Institut de Biologie StructuraleGrenoble / France

2021

New issue for the IBS Newsletter

Find the June 2021 issue (in french only).

Radical-based chemistry for the assembly of the [FeFe]-hydrogenase active site

[FeFe] hydrogenases are metalloenzymes capable of catalyzing the reversible oxidation of molecular hydrogen. They use a unique organometallic center called H-aggregate, consisting of a [Fe4S4] center linked to a binuclear iron center [2Fe]H. The latter corresponds to the hydrogen binding and conversion site. The physicochemical and structural properties of this center serve as a source of inspiration for the development of catalysts for the wider use of molecular hydrogen as a renewable energy source. IRIG researchers are unveiling the mechanisms of production and assembly of this metal center, which involve a complex radical chemistry .

The biosynthesis of [2Fe]H requires the coordinated action of at least three accessory metalloproteins HydF, HydE and HydG. HydG is responsible, from L-tyrosine, for the production of the ligands cyanide and carbon monoxide, in the form of an organometallic complex termed complex-B. The latter serves in turn as a substrate for HydE whose reaction and product remain unknown. HydF serves as a scaffold on which the [2Fe]H center is built before being inserted into the hydrogenase. Researchers from Irig are studying the catalytic mechanisms of transition metal containing metalloenzymes, but also the mechanisms of synthesis and insertion of these metal sites into the enzymes in which they are to be inserted. In collaboration with UCDavis and the University of Illinois, they published the complex-B bound HydE crystal structure, revealing for the first time both its unique (3-cysteinate)Fe(CN)(CO)2 configuration and its binding mode. Furthermore, by triggering the reaction, either directly in the crystals or just before crystallization, they were able to observe a new mononuclear pentavalent iron species, probably related to the product of HydE. Analysis of the conformational changes observed in the different structures suggests a directional movement for substrate access to the active site and product evacuation, allowing them to be protected from possible hydrolysis upon contact with the solvent. This work raises new questions about the complete mechanism of the enzyme which acts as a nano assembly line.

Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B. Rohac R, Martin L, Liu L, Basu D, Tao L, Britt RD, Rauchfuss TB, and Nicolet Y. Journal of the American Chemical Society, 2021

Contact : Yvain Nicolet (IBS/Metalloproteins Group)

SARS-CoV-2 : a new mode of transmission

Broadly speaking, cells have receptors on their surface, some of which are used only for virus attachment, while others can contribute to the cellular barrier crossing. The S-glycoprotein, located on the surface of the SARS-CoV-2 Coronavirus, allows the entry of the virus into human cells via its interaction with a receptor, the ACE2 enzyme, on the surface of infected cells.
IBS Scientists (M&P group), in collaboration with the CAID group and the IBS electron microscopy platform, as well as Spanish and Italian researchers, have demonstrated that lectin receptors (DC-SIGN, L-SIGN , MGL and Langerin) of immune cells are also able to recognize the S protein of SARS-CoV-2. This interaction involves a multi-site recognition of the S protein by exploiting the different surface glycans (sugars) of the S protein. It does not cause direct infection of cells by SARS-CoV-2 but DC-SIGN and L-SIGN are able, once they have attached the virus to the cell, to transmit it to permissive cells possessing ACE2. The S-glycoprotein thus appears to possess a whole set of keys to allow SARS-CoV-2 to proliferate.
These results, already demonstrated on pseudo viruses a few months ago in pre-publication, are now confirmed by the use of authentic SARS-CoV-2 viruses and on human respiratory cells. The researchers have also demonstrated that it is possible to inhibit this mode of transmission by using glycomimetics, molecules that can mimic the surface sugars of the virus. These glycomimetic inhibitors developed at IBS will constitute a first tool to study the relative importance of this mode of transmission. UGA press release

DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist. M. Thépaut, J. Luczkowiak, C. Vivès, N. Labiod, I. Bally, F. Lasala, Y. Grimoire, D. Fenel, S. Sattin, N. Thielens, G. Schoehn, A. Bernardi, R. Delgado, F. Fieschi. Plos Pathogens (2021) accepté

Contact : Franck Fieschi, UGA professor attached to the IBS (Membrane & Pathogens group)

Molecular insights into the bacterial cell wall elongation process

The peptidoglycan (PG) is an essential component of the bacterial cell wall, and plays a key role in shape maintenance and cell division. Due to the importance of PG for bacterial survival, its biosynthetic machinery has been a preferential target for antibiotic development for decades. However, little is known regarding how cell wall elongation is regulated. In this work we show that the scaffolding protein MreC from the human pathogen Pseudomonas aeruginosa plays a key role in regulation of cell wall elongation through its ability to self-associate and bind to different protein partners, including Penicillin-Binding Proteins (PBPs), the targets of beta-lactam antibiotics. These results were obtained in partnership with the Laboratório Nacional de Biociências in Campinas and using data collected at the Brazilian synchrotron LNLS and at the Glacios cryo-electron microscope at the IBS, pave the way for a detailed understanding of how bacteria form their cell wall as well as for the development of new antibacterial agents.

