Institut de Biologie StructuraleGrenoble / France

2017

Professor Poignard among the most cited researchers in the world

Congratulations to Professor Poignard who has been named a Thomson Reuters Highly Cited Researcher. Every year, the publishing company Thomson Reuters (now Clarivate Analytics) analyses scientific articles covering 21 disciplinary fields, published over the past 11 years in international journals. These data provide a list of about 3000 researchers (from more than 9 million researchers worldwide) who have distinguished themselves by publishing a large number of articles that rank among the 1% most cited in their respective fields. Pascal Poignard, head of the HIV and Persistent Human Viruses Group at IBS and Professor (CHUGA & UGA), is on the 2017 list of the 3,300 most cited researchers in the world (category ’Microbiology’).
The Poignard team focuses on understanding how broadly antibody responses eventually develop in a subset of HIV-infected donors. The goal is to gain knowledge from natural infection for the further design of effective immunogens and vaccine strategies to prevent HIV infection.

New light on bacteriophages, bacteria killers

The vast majority of phages, bacterial viruses, possess a capsid containing the genetic material and a tail that functions in host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. But how does the tip of the tail and the capsid communicate? Different teams of the Institute de Biologie Structurale have answered this question by determining the structure of the tail tube by combining cryo electron microscopy and crystallography. This study was published in Nature Communication.

Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection. Charles-Adrien Arnaud, Grégory Effantin, Corinne Vivès, Sylvain Engilberge, Maria Bacia, Pascale Boulanger, Eric Girard, Guy Schoehn and Cécile Breyton. Nature Communication doi:10.1038/s41467-017-02049-3

Innovative and specific painting of the pneumococcal surface

Peptidoglycan (PG) is the star molecule of the bacterial wall. In Gram-positive bacteria, teichoic acids (TA) are much less famous, although they account for about half the mass of surface molecules. These glycopolymers, anchored on the plasma membrane or on the PG, are decorated in pneumococcus with phosphorylcholines (PCho). This property was exploited to label the TA so that they could be located and tracked during the cell cycle. The labelling is carried out in two simple steps: culture of pneumococci in the presence of Propargyl-choline then coupling of modified PCho linked to TA with a fluorophore by click chemistry. This efficient and specific labelling, carried out on living bacteria, revealed the probable co-location of molecular machines for the synthesis of PG and TA. It also allows detection of the pneumococcus amongst a bacterial mixture, a pre-requisite for medical diagnostic (Figure). This work initiated within the IBS Pneumococcal Group benefited from an excellent partnership with the Département de Pharmacochimie Moléculaire of the UGA and from a significant contribution to molecular analyses from collaborators in Germany.

Specific and spatial labeling of choline-containing teichoic acids in Streptococcus pneumoniae by click chemistry. Di Guilmi AM, Bonnet J, Peiβert S, Durmort C, Gallet B, Vernet T, Gisch N, Wong YS. Chemical Commununications (Camb);53(76):10572-10575

Channelrhodopsin reveals its dark secrets

Ion channels are integral membrane proteins that upon stimulation modulate the flow of ions across the cell or organelle membrane. Channelrhodopsins (ChRs) appeared to be unusual channels. They belong to the large family of microbial rhodopsins, seven-helical transmembrane proteins containing retinal as chromophore. Photon absorption initiates retinal isomerization resulting in a photocycle, with different spectroscopically distinguishable intermediates, thereby controlling the opening and closing of the channel. In 2003, it was demonstrated that light-induced currents by heterologously expressed ChannelRhodopsin2 (ChR2) can be used to change a host`s membrane potential. This accomplishment has made ChR2 the first long thought and further used a key instrument of neuroscience. ChR2 opened a new field - optogenetics. Optogenetics is a biological technique which involves the use of light to control cells in living tissue, typically neurons, that have been genetically modified to express special light-sensitive proteins. In 2010, optogenetics was chosen as the "Method of the Year" across all fields of science and engineering by the interdisciplinary research journal Nature Methods.

