Institut de Biologie StructuraleGrenoble / France


ERC Starting Grant 2014 for Hugues Nury

The European Research Council (ERC) has awarded a "Starting Grant" to Hugues Nury for his project of structural studies of mammalian Cys loop receptors.

Hugues Nury is a research fellow at the Institute de Biologie Structurale in Grenoble (CEA / CNRS / UJF mixed research unit). His project entitled "PentaBrain" will receive € 1.5 million financial support from the ERC over 5 years. Scientific excellence at European level is one of the main criteria for the selection of these awards which recognize innovative projects of promising researchers, who earned their doctorate 2 to 7 years ago and want to create or consolidate a research team.

During his PhD at IBS, Hugues Nury studied mitochondrial membrane protein structures. He specialized in bacterial Cys-loop receptors during a first postdoc at the Institut Pasteur (France) in the laboratories of Corringer and Delarue. He then moved on to work on the mouse 5-HT3 serotonin receptor at the EPFL (Switzerland) during a second postdoc in the laboratory of Vogel. Since 2013, Hugues works at IBS and recently deciphered the X-ray structure of serotonin receptor. This collaborative study, published in Nature last year, paves the way for the design of new drugs against nausea, a main side effect of chemotherapy and anesthesia.

What is this project about ?
In the brain, Cys-loop receptors mediate fast neurotransmission. They function as allosteric signal transducers across the plasma membrane : upon binding of one or more neurotransmitter molecules to an extracellular site, the receptors undergo complex conformational transitions that result in transient opening of an intrinsic ion channel. The Cys-loop family comprises receptors activated by serotonin, acetylcholine, glycine and GABA. Mammalian receptors are also the targets of a legion of psycho-active and therapeutic compounds (including nicotine, benzodiazepines, anti-emetics, general anaesthetics). Our structural knowledge is currently limited to invertebrate homologues. Atomic structures mammalian receptors are therefore acutely missing in order to understand their physiological role in molecular terms, and to be able to develop new drugs targeting them.
The project proposes to decipher the operation mechanism, the pharmacology and conformational transitions of mammalian Cys-loop receptors. Starting with a solid body of preliminary results, the researchers will try and obtain new high-resolution structures (currently our knowledge is limited to only two family members in mammals), taking advantage of antibody-based crystallization chaperones. They will try to record for the first time a ‘molecular movie’ of the gating conformational transition in cristallo. On the way, they will also investigate the potential of antibody-based modulators of Cys-loop receptors for biomedical applications.

Keywords : neurotransmission, ionic channels, serotonine receptor

Amount of the award : €1.5 million for five years

Mini CV :
34y, 1 child
PhD at IBS in 2007
Researcher in Membrane Tansporters Group at IBS since 2013
Publications : consult google scholar profile

Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan

Researchers from the NMR group shed light on the synthesis molecular machinery of a bacterial cell wall. This study was conducted by "solid-state NMR spectroscopy" on the enzyme L, D-transpeptidase, which participates in the synthesis of the bacterial wall. The results are important for designing new antibiotic molecules against which bacteria would have no resistance mechanism.

Communique/Press release

Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Paul Schanda, Sebastien Triboulet, Cedric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur and Jean-Pierre Simorre. JACS

A quartz crystal microbalance method to study the reducing end functionalization of glycosaminoglycans

Linear polysaccharides known as glycosaminoglycans (GAGs) are ubiquitous cell surface and extracellular matrix components and, in interacting with a vast array of proteins, fulfil crucial biological functions. Ralf Richter team (CIC biomaGUNE, San Sebastian), The Département de Chimie Moléculaire (DCM Grenoble) and the SAGAG group of IBS have collaborated in the context of a chaire d’excellence of the Grenoble Nanoscience Foundation to establish oxime ligation as a facile, one-step method for the selective conjugation of GAGs at the reducing end. The work, reported in the journal ChemComm, demonstrates oxime ligation as a superior method in yield and stability in comparison to the commonly used hydrazone ligation. Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) was demonstrated as a surface-sensitive technique which enables quantitative analysis of conjugation yields, sample degradation and sample composition that is difficult to assess with conventional analytical techniques, in particular when the amount of sample is limited to a few micrograms. The methods should find broad use, as tools in the glycosciences and in biotechnological applications. In particular, the control over and stability of GAG conjugates is crucial towards the reliable preparation of GAG-functionalized surfaces and scaffolds for tissue engineering and fundamental biological studies.