Self-association of MreC as a regulatory signal in bacterial cell wall elongation. Alexandre Martins, Carlos Contreras-Martel*, Manon Janet-Maitre, Mayara M. Miyachiro, Leandro F. Estrozi, Daniel Maragno Trindade, Caique C. Malospirito, Fernanda Rodrigues-Costa, Lionel Imbert, Viviana Job, Guy Schoehn, Ina Attrée, Andrea Dessen. Nature Communication

A new HIV-1 gp41 conformation as a target for broadly neutralizing antibodies

The HIV-1 envelope glycoprotein (Env) is the key target of neutralizing antibodies, blocking virus entry. Env is a metastable trimer composed of the receptor binding domain gp120 and the fusion protein subunit gp41. Upon cellular receptor binding Env undergoes a series of conformational changes notably within gp41, which pulls viral and cellular membranes into close proximity to catalyze membrane fusion and initiate infection.
In this article, the EBEV group and collaborators from the University of the Basque Country, the University of Zurich and the University of Lorraine present the crystal structure of gp41 locked in a fusion intermediate state. This structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides (FP) and the transmembrane regions (TMR) pointing into different directions permitting a close apposition of viral and cellular membranes. Molecular dynamics simulation demonstrates the transition pathway from the intermediate state highlighted by the crystal structure into the final post-fusion conformation. Furthermore, the crystal structure conformation can be targeted by broadly neutralizing antibodies (bnAbs) recognizing the highly conserved membrane proximal external region (MPER). This corroborates that MPER bnAbs can block final steps of refolding of FP and TMR, which is required for completing membrane fusion.

Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies. Caillat C, Guilligay D, Torralba J, Friedrich N, Nieva JL, Trkola A, Chipot CJ, Dehez FL, Weissenhorn W. Elife 2021 Apr 19 ;10:e65005

Contact : W. Weissenhorn, UGA professor attached to the IBS (Entry and Budding of Enveloped Viruses Group)

Paleo biochemistry, a key to understanding the selection of enzyme properties

Studies providing insights into adaptative process of molecules to extreme conditions are of wide fundamental interest, as evolutionary processes impact the genomic organization, shape, function and phenotype of cells and their biomolecules. Thus evolutionary biochemistry allows to understand the fundamental process of exchange between the dynamic, structural and functional properties of enzymes.
In this work, scientists from the Institute of Structural Biology (IBS, Grenoble), in collaboration with the National Institute of Research in Digital Science and Technology (INRIA Rennes) and the Laboratory of Biometry and Evolutionary Biology (LBBE, Lyon), describe the evolutionary history (over a period of 500 million years) of malate dehydrogenases (MalDH) within Halobacteria, a metabolic enzyme facing extreme physicochemical conditions. They resurrected nine ancestors along the inferred halobacterial MalDH phylogeny and compared their biochemical properties with those of five modern halobacterial MalDHs. They found that a variety of evolutionary processes such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic. Unexpectedly, they analyzed that destabilizing mutations in a given circumstances could be at the origin of a gain of stability allowing a secondary adaptation in an environment with a very high pH. These researchers also showed the very important role of lateral gene transfer between species that allows a very rapid adaptive molecular response.
This work revealed that activity, stability and solubility of an enzyme are parameters that evolve independently of each other during an adaptive process.This is a fundamental finding that should be taken into account by researchers interested in protein engineering.

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering gene trajectories and changes in biochemical properties. Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti, Manolo Gouy and Dominique Madern. Molecular Biology and Evolution, msab146, https://doi.org/10.1093/molbev/msab146

Contact : Dominique Madern (IBS/Extremophiles and Large Molecular Assemblies Group)

’Green’ chemistry and biofuels : Observing a photoenzyme at work

An international consortium* of scientists, including researchers from the IBS/DYNAMOP and IBS/SYN groups, has deciphered the mechanism and dynamics of the fatty acid photodecarboxylase (FAP) enzyme, a discovery published in Science on 08/04/2021. This photoenzyme is naturally present in many microscopic algae and uses light energy to catalyse the generation of hydrocarbons from fatty acids.
To elucidate the mechanism of this unique enzyme, the research teams have combined multi-faceted experimental and theoretical approaches comprising site-directed mutagenesis, time-resolved vibrational and electronic optical spectroscopies or cryotrapping of reaction intermediates, static and kinetic crystallography at synchrotrons and an X-ray free electron laser (XFEL) and quantum chemical calculations. The elucidation of the FAP catalytic mechanism and the identification of reaction intermediates and structural elements indispensable to its activity constitute a key basis for the optimization of the enzyme for the production of ‘green’ hydrocarbon fuels and chemicals that can be easily modulated by light. Press release.