Despite the extraordinary importance of this protein, a high-resolution structure and structural mechanisms of a native ChR2 (and other ChRs) have not yet been known. A step forward was the structure of a chimera between ChannelRhodopsin1 and ChannelRhodopsin 2 (C1C2). However, recent electrophysiological and Fourier transform infrared data showed that C1C2 exhibits light-induced responses that are functionally and mechanistically different from ChR2. Given that ChR2 is the most frequently used tool in optogenetics, a high-resolution structure of ChR2 is of high importance. Deciphering the structure of the native channel would shed light on how the light-induced changes at the retinal Schiff base (RSB) are linked to the channel operation.

In this work scientist from the MEMBRANE group and their collaborators expressed ChR2 in LEXSY expression system and used in meso crystallization approach to determine the crystal structure of the wild-type ChR2 and C128T slow mutant at 2.4 and 2.7 Å, respectively. The determined structures of ChR2 and its C128T mutant present the molecular basis for the understanding of ChR functioning. They provide insights into mechanisms of channel opening and closing.

Thereby, this work shed light to the molecular mechanisms of Channelrhodopsin 2 work and opens the possibilities to make engineering of enhanced optogenetic tools more efficient.

Structural insights into ion conduction by channelrhodopsin 2. Volkov O, Kovalev K., Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V. Science: Vol. 358, Issue 6366, pp. 1000-1001.

Structure of the DNA polymerase of the vaccinia virus

Despite the eradication of smallpox virus, the most devastating virus in the poxvirus family, a risk of re-emergence is possible either through bioterrorism or the introduction of a virus from an animal reservoir. IBS researchers, in collaboration with IRBA scientists, determined the crystal structure of vaccinia virus E9 DNA polymerase at a resolution of 2.7 Å. It is 98 % identical to the one of smallpox virus and represents an important antiviral target. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Using a combination of approaches, the site of interaction with the cofactor A20/D4 has been located in a poxvirus-specific structural insertion. The high-resolution structure can be used for the design of inhibitors interfering with the assembly of the holoenzyme, just as it facilitates understanding of the mechanism of antivirals and resistance mutations.

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F. Nature Communications;8(1):1455

Resistance to antibiotics: a new target in the bacterial wall

The peptidoglycan (PG) is an essential component of the bacterial cell wall. Due to its central role in bacterial survival, its biosynthetic machinery has been a preferential target for antibiotic development for decades. MreC is a structural protein that serves as a platform during wall elongation, scaffolding other essential peptidoglycan biosynthesis macromolecules, such as Penicillin-Binding Proteins (PBP). Here, IBS researchers present the crystal structures of the soluble PBP2:MreC core elongasome complex from the human pathogen Helicobacter pylori, as well as that of uncomplexed PBP2. This work allows the visualization of how peptidoglycan machinery proteins are scaffolded, revealing interaction regions that could be targeted by tailored inhibitors.

Molecular architecture of the PBP2:MreC core bacterial cell wall synthesis complex. Contreras-Martel C, Martins A, Ecobichon C, Maragno Trindade D, Mattei PJ, El Ghachi M, Hicham S, Hardouin P, Boneca IG, Dessen A. Nature Communications

Inauguration of a Cryo-EM platform on EPN Campus

A TITAN KRIOS cryo-electron microscope has been inaugurated on November 10, at the ESRF, the European Synchrotron, in Grenoble, France. The inauguration took place in the presence of Ada Yonath, chemistry Nobel Prize laureate in 2009, Francesco Sette, Director General of the ESRF and all the partners that jointly run the facility with the ESRF: the Institut de Biologie Structurale (IBS), the European Molecular Biology Laboratory (EMBL) and the Institut Laue-Langevin (ILL). This cryo-electron microscope will provide Europe with a new, innovative and complementary facility for structural biology, serving a vibrant scientific community and addressing new biology and health challenges.

Press kit
Press release

Nobel Prize in Chemistry put structural biology on the forefront

The jury of the 2017 Nobel Prize in Chemistry put structural biology on the forefront. Jacques Dubochet, Joachim Frank and Richard Henderson, an international trio of scientists, are honored for the development of cryo-electron microscopy, a tool for the determination of the 3D structure of biomolecules. "More precisely, this technique allows to freeze biological molecules in their native structure and to observe them under the electron microscope at atomic scale," explains Guy Schoehn, head of the Methods & Electron Microscopy Group at the IBS.

