Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface

Monitoring enzymatic activities at the cell surface is challenging due to the poor efficiency of transport and membrane integration of fluorescence resonance energy transfer (FRET)-based biosensors. Therefore, we developed a hybrid biosensor with separate donor and acceptor that assemble in situ. The directed evolution and sequence-function analysis technologies were integrated to engineer a monobody variant (PEbody) that binds to R-phycoerythrin (R-PE) dye. PEbody was used for visualizing the dynamic formation/separation of intercellular junctions. We further fused PEbody with the enhanced CFP and an enzyme-specific peptide at the extracellular surface to create a hybrid FRET biosensor upon R-PE capture for monitoring membrane-type-1 matrix metalloproteinase (MT1-MMP) activities. This biosensor revealed asymmetric distribution of MT1-MMP activities, which were high and low at loose and stable cell-cell contacts, respectively. Therefore, directed evolution and rational design are promising tools to engineer molecular binders and hybrid FRET biosensors for monitoring molecular regulations at the surface of living cells. [Display omitted] •Directed evolution and rational design are used for biosensor development•PEbody can be applied to track cell-cell contact dynamics with high precision•Assembling a hybrid FRET biosensor at the cell surface enhances signal-to-noise ratio•Biosensor reveals heterogeneous activity of MT1-MMP at cell-cell contacts Limsakul et al. demonstrate that directed evolution and sequence-function analysis are promising tools for engineering molecular binders and hybrid FRET biosensors, which reveal new distinct subcellular features of MT1-MMP molecular regulations at the extracellular surface of live cells.