS, Synchrotron, EMBL…) The main objective of Grenoble Institute of Cancer is to optimize the links between the Research laboratories and the medical structure of the agglomeration. IBS in particular is involved as a technological platform.
One of the first manifestations of GIRC is the establishment of a series of seminars that will be taking place every first Tuesday of each month organized and financed by GIRC. The seminars will be taking place at different sites in the Grenoble area. T
– Amphi Dautreppe (CEA)
Vous venez de l’extérieur du CEA, merci de contacter Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr) afin de faire établir une autorisation d’entrée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS seminar room
– EMBL seminar room
Web: http://www.medit-pharma.com/
for a badge, please contact gtounkar@embl.fr
– IBS seminar room
– IBS seminar room
Innate immune responses play a critical role in the protection of organisms against pathogens. The innate immune response is triggered by pattern recognition receptors such as Toll-like receptors (TLR), intracellular RNA or DNA sensors such as Rig-I, Mda5 or DAI that recognize pathogen-associated molecular patterns. Signaling by these receptors induces the synthesis and secretion of cytokines that are important for innate and adaptive immune responses. Breakdown of signaling can lead to cancer and infection, whereas hyperactivity can result in autoimmune disease and sepsis. Here we discuss the principles of signal integration through assembly of higher order complexes and discuss recent results on structural studies of IKK kinases, central regulators of the innate immune response.
– IBS seminar room
– CIBB seminar room
DNA synthesis is a convenient way to obtain difficult-to-find cDNA clones, genes from obscure/pathogenic organisms and unnatural sequences. Additionally, during synthesis, codon use can be adapted in an attempt to improve protein expression. The rules for doing this are unclear, although a common strategy has been to use codons that are more frequently used by the host organism.
DNA2.0 have emerged as one of the more successful companies in DNA synthesis, and have sought to understand the rules for enhancement of protein expression levels. They have published their research in PLoS One and will present this in a seminar here.
– EMBL Seminar Room
– EMBL Seminar Room
– EMBL Seminar Room
– ESRF CTRM Control Room
– CNRS seminar room
Vous venez de l’extérieur du CEA, merci de contacter Odile Rossignol (tél. 04.38.78.45.63 - Email: odile.rossignol@cea.fr) afin de faire établir une autorisation d’entrée. Merci de préciser vos date, lieu de naissance, nationalité et nom de jeune fille pour les femmes. N’oubliez pas de vous munir d’une pièce d’identité.
– IBS seminar room
The complement system plays a key role in the innate immunity. Complement is a
tightly regulated immune surveillance system, capable to respond to microbial invasion,
physiological cell death or pathological cells injury, without damaging the healthy host
cells. Therefore genetic abnormalities that disturb the balance between complement
activation and regulation can induce attack on the healthy cells or inefficient elimination
of cellular debris, leading to various autoimmune, inflammatory, neurodegenerative,
ischemic, renal and age-related diseases. Deficiency of the recognition molecule of the
classical complement pathway C1q causes an autoimmune disease (systemic lupus) in
more then 90% of the affected individuals. Hyperactivity of the complement alternative
pathway central enzyme, the C3 convertase, is a hallmark of the atypical hemolytic uremic
syndrome (aHUS). Atypical HUS is a thrombotic renal disease, very similar to the HUS
observed during this year’s famous E. coli outbreak in Germany.
We screened cohorts of aHUS and lupus patients searching for mutations in complement
genes and their functional consequences in order to understand the molecular mechanisms
of these diseases. Our results for C1q in lupus and the C3 convertase in aHUS will be used
to illustrate the co-localization of the mutations hot spots with the functionally important
sites of these molecules. We used structure-function analysis for understanding the
pathophysiology of the diseases and the efficacy of novel therapeutics. On the other hand
the functionally relevant genetic changes found in patients help us to delineate important
interaction sites within studied proteins.
– IBS seminar room.
The metal ions copper, zinc and iron have been shown to be involved in Alzheimer’s disease
(AD). Cu, Zn and Fe ions are proposed to be implicated in two key steps of AD pathology:
1) aggregation of the peptide amyloid-beta, and 2) production of reactive oxygen species
induced by amyloid-beta. There is compelling evidence that Cu and Zn bind directly to
amyloid-beta in AD. This formation of Cu/Zn– amyloid-beta complexes is thought to be
aberrant as they have been detected only in AD, but not under healthy conditions. In
this context, the understanding of how these metal ions interact with amyloid-beta, their
influence on structure and oligomerization and reactivity becomes an important issue.