Amorphous/vitrious ice and high-level detection

It all began in 1988 with the will to develop electron microscopy, up to there devoted to material science, to decipher the structure of biological objects. "Indeed, the ultra vacuum present in the microscope column coupled with the irradiation of the sample by electrons destroys it very quickly!" pursues the scientist. « In cause: the water contained in these macromolecules, which evaporates under vacuum, and which coupled with the heating due to the interactions with electrons destroys the structure of the sample (the sample is literally bowling). Jacques Dubochet developed an ultra-fast freezing protocol that transforms liquid water into vitreous ice. Unlike ice crystals in our freezers, water in a vitreous ice is translucent to electrons. The first obstacle was crossed. However, the bet was not won because the samples, even at low temperature, move under the electron beam, and moreover, because the mechanical stability of an electron microscope is not perfect. Thus it was necessary to obtain more precise images (without drift or without fuzziness) to develop much faster but also more sensitive detectors with a very good signal to noise ratio, underlines Guy Schoehn. Richard Henderson took up this challenge by detecting each electron, with a rate of several hundred frames per second. Then the 3rd Nobel Prize-winning researcher, Joachim Frank, succeeded in moving from noisy cryo-electron microscopy images (recorded on photographic films at that time) to three dimensional structure of the object. The ribosome, a cellular factory translating RNA into proteins was one of the first macromolecular assemblies imaged and reconstructed by Joachim Frank.

A 2nd state-of-the-art cryo-electron microscope soon to be inaugurated in France

Electron microscopy is one of the main techniques used to decipher the structure of living organisms at the atomic scale, with crystallography and NMR (nuclear magnetic resonance). However, crystallography requires crystals and « freeze » the structure in a conformation compatible with crystallization (which is therefore not exactly in its physiological environment) and NMR is limited in size . "France did not bet on cryo-electron microscopy, unlike Germany or the United Kingdom and is far behind" the IBS researcher regrets. There is only one state-of-the-art instrument in France (a Krios electron microscope available for academic researchers in Strasbourg) by comparison with more than a dozen in UK or in Germany. Nevertheless, the most powerful electron microscope at the IBS in Grenoble (a Polara microscope installed in 2010) allows scientists to get results at atomic resolution but the risk for this microscope to become obsolete very quickly is high.
"On November 10th, a second Titan Krios cryo electron microscope will be inaugurated at the ESRF in Grenoble," he continues. "An IBS scientist, Grégory Effantin, will dedicate 80% of his time to the microscope (the team also includes an ESRF scientist, the team leader, and an EMBL scientist). I ’m also involved at approximately 20% of my time into the project". The new platform, setup and managed by ESRF, will be accessible to all ESRF state members through CryoEMbeamtime applications.

Decrypt measles, adenoviruses, phages ...
IBS scientists and their partners have used cryo-electron microscopy to decode living organisms for several years. "For example, we are working with Martin Blackledge’s team on the structure of the protein protecting the genetic information of the measles virus," explains Guy Schoehn. "Also, with Andrea Dessen we are interested in secretin, the toxins released by bacteria to infect their hosts. Another topic of interest is phages. In collaboration with Cecile Breyton, my team is studying bacteriophages, therapeutic alternatives to antibiotics." As the technique is refined and adopted more widely, researchers expect Cryo-electron microscopy will help tackle major public health questions.

Crystallophore, an all-in-one tool for protein crystallography

Macromolecular crystallography suffers from two major issues: getting well-diffracting crystals and solving the phase problem inherent to large macromolecules. Here, a collaboration involving scientists from the IBS and from the ENS-Lyon describe the firstborn of a lanthanide complex family named “Crystallophore” (Xo4). The terbium complex, Tb-Xo4, facilitates protein crystallization, improves the quality of the crystals obtained and allows structure determination thanks to its exceptional phasing power. The collaboration demonstrate the potential of this additive for crystallisation and structure determination on eight proteins, two of whose structures were unknown. Xo4 contributes to tackle both bottlenecks of crystallopgraphy.
Xo4 technology has received financial support from ANR and SATT Pulsalys and is protected by patent n°WO2017103545. An exclusive license has been granted to POLYVALAN (www.polyvalan.com), ENS-Lyon and IBS spin-off of , for the synthesis and commercialization of these molecules.

Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.
Engilberge S, Riobe F, Di Pietro S, Lassalle L, Coquelle N, Arnaud CA, Pitrat D, Mulatier JC, Madern D, Breyton C, Maury O, Girard E. Chemical Science. DOI: 10.1039/c7sc00758b

FRM team label for the Viral Replication Machines Group of Marc Jamin

The Viral Replication Machines Group of the IBS has just been certified as FRM team. About 30 french teams are certified by the "Fondation pour la Recherche Médicale" (FRM) each year.
The group will receive € 395 000 financial support from the FRM over 3 years.

What is this project about?
Protein-protein interactions are at the heart of all biological processes, including virus replication, and constitute a large and under-exploited set of therapeutic targets.Various types of interface, called "linear pattern", consisting of short sequences of contiguous amino acids are abundantly used by viruses to assemble their replicative complexes and divert molecular machines from their hosts.his project aims to: (1) characterize protein-protein interactions involving an interface of this type within the replicative machine of various viruses or host-virus interactions, (2) demonstrate that peptides mimicking these interfaces block replication of these viruses and (3) optimize these peptides by combinatorial methods of directed evolution in order to increase their affinity or to extend their spectrum of activity.

New light on fluorescent proteins dark states

Photoconvertible fluorescent proteins (PCFPs) are the most commonly used markers in super-resolution "PALM" microscopy. However, in addition to their green (native) and red (photo-converted) forms, these proteins have an unfortunate tendency to stochastically enter multiple non-fluorescent dark states, ie to “blink”. The present papers investigate dark states that are reached from the green form of PCFPs and reveal their importance for PALM microscopy. The first article shows that these dark states greatly limit the efficiency of green-to-red photoconversion. The second, in collaboration with a German team, shows that PCFPs can be divided into two categories. PCFPs of the first category blink less in their green form, and it is shown that they are amenable to “primed” green-to-red photoconversion. This is not the case for members of the second category, which blink more. It is shown that primed photoconversion, a mechanism recently discovered by a Swiss team, substantially reduces the phototoxicity of PALM experiments.

Photoswitching of Green mEos2 by Intense 561-nm Light Perturbs Efficient Green-to-Red Photoconversion in Localization Microscopy. D. Thédié, R. Berardozzi, V. Adam, D. Bourgeois. J. Phys. Chem. Lett., 2017, 8, 4424−4430

A General Mechanism of Photoconversion of Green-to-Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live-Cell Single-Molecule Imaging. B. Turkowyd, A. Balinovic, D. Virant, H. G. Gölz Carnero, F. Caldana, M. Endesfelder, D. Bourgeois, and U. Endesfelder. Angewandte Chemie International Edition England; 56, 1-7

AminoCraft :a gameplay to learn amino acids

Two associate professors at Université Grenoble Alpes (UGA) have developed an app that teaches the structure of the 20 amino acids which are the building blocks of all living creatures.

Press release

The application is available for free on Android and Apple smartphones, in English and French and it does not require a network connection to play. It provides a great way for students, and those who are curious, to have fun while quickly learning the amino acids on their smart phone, any time of the day, while commuting, in the street or on a coffee break. The development of this application was made possible thanks to funding from the Region Rhône Alpes Auvergne and assistance from Unvisersité Grenoble Aples (UGA).

Ultra-fast molecular movie: watching proteins absorbing light

Using a revolutionary method, scientists have been able to film ultra-rapid processes at work in fluorescent proteins, which are extensively used as markers in in vivo imaging. This new method, which uses enormous X-ray lasers, permits the analysis of processes such as vision, bioluminescence and other phenomena which have not been observable to date. These results are to be published in Nature Chemistry on September, the 11th, as part of an international collaboration involving scientists from the IBS, the Universities of Lille, Rennes 1 and Paris-Sud, and the Max Planck Institute for Medical Research at Heidelberg in Germany.