Stable and Terminally Functionalized Glycosaminoglycan Conjugates. Thakar D., Migliorini E., Coche-Guerente L., Sadir R., Lortat-Jacob H., Boturyn D., Renaudet O., Labbe P., and Richter R.P. Chem. Comm. 50, 15148-15151 (2014)

Finding your better half : specific oligomerization of a large 500 kDa macromolecular machine optimizes its enzymatic performance

In an innovative approach combining biochemistry, X-ray crystallography and small angle neutron scattering (SANS), the ELMA group has solved the internal structure of a hetero-oligomeric TET aminopeptidase. The specific assembly optimizes the enzymatic activity of this large 500 kDa macromolecular machine.

Small angle neutron scattering reveals the assembling mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase. Appolaire A, Girard E, Colombo M, Durá MA, Moulin M, Härtlein M, Franzetti B and Gabel F. Acta Crystallographica Section D-Biological Crystallography ;70(Pt 11):2983-93

New opportunities for data mining in structural biology

Phylogenomic analysis of extreme halophilic Archaea sheds light on osmoadaptive mechanisms : new opportunities for data mining in structural biology.

The ability to adjust to changing osmotic conditions (osmoadaptation) is crucial for the survival of organisms across the tree of life. However, significant gaps still exist in our understanding of this important phenomenon. To help fill some of these gaps, we have produced high-quality draft genomes for 59 osmoadaptation “experts” (extreme halophiles of the euryarchaeal family Halobacteriaceae). We describe the dispersal of osmoadaptive protein families across the haloarchaeal evolutionary tree. We use these data to suggest a generalized model for haloarchaeal ion transport in response to changing osmotic conditions, including proposed new mechanisms for magnesium and chloride accumulation. We describe the evolutionary expansion and differentiation of haloarchaeal general transcription factor families and discuss their potential for enabling rapid adaptation to environmental fluxes. Lastly, we challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. This result highlights the power of our dataset for making evolutionary inferences, a feature which will make it useful to the broader evolutionary community. In addition, the data base would be also useful for data mining investigations and further structural studies
The genomic dataset is accessible through a user-friendly graphical interface.
This work is due to a collaboration between scientists from Australia, France and USA.

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response. Erin A. Becker, Phillip M. Seitzer, Andrew Tritt, David Larsen,Megan Krusor, Andrew I. Yao, Dongying Wu, Dominique Madern, Jonathan A. Eisen, Aaron E. Darling, Marc T. Facciotti. Plos Genetics ;10(11)

Unexpected radical reaction on tryptophan by NosL : H-abstraction from the amino N atom

The tryptophan lyase NosL is a radical SAM enzyme responsible for the conversion of tryptophan into 3-methyl indolic acid (MIA), a building block in the synthesis of the antibiotic Nosiheptide. Combining X-ray structure determination and theoretical calculations, we have shown that the radical-based C-C bond break mechanism is not the one previously postulated. Indeed, the initial radical attack does not take place at the N atom of the indole ring of the amino acid but at its amino group instead. This is the first time that a radical SAM enzyme is shown to abstract a H-atom from a non-carbon atom. Furthermore, the NosL structure with substrate bound has defined the side chains involved in tryptophan binding at the active site pocket. Examination of their respective amino acid sequences indicates that the radical SAM tyrosine lyases HydG and ThiH are related to NosL. These proteins, respectively involved in the maturation of the active site of FeFe-hydrogenase and in the synthesis of the vitamin B1 thiazole ring, should bind their substrate as NosL does and use the same mechanism. The NosL structure will certainly be useful for the complete mechanistic analysis of MIA production. Nosiheptide is a very promising molecule against pathogens resistant to currently used antibiotics. In order to expand possible therapeutic applications, site directed mutagenesis could be used to produce unnatural Nosiheptide derivatives with novel properties.

Crystal Structure of Tryptophan Lyase (NosL) : Evidence for Radical Formation at the Amino Group of Tryptophan.
Nicolet Y, Zeppieri L, Amara P and Fontecilla-Camps JC.
Angewandte Chemie International Edition (2014) 53(44) : 11840-11844.

Overview of the 2014 Science Fair

After a break in 2013, due to the relocation of the institute,, IBS scientists resumed their participation in the Science Fair with a guided tour for general public and workshops for CM2 classes.

For the International Year of Crystallography, the Science Fair 2014 was particularly rich and original in Isere, from 26 September to 19 October 2014. The IBS could not miss this event and proposed two initiatives :

On October 02 and 03, a hundred pupils were invited to participate in one of three workshops (short experiments involving proteins and DNA) dedicated for primary schools.

