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Paul Schanda ERC Starting Grant 2012
This project will investigate the link between motion and function in two challenging systems. On the one hand, the intrinsic dynamics of a membrane protein will be studied in the light of its transport activity. Membrane proteins fulfill a wide range of functions in the cell, and are a prime drug target. Yet, our current knowledge about their structure and dynamics is very limited, due to the difficulties to obtain atomic-resolution data. Importantly, for many functions, such as transport across membranes and signaling, flexibility is a key property. In this project Paul Schanda’s team will use and develop nuclear magnetic resonance techniques to provide unprecedented insight into the intimate connection between motion and function on an atomic level. As a second target, the team will also investigate another class of challenging biological objects : very large chaperones, that assist other proteins in their folding. Their sheer size makes atomic-resolution studies of chaperones at a molecular level a significant challenge. Again, a combination of solution and solid-state NMR will be used to address the function and interaction with client proteins. The main tool used for these studies will be nuclear magnetic resonance, both in solution and in the solid state. The combination of both NMR approaches will allow to go significantly beyond the capabilities of each technique alone. The structural biologist Paul Schanda developed innovative NMR techniques during his PhD, focusing primarily at speeding up NMR data acquisition. A number of now state-of-the-art tools, have accelerated NMR by more than one order of magnitude, and allow nowadays to study short-lived protein states, such as folding intermediates in real time. For his post-doc, he switched to an emerging technique in structural biology, solid-state NMR. During his research period at ETH Zurich in B. H. Meier’s lab, he developed and applied solid-state NMR techniques for the study of protein motion in fibrillar and microcrystalline proteins. End of 2010, Paul Schanda joined IBS, where he could set up a small team funded by an ANR grant. The main goal of his team is the study of protein dynamics in challenging biological systems. *ERC Starting Grants are awarded for a five-year period to academics leading an independent team or programme who have the potential to become world-class researchers |
Pretending to be somebody elseHuman and pneumococcal cell surface glyceraldehyde-3-phosphate dehydrogenase (GAPDH) proteins are both ligands of human C1q protein. Terrasse R1, Tacnet-Delorme P, Moriscot C, Pérard J, Schoehn G, Vernet T, Thielens NM, Di Guilmi AM, Frachet P. J Biol Chem. 2012 Dec 14 ;287(51):42620-33. |
Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation
Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation. Luca Mollica, Maria Baias, Józef R. Lewandowski, Benjamin J. Wylie, Lindsay J. Sperling, Chad M. Rienstra, Lyndon Emsley, and Martin Blackledge. J. Phys. Chem. Lett., 2012, 3 (23), pp 3657–3662 |
New insight into the dynamical behavior of protein molecules
[1] Protein Surface and Core Dynamics Show Concerted Hydration-Dependent Activation. Wood K, Gallat FX, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M, Mulder FA. Angew Chem Int Ed doi : 10.1002/anie.201205898. [Epub ahead of print] |
A fluorescent protein turns to the dark side
GFP-like phototransformation mechanisms in the cytotoxic fluorescent protein KillerRed unraveled by structural and spectroscopic investigations. Eve de Rosny and Philippe Carpentier. J. Am. Chem. Soc., 2012, 134 (43), pp 18015–18021 |
Heparan sulphate helps chemokines to direct cell migration within tissues
Homeostatic and tissue reparation default in mice carrying selective genetic invalidation of CXCL12/proteoglycan interactions. Rueda P., Richart A., Récalde A., Richart A., Gasse P., Vilar J., Guérin C., Lortat-Jacob H., Vieira P., Baleux F., Chretien F., Arenzana-Seisdedos F. and Silvestre J-S. Circulation 126, 1882-1895 (2012) |
The very elongated structure of RecN revealed by a combined structural biology approach.The first quasi-atomic structure of a member of the SMC (Structural maintenance of chromosomes)-like protein family, namely the RecN protein, was assembled from three crystal structures and a low-resolution envelope by scientists from the ESRF and IBS. This structure together with biochemical studies allowed us to propose a model for the role of RecN in the repair of DNA double-strand breaks.