Press release

Chromophore twisting in the excited state of a fluorescent protein captured by time-resolved serial femtosecond crystallography. Coquelle N, Sliwa M, Woodhouse J, Schirò G, Adam V, Aquila A, Barends T, Boutet S, Byrdin M, Carbajo S, De la Mora E, Doak B, Feliks M, Fieschi F, Foucar L, Guillon V, Hilpert M, Hunter M, Jakobs S, Koglin J, Kovacsova G, Lane TJ, Lévy B, Liang M, Nass K, Ridard J, Robinson J, Roome C, Ruckebusch C, Seaberg M, Thepaut M, Cammarata M, Demachy I, Field M, Shoeman R, Bourgeois D, Colletier J-P, Schlichting I, Weik M. Nature Chemistry

NMR a tool to detect ultraweak interactions in proteins

Usually, weakly polar CH/pi interactions are inferred from the three-dimensional coordinates of proteins. The researchers of IBS in collaboration with groups of York and Ottawa universities, used solution nuclear magnetic resonance (NMR) spectroscopy in tandem with an optimized methyl (Me) isotope labeling strategy to directly observe Me/pi interactions between Methyl groups and backbone atoms of proteins. Based on the results of density functional theory (DFT) calculations and NMR spectra, the researchers provide compelling evidence of Me/pi interactions in proteins and describe how simple and unambiguous assignment of donor and acceptor groups of CH-pi pairs can be achieved. Thus, the need for an a priori knowledge of the three-dimensional structure of a protein is obviated for characterization of these weak interactions on an individual basis.

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins. Perras FA, Marion D, Boisbouvier J, Bryce DL, Plevin MJ. Angewandte Chemie-International Edition England doi: 10.1002/anie.201702626

Protein dynamics in the crystal : a subtle balance of inter- and intramolecular contacts

Recent advances in crystallographic techniques allow to obtain not only a single static picture of proteins – which are those that fill the protein data bank – but they also reveal the dynamics of protein around these « snapshots ». Knowledge of these motions may be a key to understanding protein function. But an important question remained so far poorly understood : are the protein motions in the crystal lattice representative of those in the actual biological environment ? Kurauskas et al. have combined novel solid-state NMR techniques and multi-microsecond MD simulations to reveal, for the first time, how the crystal packing influences protein dynamics on the biologically important time scale of micro/milliseconds, and lays the ground for future crystallography-based studies of protein dynamics.

Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Kurauskas V, Izmailov SA, Rogacheva O, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier JP, Skrynnikov NR, Schanda P. Nature Communications DOI:10.1038/10.1038/s41467-017-00165-8

Mechanism of transmembrane signaling by sensor histidine kinases

One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. A collaboration of scientists, including researchers from the IBS MEMBRANE group, present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Their findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.

Mechanism of transmembrane signaling by sensor histidine kinases. Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V. Science;356(6342

How plankton dominate ocean life

Photosynthesis is a unique process that allows independent colonization of the land by plants and of the oceans by phytoplankton. Although the photosynthesis process is well understood in plants, scientists are still unlocking the mechanisms evolved by phytoplankton to achieve extremely efficient photosynthesis. Researchers from the Institut de Biosciences et Biotechnologies de Grenoble (BIG), the Institut de biologie structurale (IBS), the Institut nanosciences et cryogénie (INAC), the Institut de Biologie Physico-Chimique (IBPC), ETH Zurich (Switzerland) and University of Konstanz (Germany), combine biochemical, structural and in vivo physiological studies to unravel the structure of the plastid in diatoms, prominent marine eukaryotes. The results of this study were published in Nature Communications on June 20, 2017. Press release (in french only)

Plastid thylakoid architecture optimises photosynthesis in diatoms. Flori S, Jouneau PH, Bailleul B, Gallet B, Estrozi LF, Moriscot C, Bastien O, Eicke S, Schober A, Río Bártulos C, Maréchal E, Kroth PG, Petroutsos D, Zeeman S, Breyton C, Schoehn G, Falconet D and Finazzi G. Nature Communications;8:15885.