On October 18, two visits were organized on EPN Campus. A guided tour entitled "At the heart of the living molecules" was organized in the IBS building by scientists from IBS, EMBL, UVHCI and ESRF They animated three workshops about NMR, microbiology and crystallography. Inside a marquee at the entry of the campus, crystallography activities were also put on for people of all ages. Visitors were also welcomed elsewhere on the EPN campus, at the ESRF and the ILL.

Atelier RMN/ NMR workshop
Atelier microbiologie/ Microbiology workshop
Peche aux cristaux à l’atelier Cristallographie / Crystallography workshop

In total about 40 volonteers were involved on both events to share the great pleasure of discovery with 250 people.

Do not miss this crystallographic flashmob, a performance organized specially for the Science Fair 2014 in Grenoble.

Frank Gabel nominated as co-director of the HERCULES school

Frank Gabel (IBS/ELMA) has been nominated as co-director of the HERCULES school for the biology session, together with the new general director Vincent Favre-Nicolin (CEA), and the co-directors Michael Krisch (ESRF) and David Djurado (CNRS).

The HERCULES school provides training for students, postdoctoral and senior scientists from European and non-European universities and laboratories, in the field of Neutron and Synchrotron Radiation for condensed matter studies

Please note that the registration to the 2015 HERCULES session is opened until October 15th, 2014. To know more.

Structural study of a protein-RNA complex involved in the regulation of gene expression in Drosophila sex chromosomes

In an international collaboration between Prof. Michael Sattler’s NMR group (Helmholtz Zentrum and Technische Universität München, Germany), Dr. Fátima Gebauer (Centre de Regulació Genòmica, Barcelona, Spain) and Dr. Frank Gabel (IBS and Institut Laue-Langevin Grenoble) the structure of a ternary protein-RNA complex involved in the dosage compensation mechanism in fruit flies has been solved.
The complex is a key player in gene regulation which assures the equilibrium of proteins expressed by the sex chromosome pairs XX in female and XY in male Drosophila melanogaster flies. It is composed of the proteins SXL and UNR as well as a messenger RNA sandwiched between them. It’s unusual three-dimensional arrangement represents a novel structural mechanism of gene regulation
and has been solved by a combination of nuclear magnetic resonance (NMR), crystallography and small-angle X-ray (SAXS) and neutron (SANS) scattering.

Structural basis for the assembly of the Sxl–Unr translation regulatory complex. Janosch Hennig, Cristina Militti, Grzegorz M. Popowicz, IrenWang, Miriam Sonntag, Arie Geerlof1, Frank Gabel, Fatima Gebauer & Michael Sattler.
Nature doi:10.1038/nature13693

Structure of a bacterial α2-macroglobulin reveals mimicry of eukaryotic innate immunity

Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. Surprisingly, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. The Bacterial Pathogenesis group reports, in a recent issue of Nature Communications, the crystal structures and characterization of Salmonella enterica ser. Typhimurium A2M (Sa-A2M) in different states of thioester activation. The structures reveal thirteen domains whose arrangement displays high similarity to proteins involved in eukaryotic immune defense. A structural lock mechanism maintains the stability of the buried thioester, a requirement for its protease trapping activity. These findings indicate that bacteria have developed a rudimentary innate immune system whose mechanism mimics that of eukaryotes.

Structure of a bacterial α2-macroglobulin reveals mimicry of eukaryotic innate immunity.
Wong SG, Dessen A.
Nat Commun. 2014 Sep 15 ;5:4917. doi : 10.1038/ncomms5917.

X-ray structure of the mouse serotonin 5-HT3 receptor

For the first time the X-ray structure of serotonin receptor was deciphered. The study, published online in Nature on August 03, 2014, paves the way for the design of new drugs against nausea, a main side effect of chemotherapy and anesthesia. It was conducted by IBS researchers in collaboration with researchers from the laboratory Architecture and Function of Biological Macromolecules, Swiss researchers and the participation of Théranyx.

Press release

X-ray structure of the mouse serotonin 5-HT3 receptor. Ghérici Hassaine, Cédric Deluz, Luigino Grasso, Romain Wyss, Menno B. Tol, Ruud Hovius, Alexandra Graff, Henning Stahlberg, Takashi Tomizaki, Aline Desmyter, Christophe Moreau, Xiao-Dan Li, Frédéric Poitevin, Horst Vogel and Hugues Nury. Nature, en ligne le 3 août 2014.

