Accueil > Research > Highlights > Archives > 2009
A Complex Mechanism Explains How a Fluorescent Protein Changes Colour
Photoconversion of the Fluorescent Protein EosFP : A Hybrid Potential Simulation Study Reveals Intersystem Crossings. Micka l Lelimousin, Virgile Adam, G. Ulrich Nienhaus, Dominique Bourgeois and Martin J. Field. JACS ;131(46):16814-23. |
The “gagophilic” side of chemokines
The molecular basis and functional implications of chemokine interactions with heparan sulphate. Lortat-Jacob H. Curr. Opin. Struct. Biol. 19, 543-548 |
How fluorescent proteins blink
Structural Basis of X-ray-Induced Transient Photobleaching in a Photoactivatable Green Fluorescent Protein. Adam V, Carpentier P, Violot S, Lelimousin M, Darnault C, Nienhaus GU, Bourgeois D. J Am Chem Soc. ;131(50):18063-5. |
A Unified Representation of Protein Structural Dynamics in Solution ?
Towards A Unified Representation of Protein Structural Dynamics in Solution. P.R.L. Markwick,G. Bouvignies, L. Salmon, J.A. McCammon, M. Nilges and M. Blackledge. J.Am.Chem.Soc. 131(46) : 16968-16975, 2009. |
Open Days 2009In the framework of the 2009 French science week, the IBS organized a 4-day event :
A hundred school pupils attended a general presentation about proteins, methods used to determine their structure and also careers in research. After this talk they visited laboratories and conducted experiments.
On Saturday, November 21, a large family audience (158 people) was able to enjoy a wide range of activities
About fifty volunteers were mobilized to welcome secondary school pupils and the lay public and helped to make it a successful event. |
An IBS team distinguished as "FRM Team 2009"The team of Andrea Dessen (from the Membrane Protein Laboratory) has |
Putting the squeeze on sperm DNA (Nature)Scientists discover a new way to read the histone code by studying streamlined sperm
Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. |
IBS researchers on Ushuaia TV (September 30)Researchers from the IBS are featured in the first episode of an international documentary series "Architects of Change", which will run from Wednesday, September 30 on Ushuaia TV (broadcast weekly, 10 episodes). In the first episode entitled "To innovate is to imitate," M. (Michel ?) Vivaudou presents the work of his team on a new type of biosensor. To find out more about "Architects of Change" |
Design of a hydrogenase with improved oxygen resistanceThe metalloprotein group of the LCCP has contributed to the design and the characterization of [NiFe] hydrogenase mutants that, in contrast to the wild type enzyme, retain catalytic activity in the presence of molecular oxygen. This may open the way to applications in which these enzymes are used for the clean production of molecular hydrogen, potential major energy carrier of the future, from water and sunlight. Introduction of methionines in the gas channel makes [NiFe] hydrogenase aero-tolerant. Dementin S, Leroux F, Cournac L, de Lacey AL, Volbeda A, Leger C, Burlat B, Martinez N, Champ S, Martin L, Sanganas O, Haumann M, Fernandez VM, Guigliarelli B, Fontecilla-Camps JC and Rousset M. Journal of the American Chemical Society (2009) 131(29) : 10156-10164 |
Sugar and peptide combines to fight HIVHIV normally enters cells when gp120, a protein on the surface of HIV, binds to receptors on the host cell. In this process, gp120 first binds to one receptor - CD4 - which causes the structure of the protein to change so that it can bind to a second receptor, such as CCR5 or CXCR4. Following several studies showing that this second receptor binding site also interact with heparan sulphate, Hugues Lortat-Jacob and colleagues have now made a molecule that contains a sequence of amino acids to mimic CD4 and a sequence of carbohydrates to mimic heparan sulfate to bind to both sites on gp120. This new strategy results in very effective inhibition of HIV infection in cellular assays, and so may have implications for further antiviral efforts. A synthetic CD4-HS glycoconjugate inhibits both CCR5 and CXCR4 HIV-1 attachment and entry. Baleux F., Loureiro-Morais L., Hersant Y., Clayette P., Arenzana-Seisdedos F., Bonnaffé B. Lortat-Jacob H., Nature Chem. Biol. 5, 743-748.
