Single-molecule sensing with aerolysin pore-forming toxins

Prof. Matteo Dal Peraro, Institute of Bioengineering , School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland (ospite di Prof. Matteo Masetti)

  • Data: 19 aprile 2024 dalle 14:00 alle 16:00

  • Luogo: Aula A, Farmacologia , via Irnerio 48 , Bologna BO

Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them [1].
Using integrative structural biology, i.e. combining molecular modeling and simulations along with biochemical and cryo-EM analysis, we have revealed the structure and assembly mechanism of one of the most studied bacterial pore-forming toxins [2], namely aerolysin fromA. hydrophila [3,4], recently obtaining its highest resolution structure at 2 Å by cryo-EM in nanodiscs (unpublished). Leveraging this structural and functional understanding, we have been able to characterize its properties as a molecular sensing device that can accurately discriminate nucleic acids and peptides [5], as well as detect post-translational modifications associated with validated biomarkers of neurodegenerative diseases (e.g. -synuclein phosphorylation in Parkinson’s disease)[6]. Moreover, we have explored the ability of aerolysin pores to decode the information stored in hybrid polymers with the aim of finding new, alternative solutions for the emerging problem of data storage [7]. We are further leveraging and engineering the exquisite sensitivity of aerolysin pores as well other biological pores from the same superfamily to develop the next generation of sensor devices for single-molecule proteomics and analytical chemistry.

1. Mayer, Cao, Dal Peraro, Biological nanopores for single-molecule sensing, iScience, 104145, 2022
2. Dal Peraro, van der Goot, Pore-forming toxins: ancient, but never really out of fashion, Nature Reviews Microbiology, 14(2):77, 2016
3. Degiacomi, Iacovache, … Dal Peraro, Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism, Nature Chemical Biology, 9(10):623, 2013
4. Iacovache et al., Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process, Nature Communications, 7(1):1, 2016
5. Cao, Cirauqui, Marcaida, Buglakova, Duperrex, Radenovic, Dal Peraro, Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores, Nature Communications, 10:1, 2019
6. Cao, Magalhães, …, Lashuel, Dal Peraro, Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore, ACS Nano, 18(2):1504, 2024
7. Cao, Krapp, Al Ouahabi, Konig, Cirauqui, Radenovic, Lutz, Dal Peraro, Aerolysin nanopores decode digital information stored in tailored macromolecular analytes, Science Advances, 6(50), eabc2661, 2020.