Human Immune Protein C1q Selectively Disaggregates Carbon Nanotubes

Scientists from the MEM and IRPAS group, in collaboration with LITEN and SCBM, atomistically compute the change in free energy upon binding of the globular domain of the complement protein C1q to carbon nanotubes (CNTs) and graphene in solution. Their modeling results imply that C1q is able to disaggregate and disperse bundles of large diameter multi-walled CNTs but not those of thin single-walled CNTs, and they validate this prediction with experimental observations. The results support the view of a strong binding with potential implications for the understanding of the immune response and biomedical applications of graphitic nanomaterials.

Human Immune Protein C1q Selectively Disaggregates Carbon Nanotubes. Saint-Cricq M, Carrete J, Gaboriaud C, Gravel E, Doris E, Thielens N, Mingo N, Ling WL. Nano Letters ;17(6):3409-3415

A new antifungal therapeutic strategy

Invasive fungal infections cause significant mortality, with 800,000 deaths a year. A collaborative consortium * between three research institutes in Grenoble, the Pasteur Institute and the University of Southern California has discovered that the Bdf1 protein, member of an ubiquitous family of factors regulating gene expression, is essential to the survival of pathogenic fungi. They have identified specific inhibitors of this protein capable of killing yeast. This work, published on May 18, 2017 in the journal Nature Communications, opens high hopes for the development of a new class of antifungal drugs.(Details in french)

* Team Petosa (Institut de Biologie Structurale), Jérôme Govin (Institut de Biosciences et Biotechnologies de Grenoble), Muriel Cornet (TIMC-IMAG-TheREx, CHU Grenoble Alpes), Christophe d’Enfert (Institut Pasteur) and Charles McKenna (University of Southern California, Los Angeles).

Selective BET bromodomain inhibition as an antifungal therapeutic strategy. Mietton F, Ferri E, Champleboux M, Zala N, Maubon D, Zhou Y, Harbut M, Spittler D, Garnaud C, Courçon M, Chauvel M, d’Enfert C, Kashemirov BA, Hull M, Cornet M, McKenna CE, Govin J, Petosa C. Nature Communications 8:15482.

Insights into a mechanism which inhibits root cell elongation

The Methods and Electron Microscopy group in collaboration with the Laboratoire de Biologie végétale et microbiologie environnementales Cadarache and the Leibniz Institute of Plant Biochemistry have revealed a mechanism for plant root growth arrest during low phosphate availability in soil. These results may improve crop plants resistance in acidic soil or depleted in phosphate, or increase their pollutant metal extraction properties. The results of this study were published in Nature Communications on May 15, 2017. Press release (in french only)

Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation. Balzergue C, Dartevelle T, Godon C, Laugier E, Meisrimler C, Teulon J-M, Creff A, Bissler M, Brouchoud C, Hagège A, Müller J, Chiarenza S, Javot H, Becuwe-Linka N, David P, Péret B, Delannoy E, Thibaud M-C, Armangaud J, Abel S, Pellequer J-L, Nussaume L and Desnos T. Nat. Commun. 8: 15300.

Discovery of the structure of a fundamental particle of chromatin

An international consortium has updated the complete structure of the nucleosome. This work represents a very important advance in the knowledge of the molecular organization of chromatin, which plays an essential role in many nuclear processes, such as gene expression, DNA replication and damaged DNA repair. This study was published in the journal Molecular Cell.

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Jan Bednar, Isabel Garcia-Saez, Ramachandran Boopathi, Amber R. Cutter, Gabor Papai, Anna Reymer, Sajad H. Syed, Imtiaz Nisar Lone, Ognyan Tonchev, Corinne Crucifix, Hervé Menoni, Christophe Papin, Dimitrios A. Skoufias, Hitoshi Kurumizaka, Richard Lavery, Ali Hamiche, Jeffrey J. Hayes, Patrick Schultz, Dimitar Angelov, Carlo Petosa, Stefan Dimitrov. Molecular Cell. Published: May 4, 2017. vol 66. issue 3, p384–397.

Polyvalan (IBS & ENS Lyon Spin-off company) and Pulsalys sign an exclusive exploitation contract to easily determine the 3D structure of proteins

PULSALYS, the Lyon-Saint-Etienne Technology Transfer Acceleration Company, announces the signature of an exclusive license with POLYVALAN to facilitate the determination of protein structures. POLYVALAN, which benefits from the know-how of IBS and ENS-Lyon, specializes in the development, manufacture and marketing of innovative chemical additives dedicated to structural biology. Press release (in french only).

