Neutralizing antibodies against coronaviruses
The SARS-CoV-2 virus has caused a world-wide pandemic resulting in a massive loss of lives and detrimental effects on the economies of most countries. We are using single-particle cryo-electron microscopy (cryo-EM) to solve structures of infection- and vaccination-induced antibodies complexed with the spike trimer of SARS-CoV-2 in order to elucidate the structural correlates of antibody-based immune protection. Structural comparisons allowed us to classify antibodies against the receptor-binding domain (RBD) of spike trimer into categories. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2. Our structural studies have also guided the development of a potential pan-betacoronavirus vaccine. The vaccine approach involves co-display of diverse sets of RBDs from SARS-like beta coronaviruses (sarbecoviruses) on nanoparticles (mosaic-RBD-nanoparticles) that results in increased breadth of neutralizing responses in mice compared with nanoparticles presenting only SARS-CoV-2 RBDs. This modular vaccine platform could provide protection from SARS-CoV-2 as well as potential future emergent coronaviruses that could cause pandemics.
From integrative structural biology to cell biology
Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ~52 MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving integrative modeling include expanding model representations, increasing the variety of input data and prior information, quantifying a match between input information and a model in a Bayesian fashion, inventing more efficient structural sampling, as well as developing better model validation, analysis, and visualization. In addition, two community-level challenges in integrative modeling are being addressed under the auspices of the Worldwide Protein Data Bank (wwPDB). First, the impact of integrative structures is maximized by PDB-Dev, a prototype wwPDB repository for archiving, validating, visualizing, and disseminating integrative structures. Second, the scope of structural biology is expanded by linking the wwPDB resource for integrative structures with archives of data that have not been generally used for structure determination but are increasingly important for computing integrative structures, such as data from various types of mass spectrometry, spectroscopy, optical microscopy, proteomics, and genetics. To address the largest of modeling problems, a type of integrative modeling called metamodeling is being developed; metamodeling combines different types of input models as opposed to different types of data to compute an output model. Collectively, these developments will facilitate the structural biology mindset in cell biology and underpin spatiotemporal mapping of the entire cell.
M. Joanne Lemieux
Structural studies towards the development of an oral protease inhibitor to treat SARS-CoV-2 infection
Despite progress in vaccine development, antivirals targeting SARS-Co-2 are needed for those who are immunocompromised. Proteases cleave peptide bonds of a very specific sequence making them strong drug targets. Antivirals that target proteases are already used clinically to treat HIV and Hepatitis C virus. We have developed inhibitors of the SARS-CoV-2 protease to prevent the main protease from cleaving the viral polypeptide and subsequent viral replication in cells. X-ray crystallography revealed the mechanism of inhibition, and has helped the optimisation of new derivatives. Moving forward, these inhibitors will be tested with variant proteases, followed up by studies in animals to determine efficacy and pharmacokinetics in preparation for clinical trials.
VlsE, a dual function outer surface lipoprotein from the Lyme disease spirochete
The VlsE protein from the Lyme disease spirochete Borrelia burgdorferi is an important pathogenic determinant. The protein is required for persistent infection and displays antigenic variation following infection. Continual sequence variation of VlsE allows escape from surveillance by the acquired host immune response and keeps the spirochetes one step ahead of the army of antibody molecules produced by the host. Variation of the VlsE sequence is driven by sequential gene conversion events. We developed a next generation sequencing approach to study this process. The observed changes in amino acids in the presence and absence of immune selection and the relationship to protein structure and function will be discussed. In addition, our recent findings that the VlsE protein performs a second important function will be discussed. The protein is a dermatan sulfate adhesins, which promotes transient interactions between infecting spirochetes and the microvasculature under the shear force of blood flow.
Computational, biophysical and functional analysis of calcium-mediated pseudopilus stability
Type II secretion systems are nanomachines that are found within all domains of life. In Gram negative bacteria, these nanomachines secrete folded proteins or complexes that play key roles in adaptation and virulence. Protein secretion from the bacterial periplasm across the outer membrane by the type II secretion system is coupled to dynamic assembly of an inner membrane anchored periplasmic fibre called the pseudopilus. The pseudopilus is mostly composed of multiple subunits of a protein called PulG, whose stability is dependent on calcium. As pseudopilus stability can be uncoupled from its role in protein secretion, we sought to investigate the role of calcium and cations in protein secretion. We used molecular dynamics simulations, biophysical assays and in vivo protein secretion assays to determine the influence of calcium on PulG folding and how this impacts protein secretion. Using these approaches, we identified a second calcium coordination site in PulG and determined that calcium coordination was not required for protein secretion. These findings suggest that the calcium-binding site is not involved in substrate recognition and highlight that dynamic pseudopilus assembly but not stability is required for protein secretion.
Hybrid Method Approach in Drug Discovery Pipelines- How to employ AI to fight cancer
The Stetefeld lab has a long-standing interest in exploiting the structure-property relationship of key components in extracellular higher-order signaling complexes. Starting with the very first high-resolution X-ray crystal structure of such a signaling component, the study of the basement membrane protein laminin  helped to establish the field of structural biology of higher order matrix assemblies, and it has since become a standard reference in the field. The lab expanded studies from individual domains over tandem arrangements towards signaling assemblies. For example, the unravelling of agrin-mediated neuromuscular junction formation [2,3] and the exploring of the effect of alternative mRNA splice inserts in muscular dystrophy [4,5] contributed significantly to a molecular understanding of underlying diseases. Other avenues of research included collagen assemblies via phage-based foldon systems [6,7], Cadherin super-assemblies  and integrin-snake venom lectin interactions .
Most recently, we have published work about Netrin-1 and its interaction with the dependence receptor UNC5 and Netrin-4 disrupting basement membrane networks [10,11]. Studies of these protein-protein networks are extremely important for the development of new therapeutic approaches in numerous cancers and neurodegenerative diseases. By applying AI-technology to this mostly transient protein-protein interaction networks it is envisioned to design and characterize specific mediators that allow for targeted apoptosis of specific cancer cells.
 Stetefeld et al. JMB, 1996  Stetefeld et al. Nature Structural Biology, 2001  Mascarenhas et al. EMBO J, 2003  Stetefeld et al. Structure, 2004  Stetefeld & Ruegg TIBS, 2005  Stetefeld et al. Structure, 2004  Boudko et al. JMB, 2004  Haeussinger et al. EMBO J, 2004  Eble et al. PlosBiol, 2017  Grandin et al. Cancer Cell, 2016  Reuten et al. Nature Communications, 2017