Visiting Associate Group Leader
Functional amyloids are protein fibrils produced by many organisms to carry out various physiological processes. They are especially prevalent in microbes and have been identified as key virulence factors. Microbial amyloids thus represent attractive candidates for structural characterisation aimed at discovering novel antimicrobial therapeutics. Yet amyloids present challenging systems for biochemical and structural studies due to their polymeric arrangement and aggregative, polymorphic, and partially disordered nature. As a result, high-resolution structural information on microbial functional amyloids is lacking. This is in contrast to the vast structural information gained over decades for eukaryotic amyloids involved in neurodegenerative and systemic diseases. Our lab conducts atomic-level analyses of structure–function–fibrillation relationships in bacterial amyloids and published the first atomic structures of bacterial amyloid fibrils.
Our findings thus far have exposed an extreme diversity in the structures of functional fibrils, extending beyond canonical amyloid cross-β structures and encoding different activities. This opens directions for studies of structure–function–fibrillation relationships, mechanistic studies of the interactions between fibril-forming toxic peptides and cells, modulation of fibril activity, and identifying molecular-level interactions of bacterial amyloids with human host proteins. The major challenge in achieving our goals is that the structures of these fibrils do not directly imply their function and mechanism of action. Specifically, amyloids show little to no conservation in sequence or in length, relatively rigid scaffolds, and structural polymorphisms in similar and even identical sequences. Another challenge is in the assessment of the role of fibrillation in toxic activities, and the dynamics between monomers, oligomers, and fibrils. Our working hypothesis is that a given fibril-forming sequence can form different fibril morphologies, and even different secondary structures, which show different levels of activity, selectivity, and perhaps even loss or gain of function. This is reminiscent of amyloid and prion fibril polymorphism, showing different conformations that exhibit different degrees of toxicity translating into a range of disease strains. To overcome these challenges, we leverage the unique and extensive structural knowledge accumulated in our lab on several fibrillar systems from bacteria, an amphibian, and human, which are involved in biofilm structuring, cytotoxicity, and antibacterial activities. We plan to implement new methodological approaches, including single-particle cryo-electron microscopy (cryo-EM) reconstruction and cryogenic correlative light and electron microscopy (cryo-CLEM). This will allow us to determine fibril structures in native environments, and to visualise interactions between different fibrils and of fibrils with lipid bilayers and cells, to clarify their mechanism of action.