Scientists uncover mechanism allowing bacteria to survive the human immune system

A team of scientists at the University of East Anglia (UEA) and the IBS (Metalloproteins Group) have uncovered molecular details of how pathogenic bacteria fight back against the human immune response to infection. Every step towards understanding this complex process paves the way to the possibility of developing intervention strategies that disable the response. Details

Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding. Anne Volbeda, Erin L. Dodd, Claudine Darnault, Jason C. Crack, Oriane Renoux, Matthew I. Hutchings, Nick E. Le Brun & Juan C. Fontecilla-Camps. Nature Com;8:15052

Development of innovative strategies to monitor formation of biological structures

The spontaneous formation of biological higher order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. NMR spectroscopy possesses the unique ability to monitor structural changes in real-time, however its size limitation and time resolution constraints remain a challenge when studying the self-assembly of large biological particles.
In the framework of the ERC SeeNanoLifeInAction project, scientists from IBS groups report the application of methyl specific isotopic labeling combined with relaxation-optimized NMR spectroscopy to overcome both size- and time-scale limitations. They report for the first time the self-assembly process of a half-megadalton protein complex that was monitored at the structural level, including the characterization of intermediate states, using a mutagenesis free strategy. NMR was used to obtain individual kinetics data on the different transient intermediates and the formation of final native particle. In addition, complementary time-resolved electron microscopy and native mass spectrometry were used to characterize the low-resolution structures of oligomerization intermediates.

Unraveling Self-Assembly Pathways of the 468 kDa Proteolytic Machine TET2. Pavel Macek, Rime Kerfah, Elisabetta Boeri Erba, Elodie Crublet, Christine Moriscot, Guy Schoehn, Carlos Amero, Jerome Boisbouvier. Science Advances; vol3, n4, e1601601

The remarkable complexity of vitamin B6 biosynthesis

The main enzyme responsible for the biosynthesis of vitamin B6 is the dodecameric enzyme Pdx1, whose mechanism has long been enigmatic. Pdx1 catalyses the condensation of two phosphorylated carbohydrates and ammonia into an active form of vitamin B6. The complex reaction involves more than ten catalytic steps and two distant active sites. Among the numerous intermediates that are successively formed during the reaction, several are coloured, facilitating their detection in crystallo by optical spectroscopy at the IBS/ESRF Cryobench prior to structure determination on the Structural Biology beamlines. Of particular interest is the formation of the I320 intermediate, which strongly absorbs in the UV region, and forms after the first carbohydrate and ammonia have been added. The crystallographic structure shows formation of a double covalent adduct between two distant lysine residues, one from each active site. A reorientation of one lysine later in the mechanism displaces the product from the first to the second active site. The bridging position of the I320 intermediate is an elegant solution for intermediate transfer, and represents a novel example of substrate channelling, where the use of covalent tethers prevent the loss of intermediates to surrounding solvent and maintain a high local concentration of substrate.

Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Rodrigues M, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes J, Royant A, Evans G, Sinning I, Ealick S, Begley T & Tews I. Nat. Chem. Biol.;13(3):290-294.

Insights into the first step of nucleosome formation

In eukaryotic cells, very long DNA molecules are tightly packaged and wrapped around histone proteins to form structures known as nucleosomes. While this is a useful way to store DNA, it also makes it inaccessible to many molecules that activate genes, copy DNA or perform other important cell processes. To make the DNA accessible, cells selectively disassemble particular nucleosomes and remove the histones. After DNA replication, the nucleosomes must reassemble to repackage the DNA.
A single nucleosome contains four pairs of histones, whereof two pairs consist of H3 and H4 histones. Histone chaperones assemble nucleosomes in a two-step process. First, two of H3-H4 pairs (i.e., a tetramer) interact with DNA and form a macromolecular complex. Then, two more pairs of different histones bind to complete the nucleosome. An enzyme called CAF1 is known to load the H3-H4 tetramers on DNA as the DNA is being copied. In this way, nucleosomes pack the newly made DNA. How CAF1 deposits H3-H4 tetramers onto the DNA is not known.
The EMBL laboratory lead by Daniel Panne, the Mass Spectrometry (MS) team of the IBS and scientists at Institut Curie and at Université Paris-Sud investigated the yeast CAF1 function by SEC-MALLS, AUC, SAXS and native MS. They showed that each CAF1 enzyme is able to bind a single H3-H4 pair. Then, two CAF1 enzymes bind to DNA and attach a H3-H4 tetramer onto it. The tetramer is formed in this way to ensure that the histones are correctly delivered to DNA after the DNA has been copied.
Overall, these findings explain the sequence of key events that take place when CAF1 attaches H3-H4 tetramers onto DNA which is the first step of nucleosome formation.

Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1. Sauer PV, Timm J, Liu D, Sitbon D, Boeri-Erba E, Velours C, Mücke N, Langowski J, Ochsenbein F, Almouzni G, Panne D. Elife;6. pii: e23474. doi: 10.7554/eLife.23474

Official opening of the CIBB 3D graphics room

The Official opening of a 3D graphics room took place on Friday 17 February in the Carl-Ivar Brandèn Building (CIBB).

This graphic room dedicated to master and doctoral courses in structural biology and on-site workshops offers 10 workstations operating under Debian linux with Nvidia 3D graphic displays and has the capacity to accommodate 20 students.

Located on the CIBB ground floor on EPN campus, this room has been provided by the IBS, the material has been financed by the Labex “Grenoble Alliance for Integrated Structural & Cell Biology” (GRAL) and the UFR Biology-Chemistry of University Grenoble Alpes and the installation was done by some members of the Partnership in Structural Biology (PSB).


Proton-detected solid-state NMR spectroscopy of a zinc diffusion facilitator in native nanodiscs

Membrane proteins are involved in many essential processes in living cells. However, their study is complicated by the fact that they have to be extracted from the native membrane, usually by using detergents, before they can be reinserted into model membranes, such as liposomes, bicelles or protein-bounded lipid nanodiscs. In collaboration with J. Dörr and A. Killian (Membrane Biochemistry and Biohysics, Bijvoet Center for Biomolecular Research, Utrecht, NL) we have shown that so-called native nanodiscs containing a bacterial cation diffusion facilitator (CDF) are amenable to high-resolution solid-state NMR studies. Native nanodiscs were obtained by the detergent-free extraction of the CDF protein from bacterial native membranes using Styrene Maleic Acid (SMA) copolymer. We observed favorable NMR properties that are comparable to crystalline protein preparations. This opens the way to studies of structure and dynamics of integral membrane proteins at atomic resolution in an environment that very closely resembles the native lipid bilayer.

Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs. Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Angew Chem Int Ed Engl. 2017 Jan 27. doi: 10.1002/anie.201610441.

A new NMR tool for probing functional protein dynamics

Structural biology has produced an impressive amount of high-resolution structural information on ground-state conformations of proteins. It has long been recognized, however, that biomolecules are dynamic ensembles rather than static entities, and that alternative high-energy conformations can play important functional roles, or may be responsible for the onset of misfolding and aggregation leading to cellular deregulation and disease. NMR spectroscopy is unique in its ability to study conformational dynamics over a wide range of time scales, simultaneously for a large number of individual nuclear sites in the molecule. In particular, micro- to millisecond time-scale dynamics can be accessed by relaxation−dispersion NMR, while states involving even higher energy barriers are best studied by real-time NMR methods. In this work, we have combined these two powerful NMR techniques, enabling the detection of conformational exchange dynamics in short-lived excited protein states. Application to the major folding intermediate of the amyloidogenic protein 2-microglobulin revealed the presence of a monomer-dimer exchange process that may be responsible for the early aggregation steps leading to amyloidosis in patients under hemodialysis treatment.

Probing Conformational Exchange Dynamics in a Short-Lived Protein Folding Intermediate by Real-Time Relaxation–Dispersion NMR. FrancoSergio R, Caballero G, Ayala I, Favier A and Brutscher B. Journal of the American Chemical Society; 139(3):1065-1068