Amyloid-beta is a peptide of 39 to 43 amino acids and is mostly random coil in aqueous
solution and forms amyloid type aggregated with a high content of β-sheet. The metal
ion-binding to this peptide is very dynamic and modulates the aggregation properties.
The seminar presents our recent advancements on the structural studies of complexes
between metal ions (Cu(I/II), Zn(II) and Fe(II) and amyloid-beta by a variety of methods
(1H and 13C-NMR, EPR, X-ray absorption, circular dichroism, etc) and the role of these
complexes in the production of reactive oxygen species and their interaction with other
metalloproteins.
– IBS seminar room.
CnrX est un senseur périplasmique, ancré à la membrane, appartenant au complexe CnrYXH qui
contribue à réguler l’expression des gènes impliqués dans la résistance au nickel et au cobalt chez
Cupriavidus metallidurans CH34. La résistance est induite par la libération de CnrH, un facteur
sigma de type ECF (Extracytoplasmic Function), par le complexe CnrYX en réponse à Ni et Co. Nous
avons cherché à comprendre la manière dont CnrXs, le domaine senseur de CnrX, détecte les ions
métalliques, les stratégies utilisées pour sélectionner spécifiquement Ni ou Co ainsi que la nature
du signal engendré par cette interaction. Les techniques spectroscopiques et biophysiques telles
que l’UV-visible, la RPE, le XAS et l’ITC ont permis d’étudier les sites métalliques en solution. Le
dimère de CnrXs possède quatre sites de liaison au cobalt. Deux des sites (sites F) sont retrouvés
dans la protéine entière dont nous avons maintenant un excellent modèle avec le mutant CnrXs-
H32A. Les deux autres sites (sites E) ont un signal spectroscopique atypique probablement dû à la
formation d’un complexe binucléaire de cobalt. Nous présentons également des structures à haute
résolution de CnrXs dans ses formes apo et métallées par le nickel, cobalt ou zinc. Nous avons
établi que la forme zinc est la forme inactive de la protéine et que le mécanisme de détection est
engendrée par la substitution du zinc par le nickel et le cobalt dans le site F, conduisant à une
modification majeure du site de liaison au métal. Tandis que le zinc est pentacoordiné dans une
sphère 3N2O, Ni et Co recrutent le soufre de la seule méthionine (Met123) comme sixième ligand
pour former un site octaédrique. Nous suggérons que Met123 soit l’interrupteur moléculaire dont
la liaison avec le métal fait évoluer la structure de la protéine vers une conformation active. A
notre connaissance, ces résultats constituent la première étude structurale et spectroscopique d’un
senseur de métal périplasmique impliqué dans un système de transduction du signal dépendant
d’un facteur sigma de type ECF.
– EMBL seminar room
Institut Jean Roget
Salle de Conférence, 5ème Etage
Campus Santé
38700 La Tronche
http://ijr.ujf-grenoble.fr/index.php
Institut Jean Roget
Salle de Conférence, 5ème Etage
Campus Santé
38700 La Tronche
http://ijr.ujf-grenoble.fr/index.php
Institut Jean Roget
Salle de Conférence, 5ème Etage
Campus Santé
38700 La Tronche
http://ijr.ujf-grenoble.fr/index.php
Organised by EMBL Grenoble
Cafés Sciences et Citoyens de l’Agglomération Grenobloise, 36 Rue Saint-Laurent, Grenoble
By Clément Nizak (Laboratoire Interdisciplinaire de Physique, Grenoble)
Host : T. Vernet (IBS/PG)
Holger Stark, Max-Planck Institute for Biophysical Chemistry, Gottingen, Germany
Host: Yan Nie (EMBL, Berger Group)
by Nicolas Martinez (EMBL)
EMBL seminar room
by Dr Colin KENYON, Biosciences, CSIR, Pretoria, South Africa
CIBB Seminar Room
Par Thierry Doan (Laboratoire de Chimie Bactérienne, CNRS Marseille)
hosted by Thierry Vernet (IBS/Pneumococcus Group)
IBS Seminar Room
by André Verdel (Institut Albert Bonniot, Grenoble)
Hosted by Thierry Vernet (IBS/PG)
IBS seminar room
by Keisuke Hatada (INFN Frascati, Univ. di Camerino)
Abstract
ESRF Auditorium, Central Building
Par Philippe Cinquin – TIMC - IMAG
CEA- Amphi Dautreppe
Visitors must have a registered visit prior to their arrival (send an email to Odile Rossignol (tél. 04.38.78.45.63 - Email : odile.rossignol@cea.fr) indicating your date and place of birth & your nationality). Please note that you must registered at least one week before if you are not from a CEE country. You will be asked to provide proof of your identity (e.g. passport) before being allowed to enter.
