We present a fluorogenic method to visualize misfolding and aggregation of a specific protein-of-interest in live cells using structurally modulated fluorescent protein chromophores. Combining photo-physical analysis, X-ray crystallography, and theoretical calculation, we show that fluorescence is triggered by inhibition of twisted-intramolecular charge transfer of these fluorophores in the rigid microenvironment of viscous solvent or protein aggregates. Bioorthogonal conjugation of the fluorophore to Halo-tag fused protein-of-interests allows for fluorogenic detection of both misfolded and aggregated species in live cells. Unlike other methods, our method is capable of detecting previously invisible misfolded soluble proteins. This work provides the first application of fluorescent protein chromophores to detect protein conformational collapse in live cells.

Molecular rotor-based fluorophores (RBFs) have been widely used in many fields.H owever,t he lacko fcontrol of their viscosity sensitivity limits their application. Herein, this problem is resolved by chemically installing extended p-rich alternating carbon-carbon linkages between the rotational electron donors and acceptors of RBFs.T he data reveal that the length of the linkage strongly influences the viscosity sensitivity,l ikely resulting from varying height of the energy barriers between the fluorescent planar and the dark twisted configurations.T hree RBF derivatives that span aw ide range of viscosity sensitivities were designed. These RBFs demonstrated, through ad ual-color imaging strategy,t hat they can differentiate misfolded protein oligomers and insoluble aggregates,b oth in test tubes and live cells.B eyond RBFs,i ti s envisioned that this chemical mechanismm ight be generally applicable to awide range of photoisomerizable and aggregation-induced emission fluorophores.

Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers and insoluble aggregates, a process that is associated with an increasing number of diseases that are not curable or manageable. Herein, we present a chemical toolbox, AggFluor, that allows for live cell imaging and differentiation of complex aggregated conformations in live cells. Based on the chromophore core of green fluorescent proteins, AggFluor is comprised of a series of molecular rotor fluorophores that span a wide range of viscosity sensitivity. As a result, these compounds exhibit differential turn-on fluorescence when incorporated in either soluble oligomers or insoluble aggregates. This feature allows us to develop, for the first time, a dual-color imaging strategy to distinguish unfolded protein oligomers from insoluble aggregates in live cells. Furthermore, we have demonstrated how small molecule proteostasis regulators can drive formation and disassembly of protein aggregates in both conformational states. In summary, AggFluor is the first set of rationally designed molecular rotor fluorophores that evenly cover a wide range of viscosity sensitivities. This set of fluorescent probes not only change the status quo of current imaging methods to visualize protein aggregation in live cells but also can be generally applied to study other biological processes that involve local viscosity changes with temporal and spatial resolutions.

While organic donor‐acceptor (D‐A) molecules are widely employed in multiple areas, the application of more D‐A molecules could be limited because of an inherent polarity sensitivity that inhibits photochemical processes. Presented here is a facile chemical modification to attenuate solvent‐dependent mechanisms of excited‐state quenching through addition of a β‐carbonyl‐based polar substituent. The results reveal a mechanism wherein the β‐carbonyl substituent creates a structural buffer between the donor and the surrounding solvent. Through computational and experimental analyses, it is demonstrated that the β‐carbonyl simultaneously attenuates two distinct solvent‐dependent quenching mechanisms. Using the β‐carbonyl substituent, improvements in the photophysical properties of commonly used D‐A fluorophores and their enhanced performance in biological imaging are shown.

Aberrant protein aggregation leads to various human diseases, but little is known about the physical chemical properties of these aggregated proteins in cells. Herein, we developed a boron-dipyrromethene (BODIPY)-based HaloTag probe, whose conjugation to HaloTag-fused proteins allows us to study protein aggregates using both fluorescence intensity and lifetime. Modulation of BODIPY fluorophore reveals key structural features to attain the dual function. The optimized probe exhibits increased fluorescence intensity and elongated fluorescence lifetime in protein aggregates. Fluorescence lifetime imaging using this probe indicates that protein aggregates afford different viscosity in the forms of soluble oligomers and insoluble aggregates in live cells. The strategy presented in this work can be extended to enable a wide class of HaloTag probes that can be used to study a variety of physical properties of protein aggregates, thus helping unravel the pathogenic mechanism and develop therapeutic strategy.