* In France, this study mobilized researchers from the Institut de Biosciences et Biotechnologies Aix-Marseille in Cadarache, the Institut de Biologie Intégrative de la Cellule in Gif-sur-Yvette, the Institut Polytechnique de Paris in Palaiseau, the Institut de Biologie Structurale in Grenoble, the Universities of Lille and Rennes, the European Synchrotron Radiation Facility and the Institut Laue-Langevin. Abroad, researchers from the Max-Planck Institute in Heidelberg, Moscow State University and the SLAC National Accelerator Laboratory in Stanford are involved.

Mechanism and dynamics of fatty acid photodecarboxylase. Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin S, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier J-P, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, Beisson F. Science 2021 ; 372:eabd5687 (https://science.sciencemag.org/content/372/6538/eabd5687/tab-pdf)

IBS Contact : Martin Weik

An Unexpected P-Cluster like Intermediate En Route to the Nitrogenase FeMo-co

Nitrogenase is a key metalloprotein that catalyzes the reduction of nitrogen to ammonia at room temperature and ambient pressure. It thus plays a major role in the global nitrogen cycle. It uses two metal centers : the P-cluster, an atypical [Fe8S7] center, which allows electron transfer to the active site itself, which is an organometallic [MoFe7S9C-(R)-homocitrate] center. Its biosynthesis requires the action of a dozen accessory proteins that constitute the NIF (for NItrogen Fixation) assembly machinery. The NifB protein is the key enzyme in this mechanism because it is responsible for the fusion of two [Fe4S4] centers combined with a carbide ion insertion and the addition of a sulfide ion to produce a [Fe8S9C] precursor termed NifB-co. Recently, American colleagues published a crystal structure of the NifB protein with all its metal centers. Unfortunately, they did not model their crystallographic data well and missed the identity of cluster bound to the active site. By reusing these data, we were able to highlight the presence of a unique [Fe8S8] center resulting from the fusion of [Fe4S4] centers. This crystal structure allowed us to redefine the order of the reaction steps showing that the FeS center fusion must take place before the carbide ion insertion. The particular coordination of this intermediate highlights the role of the protein matrix in the organization of the NifB-co biosynthetic steps, thus revealing the mechanism of the enzyme.

An unexpected P-cluster like intermediate en route to the nitrogenase FeMo-co. Leon P. Jenner, Mickael V. Cherrier, Patricia Amara, Luis M. Rubio and Yvain Nicolet. Chemical Science DOI : 10.1039/D1SC00289A

Contact : Yvain Nicolet (IBS/Metalloproteins Group)

IBS benefits from exceptional funding from the 3rd French Investment Program ’EquipEx+’

The 3rd French Investment Program ’EquipEx+’ aims to support new research equipment of international standard, to strengthen the excellence and competitiveness of French scientific research. Following a call for research proposals launched mid-2020, 50 proposals out of 135 were selected by an international jury end of 2020 for a total amount of 422 million euros.

IBS is associated with two of the winning projects :

  • the FranceCryoeEM project for a "National instrumentation in cryo-electron microscopy" : 3 ultra-efficient and ultra-stable high-energy electron cryo-microscopes will be installed in France, one of them managed by IBS for the observation of macromolecules at atomic level,
  • the MAGNIFIX project for a "Global upgrading and New French Hard X-Ray Investigation Infrastructures" : this project will give the French academic and industrial community privileged access to the new EBS-ESRF fourth generation synchrotron source (the most efficient in the world), through the upgrading of 5 French CRG "Collaborative Research Groups" beamlines (one managed by IBS) (total investment of 12 million euros over 2021-2025).

Pas de deux : how polymers keep dry proteins active

© Yann Fichou/IBS/CEA/CNRS/UGA

Dancing water molecules on the surface of soluble proteins provide the essential lubricant for macromolecular function. Surprisingly, polymers attached to protein surfaces have been reported to replace hydration water and bring inactive dry proteins back to life. The mechanism behind polymer-assisted functional protein motions has now been revealed by researchers from the Institut de Biologie Structurale in Grenoble, the Universities of Bordeaux, of California Irvine, of Bristol and of Perugia and from the Heinz-Maier Leibnitz Zentrum in Garching. The consortium applied neutron spectroscopy and molecular dynamics simulations to shed light on the motions animating proteins and polymers in the water-free hybrid. Separating them was possibly by selectively masking the signal from either the polymer or the protein by replacing hydrogen by deuterium atoms, the latter scattering neutrons two orders of magnitude less than the former in spectroscopy experiments. Surprisingly, protein and polymer motions turned out to be qualitatively similar, in stark contrast to protein and water motions being qualitatively different ; segmental polymer motions appear to substitute for hydration-water translational motions. Even if this substitution keeps dry proteins biologically active, certain dynamical modes are suppressed in the protein, possibly explaining the generally observed decrease in activity when hydration water is substituted by polymer coating. The study suggests ways to fine-tune polymer properties so that the loss in protein activity can be minimized. This will be particularly important for rationally designing protein-polymer hybrids for specific biotechnological applications, such as in medicine and cosmetics.