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Electronic tongue for protein analysis
Continuous Evolution Profiles for Electronic Tongue Based Analysis. Hou Y., Genua M., Tada Batista D., Calemczuk R., Buhot A., Fornarelli P., Koubachi J., Bonnaffé D., Saesen E., Laguri C., Lortat-Jacob H. and Livache T. Angew Chem Int Ed Engl. 51 (41), 10394-10398 (2012). |
Science Fair 2012
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Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution by NMR
Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution. Ozenne V, Schneider R, Yao M, Huang JR, Salmon L, Zweckstetter M, Jensen MR, Blackledge M. J Am Chem Soc. ;134(36):15138-48 |
A channeling mecanism is involved in the pathway of the biotin synthesis in plants
Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase : Evidence for Substrate Channeling in Biotin Synthesis, Cobessi, D., Dumas, R., Pautre, V., Meinguet, C., Ferrer, J.-L., Alban, C., Plant Cell ;24(4):1608-25 |
Molecular basis of genetic diseases revealed by functional and dynamic studies of the mitochondrial ADP/ATP carrier
Impaired Transport of Nucleotides in a Mitochondrial Carrier Explains Severe Human Genetic Diseases. Stéphanie Ravaud, Axel Bidon-Chanal, Iulia Blesneac, Paul Machillot, Céline Juillan-Binard, François Dehez, Chris Chipot and Eva Pebay-Peyroula. ACS Chem. Biol., 2012, 7 (7), pp 1164–1169 |
Insights into the mechanism of Helicobacter pylori cytotoxin cagA internalization by host cells
Structural insights into Helicobacter pylori CagA interaction with β1 integrin. Kaplan Türköz B, Jiménez-Soto LF, Dian C, Ertl C, Remaut H, Louche A, Tosi T, Haas R and Terradot L. Proc. Natl. Acad. Sci. ;109(36):14640-5. |
A new method for understanding conformational exchange processes in solid protein samples : application to hidden states in a cristalline protein
Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy. Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. J Am Chem Soc. 2012 Sep 12 ;134(36):14800-7 |
Neutron scattering explains how myoglobin can perform without water
A Polymer Surfactant Corona Dynamically Replaces Water in Solvent-Free Protein Liquids and Ensures Macromolecular Flexibility and Activity. François-Xavier Gallat, Alex P. S. Brogan, Yann Fichou, Nina McGrath, Martine Moulin, Joachim Wuttke, Stephen Mann, Giuseppe Zaccai, Colin J. Jackson, Adam W. Perriman, and Martin Weik. Journal of the American Chemical Society ;134(32):13168-71. |
Contamination from affinity column : a new villain in the world of membrane protein crystallization
Contamination from affinity column : a new villain in the world of membrane protein crystallization. R. Panwar, A. Deniaud and E. Pebay-Peyroula. Acta Crystallogr D Biol Crystallogr. 2012 Oct ;68(Pt 10):1272-7 |
A key cell cycle kinase of the pneumococcus
Mutational dissection of the S/T-kinase StkP reveals crucial roles in cell division of Streptococcus pneumoniae. Fleurie A, Cluzel C, Guiral S, Freton C, Galisson F, Zanella-Cleon I, Di Guilmi AM, Grangeasse C. Mol Microbiol. ;83(4):746-58. doi : 10.1111/j.1365-2958.2011 |
Better understanding of the role of the NS5A protein during hepatitis C virus infectionThe NS5A protein of hepatitis C virus plays an important role in virus replication and particle formation. In collaboration with the research group of D. Willbold (FZ Jülich, D) we have investigated the structure and dynamics of an intrinsically disordered fragment (188 residues) of NS5A comprising interaction sites with a large number of other viral and host proteins. Our study reveals the presence of transient a-helical structures in 3 regions of the peptide sequence that are partly stabilized by long-range tertiary interactions. Two of these transient a-helices form a non-canonical binding motive which allows low affinity binding to the SH3 domain of the tumor suppressor protein Bin-1. Our results contribute to a better understanding of the role of the NS5A protein during hepatitis C virus infection. Transient structure and SH3 interaction sites in an intrinsically disordered fragment of the hepatitis C virus protein NS5A. Sophie Feuerstein, Zsofia Solyom, Amine Aladag, Adrien Favier, Silke Hoffmann, Dieter Willbold, Bernhard Brutscher. Journal of Molecular Biology ; 420(4-5):310-23 |