Par Cedric Allier- CEA/LETI/DTBS
CEA- Amphi Dautreppe
Visitors must have a registered visit prior to their arrival (send an email to Odile Rossignol (tél. 04.38.78.45.63 - Email : odile.rossignol@cea.fr) indicating your date and place of birth & your nationality). Please note that you must registered at least one week before if you are not from a CEE country. You will be asked to provide proof of your identity (e.g. passport) before being allowed to enter.
by Christophe Masselon de l’iRTSV
Seminar of interest for IBS, iRSTV and PSB
IBS Seminar room
presented by Rasa Sukackaite (EMBL)
EMBL Seminar Room
CANCELLED
presented by Cristina Martinez (EMBL)
EMBL Seminar Room
by Oana BUNAU of CNRS - IMPMC Paris
room 337, Central Building
By Shahid Mehmood (IBS/Membrane & Pathogens Group)
IBS seminar room
by Eejfan Breukink (Dept. Chemical Biology and Organic Chemistry,Utrecht University, Netherlands)
Host : T. Vernet (IBS/PG)
IBS seminar room
by Odile Filhol-Cochet – iRTSV/BCI-KIN
CEA- Amphi Dautreppe
Visitors must have a registered visit prior to their arrival (send an email to Odile Rossignol (tél. 04.38.78.45.63 - Email : odile.rossignol@cea.fr) indicating your date and place of birth & your nationality). Please note that you must registered at least one week before if you are not from a CEE country. You will be asked to provide proof of your identity (e.g. passport) before being allowed to enter.
presented by Manikandan Karuppasamy (EMBL)
EMBL Seminar Room
by Burkhard Schillinger, Michael Schulz (FRM II – TU München - Germany)
Room 7/8 - ILL 1
Participants without entrance to the ILL site are asked to contact : dubouloz@ill.fr
By Michel Viso (CNES, Paris)
Host : P. Vauclare (IBS/ELMA)
Seminar for all audiences
IBS Seminar room
By Pierre Cornelis (Vrije Universiteit Brussel, Microbiology)
Host : E. de Rosny (IBS/METALLO)
IBS Seminar room
by Rong Li- Stowers Institute for Medical Research - Kansas City, USA
Seminar room at the main entrance of the CEA Grenoble - no entry pass needed
By Gregg Siegal (Gorlaeus Laboratory, Leiden University, Netherlands)
Host : C. Vivès (IBS/M&P)
Abstract
_ by Gemma NEWBY of Warwick University
Hosted by N. Theyencheri (narayan@esrf.fr)
room 500 - 501, Central Building
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Eva Jahn-Feppon tel +33 (0)476 88-26-19. Requests made by e-mail will be confirmed. If you do not receive a confirmation e-mail, please contact us by phone.
