BPS2026 – Detection and characterization of single proteins via membrane deformations

Label-free characterization of protein species within their native, dynamic interactomes remains a significant challenge, particularly for membrane-associated systems. In cells, many functional interactomes are transiently or permanently confined to membranes. Here, we demonstrate that protein identities, interactions and activities can be obtained from their membrane deformation footprints. Utilizing a soft-elastic membrane nanotube (seNT) as an electric biosensor, we detect molecular-size deformations through changes in luminal electrical current. The deformation footprints by small proteins and lipid-like molecules were resolved. Structure-based modeling of the deformations enabled robust identification of single protein species, their membrane interactions, dynamic structural modifications and oligomeric states. As a proof of principle, we show how seNT sensor tracks in real time self-assembly of dynamin1 molecular machine from dimeric building blocks followed by cyclic conformational rearrangements of the machine driven by GTP hydrolysis. Our approach thus uncovers the extensive informational capacity of membrane deformations, with implications as for molecular sensing technologies as for mechanistic understanding of the membrane roles in the intracellular metabolic and signaling pathways. This work was partially supported by the Spanish Ministry of Science and Innovation under grant PID2024-159156NB-I00.