Diffusive-like motions in a solvent free protein-polymer hybrid. Schirò G, Fichou Y, Brogan APS, Sessions R, Lohstroh W, Zamponi M, Schneider GJ, Gallat F-X, Paciaroni A, Tobias DJ, Perriman A, Weik M. Physical Review Letters 126, 088102

Contact : Martin Weik & Giorgio Schirò (Dynamics and kinetics of molecular processes Group)

Supramolecular assembly of the Escherichia coli LdcI upon acid stress

Bacteria possess a sophisticated arsenal of defense mechanisms that allow them to survive in adverse conditions. Adaptation to acid stress and hypoxia is crucial for the enterobacterial transmission in the gastrointestinal tract of their human host. Using three-dimensional superresolution fluorescence microscopy and electron cryo-microscopy, the researchers of the MICA group, in collaboration with the PIXEL team and the M4D platform at the IBS, have shown that in response to acid stress, the enzyme lysine decarboxylase (LdcI) forms supramolecular assemblies in vivo in E. coli and polymerizes into filaments. They determined the atomic structure of those filaments in vitro and proposed a mechanistic model for LdcI function and offer tools for further in vivo investigations. This work has also made it possible to develop tools applicable to all types of cells, to study molecular assemblies by combining the two types of microscopy while preserving their structural integrity and their interactions with cellular partners.

Supramolecular assembly of the Escherichia coli LdcI upon acid stress. Jessop M, Liesche C, Felix J, Desfosses A, Baulard M, Adam V, Fraudeau A, Huard K, Effantin G, Kleman JP, Bacia-Verloop M, Bourgeois D, Gutsche I. Proc Natl Acad Sci U S A. 2021 Jan 12 ;118(2):e2014383118.

Congratulations to Andrea Carfi, former IBS PhD student, for the development of the Moderna’s COVID-19 vaccine

Photo credits : https://masscpr.hms.harvard.edu/vaccines

We are proud to announce that Andrea Carfi, currently VP & Head of Research for Infectious Disease at Moderna, Cambridge, MA, USA, is an IBS alumnus.

After receiving his doctorate under the direction of Otto Dideberg (retired) at the IBS in 1997 he completed his training as a postdoctoral fellow in Prof. Don Wiley’s group at Children’s Hospital (Harvard University) in Boston, MA, where he met the current IBS director Prof. W. Weissenhorn. Andrea Carfi then moved to industry, joining Merck in 2002. He returned to Cambridge (USA) in 2010 as a senior manager first at Novartis Vaccines and then GSK vaccines. He joined Moderna in 2017, where he contributed to the development of Moderna’s COVID-19 mRNA vaccine that was recently approved for use by the European Medicines Agency (https://www.ema.europa.eu/en/news/ema-recommends-covid-19-vaccine-moderna-authorisation-eu). The Moderna’s COVID19 vaccine has been approved and used in France since 11 January

To know more :

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Corbett KS, Edwards DK, Leist SR, Abiona OM, Boyoglu-Barnum S, Gillespie RA, Himansu S, Schäfer A, Ziwawo CT, DiPiazza AT, Dinnon KH, Elbashir SM, Shaw CA, Woods A, Fritch EJ, Martinez DR, Bock KW, Minai M, Nagata BM, Hutchinson GB, Wu K, Henry C, Bahl K, Garcia-Dominguez D, Ma L, Renzi I, Kong WP, Schmidt SD, Wang L, Zhang Y, Phung E, Chang LA, Loomis RJ, Altaras NE, Narayanan E, Metkar M, Presnyak V, Liu C, Louder MK, Shi W, Leung K, Yang ES, West A, Gully KL, Stevens LJ, Wang N, Wrapp D, Doria-Rose NA, Stewart-Jones G, Bennett H, Alvarado GS, Nason MC, Ruckwardt TJ, McLellan JS, Denison MR, Chappell JD, Moore IN, Morabito KM, Mascola JR, Baric RS, Carfi A, Graham BS. (2020). Nature ; 586(7830):567-571.

https://news.harvard.edu/gazette/story/2020/04/harvards-coronavirus-vaccine-efforts/ & https://masscpr.hms.harvard.edu/vaccines