presented by Mathieu Botte
EMBL Seminar Room
By Dr Sonja Welch (EMBL Heidelberg)
For site entry please contact : Rokhaya Gisele TOUNKARA (gtounkar@embl.fr)
By Bridgette Janine Connell (IBS/Structure and Activity of Glycosaminoglycans Group)
IBS seminar room
By Prof. Dr. Ian Collinson, University of Bristol, UK
Host : Christiane Schaffitzel
EMBL seminar room
by Prof. Dr. Hans-Georg Koch , University of Freiburg, Germany
Host : Christiane Schaffitzel
EMBL seminar room
By Jean-Luc Parouty (IBS/DIR)
Seminar for all audiences
IBS seminar room
by Eve de Rosny (IBS/Metalloproteins Group)
IBS Seminar room
Par Gilles Peltier – CEA DSV / IBEB
Invité par iRTSV/PCV (UMR5168 - CEA/CNRS/UJF/INRA)
salle - Accueil CEA
Par Olivier Hamant- ENS Lyon
By: Nolwenn Jouvenet, Pasteur Institute, Paris
Host: Rob Ruigrok/Winfried Weissenhorn
Salle: ILL Chadwick
By: Dr. Boris Eliseev, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences (RAS)
Hosted by: Christiane Schaffitzel
Salle: EMBL Seminar Room
by Sigolene Lecuyer (Laboratoire Interdisciplinaire de Physique (LIPhy), Saint Martin d’Hères)
Hosted by C. Morlot (IBS/Pneumococcus group)
IBS seminar room
By Françoise Jacob-Dubuisson (Centre d’Infection et d’Immunité & Institut Pasteur, Lille)
Hosted by C. Ebel (IBS/Membrane & Pathogens Group)
IBS Seminar Room
By Jean-Louis Baneres (Institut des Biomolécules Max Mousseron (IBMM), Montpellier)
_Hosted by F. Fieschi(IBS/membrane & pathogen Group)
IBS Seminar Room
By Lina Siauciunaite (IBS/Membrane &Pathogens Group)
IBS seminar room
By Hiá »ƒn Anh Nguyá »…n (IBS/Membrane & Pathogens Group)
IBS seminar room
By Carolin Seuring (Swiss Federal Institute of Technology (ETH) - Zurich)
_Hosted by D. Bourgeois (IBS/Dynamop Group)
IBS Seminar Room
By Fred Chang – Columbia university, NY
Room at the entry site of the CEA
by Daniel Panne (EMBL)
EMBL Seminar Room
by Isabelle Schalk (University of Strasbourg)
IBS seminar room
Abstract : Siderophores are small molecules having an extremely high affinity for iron and produced by bacteria in order to get access to this metal. Their biosynthesis requires the coordinated action of cytoplasmic, periplasmic, and membrane proteins. Using chromosomal replacement to generate bacteria producing fluorescent fusions with enzymes involved in the siderophore pyoverdine biosynthesis, we were able to show that these enzymes were clustered at the old cell pole of bacteria. This observation indicates a polar segregation of the proteins and of siderophore biosynthesis in Pseudomonas aeruginosa.
Concerning iron acquisition by siderophore, the E. coli ferrichrome and enterobactin pathways have been the archetype in the field for years. It was believed that the mechanisms involved in these two pathways were probably common to all siderophores pathways in Gram-negative bacteria. We have investigated at the molecular level iron uptake by three different siderophore in Pseudomonas aeruginosa (pyoverdine, pyochelin and ferrichrome) and came to the conclusion that diversity is found in the molecular mechanisms involved in siderophores pathways in Gram-negative bacteria. The ferrichrome uptake pathway in P. aeruginosa was very similar to the one shown in E. coli except for the type of protein involved in the transport across the inner membrane. For the pyoverdine pathway in P. aeruginosa, we have shown a completely different mechanism as was described for other siderophore pathways. Iron is released from the siderophore in the periplasm and not in the cytoplasm as for ferrichrome and the mechanism involves no chemical modification of the siderophore, but only iron reduction. Apo pyoverdine is then recycled from the periplasm into the extracellular medium by a specific efflux pump PvdRT-OpmQ. Recent data showed that this pump also plays a key role in the control of the metal specificity of this iron uptake pathway. All these different mechanisms involved in iron acquisition by siderophores will be discussed and compared.