|
Unexpected electron transfer in the mechanism of radical SAM-dependent proteinsRadical S-adenosine-L-methionine (SAM or AdoMet) proteins are involved in chemically difficult reactions including the synthesis of cofactors, the generation of protein radicals, and the maturation of complex organometallic catalytic sites. In the first and common step of the reaction, a conserved [Fe4S4] cluster donates an electron to perform the reductive cleavage of AdoMet into methionine and a reactive radical 5’dA. species. We have used protein crystallography and theoretical calculations to show that regardless whether AdoMet serves as a cofactor or a substrate, the 5’-dA. generating mechanism should be common to the radical SAM proteins studied so far, and that electron transfer is mediated by a unique Fe from the conserved [Fe4S4] cluster. Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins. |
Structure and functional relevance of the Slit2 homodimerization domainSlit proteins are secreted proteins that interact with- and signal through- the Roundabout (Robo) receptors, in a heparan sulphate dependant manner. They mediate a change in axonal response from attraction to repulsion, and provide important guidance cues during neuronal development. To better understand the role of Slit domains in signalling, the crystal structure of the fourth Slit2 domain (D4) was determined and its effect on chick retinal ganglion cell axons was examined. The Slit2 D4 domain forms a stable non-symmetrical dimer through highly conserved residues on its concave face. Functional studies showed that Slit2 dimerization is functionally relevant and that heparan sulphate can inhibit the collapse response of chick retinal ganglion cell growth cones to Slit2 D4 Structure and functional relevance of the Slit2 homodimerization domain. |
Origins of life : IBS researchers provide an update on ancestral enzymes in Nature journalStructure-function relationships of anaerobic gas-processing metalloenzymes. Podcast (Insight reviews). |
A stunning mechanism explains the functionning of a red fluorescent protein.Fluorescent proteins are invaluable fluorescent markers in cell biology. We have studied the red fluorescent protein Keima, which exhibits a huge Stokes shift of 180 nm, an extremely useful property for multicolor experiments. Combining X-ray crystallography with absorption, fluorescence and Raman spectroscopy, we have discovered a fascinating property of Keima : the higher the pH, the more protonated the chromophore becomes. This very strange property allows explaining the large Stokes shift of the protein at physiological pH. Reverse pH-Dependence of Chromophore Protonation Explains the Large Stokes Shift of the Red Fluorescent Protein mKeima |
Studying the mechanism of protein denaturation using SANS and SAXSCharacterization of the conformational properties of denatured proteins is essential to our understanding of the molecular basis of protein folding and stability. Here we combine small angle neutron and X-ray scattering to study the interaction of urea with the protein ubiquitin. Comparing coherent intensities scattered at zero angle, and exploiting the scattering densities of H(2)O, D(2)O, ubiquitin, and urea for X-rays and neutrons, we quantitatively determine the number of urea molecules preferentially bound during unfolding of ubiquitin. We find that a pH change from 6.5 to 2.5 triggers recruitment of approximately 20 urea molecules from bulk solution per ubiquitin molecule during the unfolding process. Quantitative modelfree analysis of urea binding to unfolded ubiquitin using a combination of small angle X-ray and neutron scattering. Gabel F, Jensen MR, Zaccaï G, Blackledge M. JACS 2009 Jul 1 ;131(25):8769-71 |
Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus EpIn order to understand the principles that guide emergence of public T cell responses against cytomegalovirus, we have performed structural, biophysical and functional analyses of an immunodominant public T cell receptor (RA14 TCR) directed against a major HLA-A*0201-restricted HCMV antigen (pp65495-503) and selected in vivo from a diverse repertoire after chronic stimulations. The RA14 TCR interacts with the full array of available peptide residues indicating that its emergence out of an oligoclonal antigen-specific response after repeated viral stimulations is based on a high structural complementarity with the antigen. These results highlights key parameters underlying selection of a protective T cell response against HCMV infection, which remains a major health issue in patients undergoing bone marrow transplantation. Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope. |
A project from the IBS awarded in a national competition for innovative projectsSince 1998 a French national competition organized by the French Ministry of Research and OSEO-ANVAR has identified and helped finance the creation of startup companies with innovative technological products. The NatX-Ray project was one of the winners of the 2009 edition in the "creation/development" category. The NatX-ray company commercialize automated systems initially developed by an IBS team for the CRG FIP beamline at ESRF, that significantly reduce the time required for the collection and analysis of X-ray diffraction data. Potential customers include synchrotron research facilities, academic laboratories and the pharmaceutical industry. |
Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solutionRNAs play key roles in many cellular processes, e.g. transfer of genetic information to the ribosome, translation, catalytic ribosome activity, and regulation of gene expression. This functional versatility requires distinct three-dimensional structures and local flexibility. These properties can be studied at atomic resolution by multidimensional NMR spectroscopy. Unfortunately, solution NMR studies are currently limited to relatively small nucleic acids at high concentrations. Here we introduce new longitudinal relaxation optimized NMR experiments for the characterization of RNA base pairing interactions, RNA-ligand binding, and real-time studies of conformational transitions, that yield over a 2-fold increase in sensitivity compared to conventional pulse schemes. This allows extending the applicability of NMR to larger or less concentrated RNA samples, and addressing new questions of biological relevance. Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution. |
Quantitative determination of protein-backbone motions