Observing transient states of proteins at atomic résolution

The three-dimensional shape of a protein determines its function. In many cases, however, the conformational states that are actually relevant for function are only transient and populated to a small extent at any given time, and therefore difficult to grasp by existing methods. A new method based on solid-state NMR spectroscopy, developed by researchers at IBS, allows detecting transient protein states even in large or insoluble proteins.

Proteins fulfill an impressively wide range of tasks in the cell, and their function is tightly bound to their shape. Biologists use techniques such as Nuclear Magnetic Resonance (NMR) to determine these structures. But proteins do not have only one rigid conformation, but they continuously exchange between different conformations. In many cases proteins perform their tasks within milliseconds or even faster, such that relevant conformational states may only last for a tiny fraction of a second, and in a given sample only a small part of the molecules may be in some of these functional states. NMR spectroscopic techniques developed over the last decade are able to provide information about such short-lived states for proteins in solution, even though they are transient and rare, but extending this to large or insoluble proteins (such as membrane proteins) remained so far very challenging. Researchers from IBS Grenoble, in collaboration with Forschungszentrum Jülich (Germany) have developed a new method that overcomes these limitations and allows studying proteins in the solid state, which opens the possibility to see motion in proteins that were so far out of reach. The methodology provides insight into these rare and transient states, in terms of their structural changes, as well as into the kinetics and thermodynamics of these dynamic fluctuations. The techniques was first demonstrated on a well-established protein, ubiquitin. It had been known before that this protein exists in two slightly different conformational states, as seen in different crystal structures. With the new technique, the IBS researchers could show that both states co-exist in the crystal, i.e. the protein constantly “hops” from one state to the other, making it thereby able to expose conformations that are preorganized for their binding partners. The method, which is currently being applied to large challenging systems, is expected to also help understanding how potentially medically relevant proteins, such as membrane receptors or large enzymes function.

Probing Transient Conformational States of Proteins by Solid-State R11 Relaxation-Dispersion NMR Spectroscopy.Peixiang Ma, Jens D. Haller, J-r-my Zajakala, Pavel Macek, Astrid C. Sivertsen, DieterWillbold, J-er-ome Boisbouvier, and Paul Schanda. Angew Chem Int Ed Engl. 2014 Apr 22 ;53(17):4312-7. doi : 10.1002/anie.201311275. Epub 2014 Mar 18.

Official inauguration of the new IBS building

Friday 21 February saw the official opening of the new IBS building which was funded by local and regional authorities within the framework of a CPER contract (Contrat de Projets Etat-Région) and the Plan Campus.

The opening ceremony was attended by the French Minister for Higher Education and Research, Geneviève Fioraso, the president of the Rhône-Alpes region, Jean-Jack Queyranne, the President of Grenoble Alpes Metropole, Marc Baïetto, the Deputy Mayor of Grenoble, Jérôme Safar, the Vice President for Economic Development and Tourism in the General Council of Isère, Christian Pichoud (representing Andre Vallini, President of the General Council) and the President of the combined Universities of Grenoble, Bertrand Girard. The directors of two French national research agencies, the CNRS and the CEA, and Grenoble’s Joseph Fourier University, were also present in their capacities as funders and supporters of the new IBS project.

Built on the EPN Science Campus in the heart of Giant, the new 5600 m2 building offers a unique environment for researchers to decipher the living world at a molecular level. The IBS’s location close to its PSB partners (Partnership for Structural Biology) allows access to cutting-edge facilities and constitutes a further step in the development of the region as an International centre of excellence for structural biology.

As 2014 has been declared by Unesco the "International Year of Crystallography", the IBS groups now have at their disposal a unique environment for furthering knowledge about the molecular and cellular architecture and dynamics of living organisms.

Accueil dans le hall de l’IBS/ Welcome
Quelques explications sur les recherches menées à l’IBS/ Explanation about IBS research
Visite zone laboratoires par Genevieve Fioraso, Ministre de l’enseignement supérieur et de la recherche, et Eva Pebay-Peyroula, Directrice de l’IBS/ Labs visit by the French Minister for Higher Education and Research, Geneviève Fioraso and the IBS Director, Eva Pebay-Peyroula
Visite d’un laboratoire/ Labs visit
Viste de la salle des spectrometres RMN/ NMR spectrometers room
Allocution de Madame la Ministre en salle des séminaires / Speech of the French Minister for Higher Education and Research in the IBS seminar room