by Irina Gutsche, UVHCI
EMBL Seminar room
PARTICIPANTS WHO HAVE NO BADGES ALLOWING ENTRANCE TO THE ILL-ESRF SITE ARE REQUESTED TO CONTACT Irina Gutsche
by Eric Chabrol (IBS/MP)
IBS Seminar room
Par Thomas Iwena, GRI, Groupe de recherche en immunopathologies et maladies infectieuses, Université de la Réunion
Hosted by Nicole Thielens (IBS/IRPAS)
Salle des séminaires de l’IBS
Par Romain Talon (IBS/ELMA)
IBS Seminar room
by Daniel Picot (Institut de Biologie Physico-Chimique, Paris)
Hosted by E. Girard(IBS/ELMA)
IBS Seminar room
by Ali Flayhan (IBS/Membrane & Pathogens Group)
_ IBS seminar room
by Vera Moiseeva (IBS/Membrane Transporters Group)
_ IBS seminar room
by Olivier Berteau (INRA, Jouy en Josas)
hosted by : J. Fontecilla (IBS/Metallo)
IBS seminar room
presented by Kyle Muir (EMBL)
EMBL Seminar Room
Dr. Federico Katzen, Unit Head, Life Technologies/Invitrogen, Carlsbad, USA
Host : Imre Berger (iberger@embl.fr)
EMBL Seminar Room, EMBL Grenoble
presented by Laurence Pearl, University of Sussex
_Host : Daniel Panne
ILL Chadwick
presented by Dr. Federico Katzen, Unit Head, Life echnologies/Invitrogen, Carlsbad
Host : Imre Berger
EMBL Seminar Room
presented by Esther Ortega
EMBL Seminar Room
by Prof Hélène Joliot-Curie (Institut de Physique Nucléaire, Orsay)
CHADWICK AMPHI
External visitors may ask for a site access to Karine Sultan (sultan@ill.fr)
By Laurent Kremer (Dynamique des Interactions Membranaires Normales et Pathologiques, Montpellier)
Hosted by : C. Bougault (IBS/NMR)
IBS seminar room
Par Jean-Luc Pellequer (Institut de biologie environnementale et biotechnologie (CEA/DSV/IBEB), Service de biochimie et toxicologie nucléaire (SBTN) - Marcoule
Hosted by : M. Weik (IBS/DYNAMOP)
IBS seminar room
Glen Ramsay (Aviv Technology) will make this lecture
room 4225 IBS
by Prof. Franck Duong (University of British Columbia, Vancouver, Canada)
hosted by Christiane Schaffitzel (EMBL)
EMBL seminar room
by Dror Warschawski (IBPC -Paris)
hosted by J. Boisbouvier (IBS/NMR)
_ IBS seminar room
Par June Kwak – Department of Cell Biology & Molecular Genetics, University of Maryland, USA
– CEA entrance
presented by Thomas Saijo (EMBL)
by Prof. Henry R. Glyde (Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA)
Seminar Room 1rst floor, ILL 4
by Prof Catherine PICART (LMGP in Minatec, Grenoble Institute of Technology and CNRS, Grenoble)
CHADWICK AMPHI, ILL4, Ground Floor
by Dr Giorgio SCHIRO (Department of Physics, University of Palermo, Italy)
EMBL Seminar Room
by Rita Giordano (ESRF) abstract
ESRF Auditorium, Central Building
by John Tomkinson (ISIS Facility, UK)
Seminar Room 1rst floor, ILL 4
presented by Pierre-Yves Lozach, Institut für Biochemie, ETH-Hönggerberg, Zürich
EMBL Seminar Room
presented by Dr. Oliver Daumke, Max-Delbrück-Centrum for Molecular Medicine, Berlin
EMBL Seminar Room
By Markus Sauer (Julius-Maximilians-University Würzburg, Germany)
Hosted by Virgile Adam (IBS/DYNAMOP)
IBS Seminar Room
by Andrew Aquilina (University of Wollongong, Australia)
Hosted by E. Boeri Erba (IBS/VIC)
_ IBS seminar Room
by Dr Stefania Galdiero from University of Naples "Federico II", Italy
ILL Oval Room (ILL Main Building ILL4 - First Floor - Door 163)
by Mélanie Verneret (IBS/IRPAS)
IBS Seminar room
by Yasser Heidari (IBS/GSY)
IBS Seminar room
by Mickael Jacquet (IBS/IRPAS)
IBS Seminar room
by Aline Faro (IBS/DYNAMOP)
IBS Seminar room
by Dr. Andres Ramos (MRC, National Institute for Medical Research, London, United Kingdom)
Hosted by Nikolas Mathioudakis (EMBL/Cusack Group)
EMBL seminar room
By Martha BRENNICH of Institute for X-Ray Physics, Georg-August-Universität Göttingen, Germany
Hosted by Petra Pernot (rejma@esrf.fr)
Abtsract
Room 500 - 501, Central Building
by Wiebke Knoll (ILL)
EMBL seminar room
Par Antoine Nigues of ESRF Grenoble, France
ESRF Auditorium, Central Building
by Alessandro SPILOTROS of University of Palermo Dept. Physics Via Archirafi 36 90123 Palermo (Italy)
CTRM Control Room
presented by Gergely Papp
EMBL Seminar Room
presented by Jorge Dias
EMBL Seminar Room