Protein conformational flexibility from structure-free analysis of NMR dipolar couplings : quantitative and absolute determination of backbone motion in ubiquitin.Loïc Salmon, Guillaume Bouvignies, Phineus Markwick, Nils Lakomek, Scott Showalter, Da-Wei Li, Korvin Walter, Christian Griesinger, Rafael Brüschweiler, Martin Blackledge. Angew Chem Int Ed Engl. 2009 ;48(23):4154-7 |
Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplingsThe description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 kM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy is the technique of choice for studying low affinity protein-protein interactions. Residual dipolar couplings (RDCs) provide powerful constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDCs seriously complicates their exploitation for weakly interacting partners. We have developed an approach for the exploitation of the unique orientational information available from RDCs in the case of weak interaction and rapid exchange between free and bound forms. The approach relies on the measurement of RDCs in different equilibrium mixtures of partially aligned free and complex forms of the proteins, and on novel analytical approaches to determine and normalize the effective level of alignment in all equilibrium mixtures. We show that this results in the simple extraction of precise RDCs for bound forms of both partner proteins. The approach is applied to determine the three dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd=132±13 µM). We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings : application to the CD2AP SH3-C:ubiquitin complex. J. L. Ortega-Roldan, M. R. Jensen, B. Brutscher, A. I. Azuaga, M. Blackledge, N. A. van Nuland. Nucleic Acids Res. (2009). 2009 May ;37(9):e70
|
An Infrared fluorescent protein for whole-body imaging (Science)GFP has revolutionized cell biology, but has met limited success in whole-body imaging, because hemoglobin and oxy-hemoglobin present in tissues tremendously absorb light below 650 nm, i.e. from UV to red. Above, there is a so called ‘optical window’, limited at around 900 nm by water absorption, in which fluorescence imaging on animal is achievable. A scientist from the IBS has contributed in Roger Tsien’s lab at the University of California San Diego to the development of a fluorescent protein suitable for whole-body imaging, based on the directed evolution of a truncated phytochrome from Deinoccus radiodurans. The latter binds biliverdin, a heme breakdown product which is abundant in the organism. Fluorescence Molecular Tomography imaging of mice infected by an adenovirus expressing the Infrared fluorescent protein and specifically targeting the liver has demonstrated the potential of this genetically-encoded marker.
|
CNRS 2009 Cristal awarded to Jacques Joly (LCCP)Jacques Joly (LCCP) is the recipient of one of the CNRS "Crystals" for the year 2009. This distinction created in 1992 is given annually to a dozen engineers, technicians and administrative staff of the CNRS for their creativity and innovative contribution to research (list of winners 2009). |
The true accuracy of NMR restraints measured in liquid crystalline mediaA detailed study carried out at the IBS describes the experimental parameters that are necessary to overcome problems of conformational degeneracy and to obtain protein structures with improved accuracy and precision. 16-fold degeneracy of peptide plane orientations from residual dipolar couplings : Analytical treatment and implications for protein structure determination. |
Gergely Katona winner of the ESRF Young scientist Award 2009Gergely Katona received the prize for his innovative experiments in the field of structural dynamics of proteins by using synchrotron radiation. The jury awarding the prize acknowledged the combination of X-ray crystallography, time-resolved Laue diffraction, time resolved wide angle X-ray scattering and Raman spectroscopy in his research, a method developed when he was part of the Laboratoire de Cristallographie et Cristallogénèse des Protéines (IBS/LCCP). |
A New Method To Tackle Structural And Dynamics Change in Molecular NanoMachinesRecently IBS researchers have developed a new technique to reduce the time required to probe large biomolecular using Nuclear Magnetic Resonance spectroscopy (NMR). The experimental time has been reduced from minutes or hours to seconds time scale. This new method offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nanomachines while they perform their biological function in vitro. This technique may also prove useful for real-time investigation of macromolecular folding and self-assembly. Fast Two-Dimensional NMR Spectroscopy of High Molecular Weight Protein Assemblies. Carlos Amero, Paul Schanda, Asunción Durá, Isabel Ayala, Dominique Marion, Bruno Franzetti, Bernhard Brutscher & Jérôme Boisbouvier. Journal of the American Chemical Society ; 131(10):3448-9.
|
The crystallographic structure of Light-Harvesting Complex II shows the active energy-transmitting state
Under high light conditions, plants use a non-photochemical quenching mechanism to dissipate excess excitation energy as heat in order to limit the generation of reactive oxygen species that could jeopardize survival. Until recently, it was a common assumption that this mechanism should involve a conformational change within light harvesting complex II within photosynthetic membranes. Scientists from the Max Planck Institute, Frankfurt, the University of Frankfurt and the Institut de Biologie Structurale, Grenoble, have obtained new data which allow excluding the possibility of such conformational changes as part of the quenching mechanism. Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state. |
IBS at the Days of the CEA-GrenobleOn the 23rd and 24th January 2009, the IBS participated at a symposium organized by the CEA-Grenoble, the aim of which was to present the current and future activities of the CEA-Grenoble within the framework of the projects "Scientific Peninsula" and "Operation Campus". On the 23rd a General Assembly was hold for personnel of the CEA and its partners, whereas the 24th was devoted to an exhibition describing the Scientific Peninsula project and illustrating the activities of the CEA’s Institutes. The exhibition was open between 10 to 18h for CEA personnel and their families and had stands devoted to both fundamental and applied research. The IBS presented a stand in the zone dedicated to fundamental research.
|
French Structural Biology DayLyon-Gerland, January 15th, 2009 The purpose of the meeting is to take stock of the current state of structural biology in France in terms of ongoing projects, positioning within the wider European context, and long-term vision. Program. Organizing committee :
|