VIB today introduces an upgrade to its toolbox for structural analysis of biological molecules, leading the way for drug development. These tools help to overcome critical obstacles that limit the resolution of cryo-electron microscopy (cryo-EM) reconstructions. The latest upgrade is the use of generic MegaBodies™ as chaperones for 3D reconstructions of difficult proteins, including membrane proteins in their native state. This technology is made available via the VIB-VUB team of Professor Jan Steyaert. The Steyaert lab is recognized worldwide for pioneering applications of Nanobodies® in Structural Biology and structure-based drug discovery. Today, Nature Methods publishes a new paper on novel engineered Nanobodies®, optimized for applications in the fast growing field of cryo-EM.
Structural insights into drug targets
Despite the crucial importance of proteins for the efficacy of medicines, our knowledge of the function of human proteins extends to only one-third of these. Our understanding of their mode of action is hampered mostly because the molecular structure of only one in ten is known. Accordingly, solving protein structures by single particle cryo-EM has become a crucial tool to discover novel drugs directed to challenging yet highly valuable human drug targets. Moreover, these 3D-structures enable the rational design of safer and more specific drugs with less side-effects.
Picture: ©VUB 2018-Saskia Vanderstichele
Although cryo-EM is booming business in structural biology, the technology still has major limitations. To overcome these bottlenecks, the Steyaert lab developed the MegaBody™ technology to overcome three key obstacles that limit the resolution of single-particle cryo-EM reconstructions:
- Small protein size: the binding of the large and rigid MegaBodies™ to small targets generates larger particles that are visible under the microscope;
- Preferential orientation: MegaBodies™ allow to overcome the preferential orientation of single particles that is often observed at the water-air interfaces of frozen samples;
- Highly flexible particles: MegaBodies™ lock proteins in a unique functional state to produce more homogenous particles.
The Steyaert lab also developed the so-called MSP MegaBodies™. These proprietary engineered VHHs bind the belt proteins of Nanodisks and allow the structural characterization of native membrane proteins embedded in Nanodisks at high resolution.
In the new Nature Methods paper, the Steyaert lab describes the methodology to make Megabodies™. In three earlier Nature papers in collaboration with Radu Aricescu (MRC Laboratory of Molecular Biology in Cambridge) the scientists have thoroughly validated the technology. They succeeded to make the first high resolution 3D-reconstructions of the human GABAA receptor by applying different MegabodiesTM. GABAA receptors are important neurotransmission mediators in the human brain and are targets for clinically-relevant drugs including benzodiazepines and general anaesthetics.
Tools to maximize the huge potential of cryo-EM
The VIB toolbox for cryo-EM now includes a series of technologies, developed by the VIB labs of Professors Jan Steyaert, Rouslan Efremov and Nico Callewaert, to enable structural and functional analysis of challenging target proteins.
Next to the MegaBodies™ chaperones, VIB’s world-leading expertise in glyco-engineering technology adds up to the toolbox. With the VIB-UGent lab of Nico Callewaert, VIB has a broad IP portfolio and extensive know-how in eukaryotic cell-based glyco-engineering in house.
Specifically, the toolbox consist of:
- The MegaBody™ technology: large and rigid equivalents of Nanobodies® acting as chaperones
- MSP-MegaBodies™: generic MegaBodies™ against membrane proteins in MSP-based nanodiscs
- Glyco-engineering: technologies to reduce the sugar moieties on proteins which often cause problems for high resolution structure determination
- Co-express: a combination of glyco-engineering and Nanobodies® as protein chaperones
Jan Steyaert adds: "The MegaBody™ technology has enormous potential to stimulate the rapidly growing field of drug discovery using single particle cryo-EM. With this toolbox, we put in motion a coordinated approach for facilitating high resolution structural analysis of difficult yet highly valuable targets, such as eukaryotic membrane proteins."
Enabling tools for cryo-EM now available at VIB
The ‘VIB-VUB facility for Bio Electron Cryogenic Microscopy’ (BECM) hosts the newest kinds of electron cryogenic microscopes that allow for high-resolution protein structure reconstruction using single particle cryo-EM. This combination of drug discovery platforms, technology and expertise can now be accessed at VIB.
Tim Van Acker, Business Development Manager at VIB: “VIB is actively partnering with industry, putting its cryo-EM toolbox at the service of companies so they can push forward their structure-based drug discovery programs through a combination of state of the art technologies.”
Tomasz Uchański, Simonas Masiulis, Baptiste Fischer, Valentina Kalichuk, Uriel López-Sánchez, Eleftherios Zarkadas, Miriam Weckener, Andrija Sente, Philip Ward, Alexandre Wohlkönig, Thomas Zögg, Han Remaut, James H. Naismith, Hugues Nury, Wim Vranken, A. Radu Aricescu, Els Pardon & Jan Steyaert. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Nature Methods.