By Ranieri Bizzarri (Scuola Normale Superiore and Istituto Nanoscienze
Pisa, Italy)
IBS Seminar room
presented by Irina Gutsche, UVHCI
EMBL Seminar Room
presented by Catarina Silva, EMBL
EMBL Seminar Room
presented by Nikolaos Mathioudakis, EMBL
EMBL Seminar Room
presented by Charlotte Sueur, UVHCI
EMBL Seminar Room
presented by Rasa Sukackaite, EMBL
EMBL Seminar Room
by Vadim Cherezov (The Scripps Institute, La Jolla, USA)
Hosted by V. Gordeliy (IBS/MEMBRANE)
IBS seminar room
by Yvain Nicolet (IBS/Metalloproteins Group)
IBS seminar room
by Marion Sevajol (IBS/Immune response to pathogens and altered-self Group)
IBS seminar room
By Claire Durmort (IBS/Pneumococcus Group)
IBS seminar room
By Rut Carballido-Lopez (Institut Micalis, INRA, Jouy-en-Josas)
Hosted by T. Vernet (IBS/ Pneumococcus Group)
IBS seminar room
By Jean-Baptiste Reiser (IBS/Immune response to pathogens and altered-self Group)
IBS seminar room
By Jérôme Nigou (Institut de Pharmacologie et de Biologie Structurale, Toulouse)
Hosted by H. Lortat-Jacob (IBS/SAGAG) & J.P. Simorre (IBS/NMR)
IBS seminar room
presented by Kuan-Ming Chen
EMBL Seminar Room
by Jean Jacque Hublin, Max Planck Institute for Evolutionary Anthropology, Leipzig (Germany)
_ Chadwick amphitheatre, ILL
presented by Ottilie Von Loeffelholz
EMBL Meeting Room
presented by Eva Geenen
EMBL Seminar Room
presented by Prof. Dr. Mikel Valle, Structural Biology Unit, CICbioGUNE
CIBB Seminar Room
presented by Boris Eliseev
By Samuel T. Hess (University of Maine, USA)
IBS seminar room
by Lauriane Lecoq (IBS/NMR spectroscopy Group)
IBS seminar room
by Prof. Boris Noskov, St Petersburg State University, Russian Federation
CIBB Seminar Room
by Dr. Aleksandra Dabkowska, Lund University, Sweden
EMBL Seminar Room
by Dr. Marité Cárdenas, Copenhagen University, Denmark
EMBL Seminar Room
by Prof. Karl-Peter Hopfner (Gene Center, Munich)
Hosted by Joanna TIMMINS (IBS/VIC)
IBS seminar room
by Joanna TIMMINS (IBS / Virus Infection & Cancer Group / DNA Damage & Repair Team)
IBS seminar room
By Martin R. Fuchs of MX Group, Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
Auditorium, Central Building
Par Anne Laure Favier (Centre de Recherches du Service de Santé des Armées, La Tronche)
Host : N. Thielens (IBS/Groupe IRPAS)
IBS seminar room
by Ambroise Desfosses (UVHCI)
amphiteatre Chadwick
By Valéry Ozenne (IBS/Protein Dynamics and flexibility by NMR Group)
IBS Seminar room
by Pascal Poignard, Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California
ILL Chadwick
by Vanessa Delfosse (Centre de Biochimie Structurale, Montpellier) - Hôte : B. Franzetti (IBS/Groupe ELMA)
_Please note that the following IBS seminar is cancelled
presented by Dr. Maria Carla Saleh (Viruses and RNAi Group, Institut Pasteur)
EMBL Seminar Room
by Christine Ebel (IBS/M&P)
IBS Seminar room
by Winnie Ling (IBS/MEM)
IBS seminar room
by Antoine Royant (IBS/DYNAMOP)
IBS seminar room
by Paul Schanda (IBS/NMR)
IBS seminar room
by Cécile Breyton (IBS/M&P)
IBS seminar room
by Jacques Colletier (IBS/DYNAMOP)
IBS seminar room
by Christiane Schaffitzel (EMBL)
IBS seminar room
by Malène Jensen (IBS/FDP)
IBS seminar room
In the context of the Enzymology course in Master 2, Jean-Marie Frère from the University of Liège will give on monday 26th from 13h30 to 16h30 in the EMBL seminar room a lecture entitled : "Les aventures d’un cinéticien au pays de beta-lactamines". For those of you who would like to know more about the enzymes that are targeted by penicillin and other beta-lactam antibiotics and about the resistance mechanisms developped by the bacteria, the lecture is opened and you are welcome to participate
EMBL Seminar room
By Ieva Sutkeviciute (IBS/Membrane and Pathogens Group)
CERMAV seminar room
by Pierre-Emmanuel Milhiet (Centre de Biochimie Structurale, Montpellier)
Hôte : J.M. Jault (IBS/Membrane and Pathogens Group)
IBS Seminar room
by Daniel Marc, UMR-1282, Infectiologie et Santé Publique, INRA, Tours
CIBB Seminar room
by Gaë l GORET (ESRF)
ESRF, room 500 - 501
by Bruce Turnbull (University of Leeds)
