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Institut de Biologie StructuraleGrenoble / France

Highlights

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.