Structure of ExoU, toxin of the human pathogen Pseudomonas aeruginosaThe human pathogen Pseudomonas aeruginosa employs its type III secretion system in order to initiate acute infection. One of the toxins injected into cells by this system, ExoU, causes massive cell damage rapidly through phospholipolysis of target membranes. Here, we have solved the structure of ExoU in complex with a partner molecule and identified that it folds into three independent domains. Fluorescence microscopy experiments indicate that once injected, the cell attempts to clear the toxin from the cytosol by introducing it into the endosomal pathway, but this defense action is not quick enough and membranes get degraded in few minutes by ExoU’s phospholipase action, explaining the aggressiveness of Pseudomonas strains that express this toxin. Structural Basis of Cytotoxicity Mediated by the Type III Secretion Toxin ExoU from Pseudomonas aeruginosa. Gendrin C, Contreras-Martel C, Bouillot S, Elsen S, Lemaire D, Skoufias DA, Huber P, Attree I, Dessen A. PLoS Pathogens 8, e1002637. |
Dynamics of a bacterial multidrug ABC transporter in the inward and outward facing conformations
Dynamics of a bacterial multidrug ABC transporter in the inward and outward facing conformations. Mehmood, S., Domene, C., Forest, E. & Jault, J.-M. Proc Natl Acad Sci U S A. 2012 Jul 3 ;109(27):10832-6 |
(IscS-IscU)2 Complex Structures Provide Insights into Fe2S2 Biogenesis and Transfer
(IscS-IscU)2 Complex Structures Provide Insights into Fe2S2 Biogenesis and Transfer. Elodie N. Marinoni, Jaim S. de Oliveira, Yvain Nicolet, Estella C. Raulfs, Patricia Amara, Dennis R. Dean, and Juan C. Fontecilla-Camps. Angewandte Chemie International Edition ;51(22):5439-42 |
7th IBS scientific day and 20th anniversaryOn June 08, 2012, IBS organized its 7th Science Day, which brought together most of the staff (about 200 people) in the Weil Amphitheater on the campus. Former permanent people were also invited as IBS celebrates its 20th anniversary in 2012.
Note that the IBS will held a ‘Midi Minatec’ conference on October 05, 2012 to celebrate 20 Years of research with all its partners. |
Detailed Characterisation of the Conformational Energy Landscape of the SH3C domain of CD2AP by NMR
Multi-Timescale Conformational Dynamics of the SH3 Domain of CD2-Associated Protein using NMR Spectroscopy and Accelerated Molecular Dynamics. Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. Angew Chem Int Ed Engl. ; 51(25):6279. |
Putting a stop to L,D-transpeptidases
Dynamics induced by β-lactam antibiotics in the active site of Bacillus subtilis L,D-transpeptidase. Lecoq L, Bougault, C., Hugonnet J.-E., Veckerlé C., Pessey O., Arthur, M., Simorre J.-P. Structure ; 20(5):850-61. |
Real-Time NMR Characterization of Structure and Dynamics in a Transiently-Populated Protein Folding Intermediate
Real-Time NMR Characterization of Structure and Dynamics in a Transiently-Populated Protein Folding Intermediate. Enrico Rennella, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge, and Bernhard Brutscher. Journal of the American Chemical Society, 2012 May 16 ;134(19):8066-9. Epub 2012 May 7. |
A combination of methods to develop a high resolution description of the unfolded state of the protein ubiquitinNuclear magnetic resonance (NMR) spectroscopy is increasingly recognised as the most powerful experimental tool for studying protein folding and stability. In a recent study researchers at the IBS used extensive experimental NMR data, in combination with small angle scattering and a unique tool for the description of dynamic conformational equilibria, to develop a high resolution description of the unfolded state of the protein ubiquitin, providing sequence specific details of the interaction between the denaturant and the protein. In related studies the same methodology was applied, in collaboration with researchers at the Goethe university in Frankfurt, to understand the folding pathway of the protein Lysozyme. Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering data. Huang JR, Gabel F, Jensen MR, Grzesiek S, Blackledge M. J Am Chem Soc. 2012 Mar 7 ;134(9):4429-36. Modulation of structure and dynamics by disulfide bond formation in unfolded States. Silvers R, Sziegat F, Tachibana H, Segawa S, Whittaker S, Günther UL, Gabel F, Huang JR, Blackledge M, Wirmer-Bartoschek J, Schwalbe H. J Am Chem Soc. 2012 Apr 18 ;134(15):6846-54. |