_ IBS Seminar Room
by Thomas Cutuil (IBS/Biomolecular NMR Spectroscopy Group)
IBS Seminar Room
presented by Nataliia Aleksandrova
EMBL Seminar Room
presented by Srinavasan Rengachari, University of Graz
[Host : Daniel Panne]
EMBL Seminar Room
presented by Prof. Dr. Marc Timmers, Molecular Cancer Research, University Medical Center Utrecht
[Host : Imre Berger]
EMBL Seminar Room
presented by Yan Nie
EMBL Seminar Room
by Olivier Genest (Laboratory of Molecular Biology, National Cancer Institute, Bethesda, USA)
Host : J.M. Jault (IBS/Groupe Membrane & Pathogènes)
IBS seminar room
by Neil Hunter (Department of Molecular Biology and Biotechnology, The University of Sheffield, UK)
Hosted by D. Bourgeois (IBS/DYNAMOP)
IBS seminar room
by Erwan Gueguen (Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Marseille)
Hosted by C. Cavazza (IBS/Metalloproteins)
_ IBS seminar room
by Jacques Colletier (IBS/DYNAMOP)
IBS Seminar room
By Els Saesen (IBS/Structure and Activity of Glycosaminoglycans Group)
IBS Seminar room
Presented by Nadia Rosenthal and Alex Mauron, Australian Regenerative Medicine Institute, Monash, and University of Geneva
[Host: Halldór Stefánsson]
For more information check here
By Alexandre MJJ Bonvin
Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands.
Contact: a.m.j.j.bonvin@uu.nl
Protein-protein interactions underlie most cellular processes, including signal transduction and apoptosis. Understanding how the cell works requires describing these at molecular level, which is bound to have a dramatic impact on current and future structure-based drug design. Computational methods may assist in this task, particularly when some experimental data can be obtained.
I will first describe our information-driven docking approach HADDOCK (http://haddock.science.uu.nl), illustrating it with various examples including results from the CAPRI blind scoring experiment. I will then discuss the problem of binding affinity prediction, showing that current scoring functions in macromolecular docking fail at predicting the affinity of protein-protein complexes. For binding affinity calculation, the surface buried upon complexation is not the absolute determinant and inclusion of additional structural parameters, previously neglected is deemed mandatory for near-accurate predictions. In conclusion, current biophysical models are far more adequate in predicting accurate conformations of protein-protein complexes rather than assessing the affinity of their interactions.
References
• S.J. de Vries, A.S.J. Melquiond, P.L. Kastritis, E. Karaca, A. Bordogna, M. van Dijk, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin (2010). Strengths and weaknesses of data-driven docking in CAPRI. Proteins: Struc. Funct. & Bioinformatic, 78, 3242-3249.
• P.L. Kastritis and A.M.J.J. Bonvin (2010). Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Res., 9, 2216-2225.
• P.L. Kastritis, I.H. Moal, H. Hwang, Z. Weng, P.A. Bates, A.M.J.J. Bonvin and J. Janin (2011). A structure-based benchmark for protein-protein binding affinity. Prot. Sci., 20, 482-41.
• A.S.J. Melquiond, E. Karaca, P.L. Kastritis and A.M.J.J. Bonvin (2012). Next challenges in protein-protein docking: From proteome to interactome and beyond. WIREs Computational Molecular Science 2, 642-651.
To consult the list of upcoming seminars organised by the PSB Partners check the following links:
IBS seminars
EMBL seminars
ESRF Seminars
ILL seminars
For other scientific seminars organised in the Grenoble area, please check HERE (in french only)
To consult the list of upcoming seminars organised by the PSB Partners check the following links:
IBS seminars
EMBL seminars
ESRF Seminars
ILL seminars
For other scientific seminars organised in the Grenoble area, please check HERE (in french only)
To consult the list of upcoming seminars organised by the PSB Partners check the following links:
IBS seminars
EMBL seminars
ESRF Seminars
ILL seminars
For other scientific seminars organised in the Grenoble area, please check HERE (in french only)