Rational design of a remarkably efficient cyan fluorescent proteinResearchers from the IBS (Institut de biologie structurale, CEA-CNRS-UJF) and the ESRF (European Synchrotron Radiation Facility), in collaboration with groups from the Universities of Amsterdam and Oxford, have managed to design a new cyan fluorescent protein (CFP) whose fluorescence efficiency is unmatched among this family of proteins, using a combination of structural biology and genetic engineering. Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%, J. Goedhart, D. von Stetten, M. Noirclerc-Savoye, M. Lelimousin, L. Joosen, M. A. Hink, L. van Weeren, T. W. Gadella Jr, and A. Royant, Nat. Commun. 2012 Mar 20 ;3:751 |
The IBS actor of INSTRUCT, the European integrated biology infrastructureBreakthroughs in biomedical science are a step closer, with the launch, on February 23rd, 2012, of a new distributed research infrastructure for the science of structural biology. The launch of ‘Instruct’ will give academic and commercial scientists across Europe access to a full portfolio of integrated technologies, thanks to the collaboration of leading european structural biology research institutes. Instruct provides access to some of the most advanced technology in the world. A full catalogue of the accessible technology is available on the Instruct Hub at www.structuralbiology.eu. The Hub includes adverts for jobs and academic programmes, a comprehensive calendar of events and discussion forums, with plans for virtual workspaces for collaborative projects in the near future. The Hub is also home to a number of networks of scientists with a common interest or objective. Grenoble (PSB) and Strasbourg (IGBMC) are the two French Instruct centers among 15 Instruct centers. The Institut de Biologie Structurale provides access to high-tech instruments and cutting-edge know-how through a number of platforms (Cryo EM, MP3 et NMR). |
A peptide to mimic a sugar and inhibit the entry of HIV into cells
A synthetic heparan sulfate-mimetic peptide conjugated to a mini CD4 displays veryhigh anti-HIV-1 activity independently of coreceptor usage. Connell B.J., Baleux F., Coic YM., Clayette P., Bonnaffé D and Lortat-Jacob H. Chemistry & Biology 19 (1) 131-139 (2012) |
Molecular mechanisms of the biogenesis of Streptococcus pneumoniae pilus
Streptococcus pneumoniae is a major human pathogen, responsible for ear infections, pneumonia, septicemia and meningitis. Recently pilus-like structures were identified on the surface of S. pneumoniae, which play an important role in the initial stages of colonization of host tissues. Six genes are involved in the formation of this structure. Three of them encode structural proteins or pilins (RrgA, RrgB and RrgC) whereas three other genes code for enzymes called sortases, catalyzing the covalent association of pilins (SrtC-1, SrtC-2 and SrtC-3 ). The structural characterization of pilins RrgA, RrgB and RrgC was completed owing a collaboration between the pneumococcus and the Bacterial Pathogenesis Groups of the IBS. It revealed the presence of a new type of posttranslational modification : intramolecular bridges between Lys-Asn residues. The stabilizing effect on each pilins of these unusual covalent bonds has been established. Furthermore, the crystallographic structures of RrgA and RrgB has elucidated some aspects of the pilus assembly process and its adhesive properties. To define the substrate specificity of each of the three sortases, we have developed a platform of co-expression of pilins and sortases in the E. coli recombinant system. This study identified the specific sortases catalysing the formation of complexes between pilins and sortases. Overall this work has revealed key insights in our understanding of the biogenesis of the pilus in S. pneumoniae allowing us to propose a new model of pilus assembly.
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Inhibition of HIV infection in human uterine tissue samplesMore than 18 months ago, our team has contributed, in the context of a European network, to the demonstration that some molecules inhibiting DC-SIGN, that are produced within our network (glycomimic dendrons), had the potency to block DC-SIGN-mediated HIV trans-infection of T lymphocytes. DC-SIGN is a receptor of dendritic cells present in epithelium and mucosa that is hijacked by HIV in order to be transmitted through the genital mucosal barrier. A glycomimetic compound inhibits DC-SIGN-mediated HIV infection in cellular and cervical explant models. Berzi A, Reina JJ, Ottria R, Sutkeviciute I, Antonazzo P, Sanchez-Navarro M, Chabrol E, Biasin M, Trabattoni D, Cetin I, Rojo J, Fieschi F, Bernardi A, Clerici M. AIDS. 2012 Jan 14 ;26(2):127-137. |