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1. A single point mutation converts a proton-pumping rhodopsin into a red-shifted, turn-on fluorescent sensor for chloride

   https://doi.org/10.1039/D0SC06061E  

   Tutol, Jasmine N.; Lee, Jessica; Chi, Hsichuan; Faizuddin, Farah N.; Abeyrathna, Sameera S.; Zhou, Qin; Morcos, Faruck; Meloni, Gabriele; Dodani, Sheel C. (April 2021, Chemical Science)

   null (Ed.)

   The visualization of chloride in living cells with fluorescent sensors is linked to our ability to design hosts that can overcome the energetic penalty of desolvation to bind chloride in water. Fluorescent proteins can be used as biological supramolecular hosts to address this fundamental challenge. Here, we showcase the power of protein engineering to convert the fluorescent proton-pumping rhodopsin GR from Gloeobacter violaceus into GR1, a red-shifted, turn-on fluorescent sensor for chloride in detergent micelles and in live Escherichia coli . This non-natural function was unlocked by mutating D121, which serves as the counterion to the protonated retinylidene Schiff base chromophore. Substitution from aspartate to valine at this position (D121V) creates a binding site for chloride. The binding of chloride tunes the p K a of the chromophore towards the protonated, fluorescent state to generate a pH-dependent response. Moreover, ion pumping assays combined with bulk fluorescence and single-cell fluorescence microscopy experiments with E. coli , expressing a GR1 fusion with a cyan fluorescent protein, show that GR1 does not pump ions nor sense membrane potential but instead provides a reversible, ratiometric readout of changes in extracellular chloride at the membrane. This discovery sets the stage to use natural and laboratory-guided evolution to build a family of rhodopsin-based fluorescent chloride sensors with improved properties for cellular applications and learn how proteins can evolve and adapt to bind anions in water. 

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2. Excitation ratiometric chloride sensing in a standalone yellow fluorescent protein is powered by the interplay between proton transfer and conformational reorganization

   https://doi.org/10.1039/D1SC00847A  

   Chen, Cheng; Tutol, Jasmine N.; Tang, Longteng; Zhu, Liangdong; Ong, Whitney S.; Dodani, Sheel C.; Fang, Chong (January 2021, Chemical Science)

   null (Ed.)

   Natural and laboratory-guided evolution has created a rich diversity of fluorescent protein (FP)-based sensors for chloride (Cl − ). To date, such sensors have been limited to the Aequorea victoria green fluorescent protein (avGFP) family, and fusions with other FPs have unlocked ratiometric imaging applications. Recently, we identified the yellow fluorescent protein from jellyfish Phialidium sp. (phiYFP) as a fluorescent turn-on, self-ratiometric Cl − sensor. To elucidate its working mechanism as a rare example of a single FP with this capability, we tracked the excited-state dynamics of phiYFP using femtosecond transient absorption (fs-TA) spectroscopy and target analysis. The photoexcited neutral chromophore undergoes bifurcated pathways with the twisting-motion-induced nonradiative decay and barrierless excited-state proton transfer. The latter pathway yields a weakly fluorescent anionic intermediate , followed by the formation of a red-shifted fluorescent state that enables the ratiometric response on the tens of picoseconds timescale. The redshift results from the optimized π–π stacking between chromophore Y66 and nearby Y203, an ultrafast molecular event. The anion binding leads to an increase of the chromophore p K a and ESPT population, and the hindrance of conversion. The interplay between these two effects determines the turn-on fluorescence response to halides such as Cl − but turn-off response to other anions such as nitrate as governed by different binding affinities. These deep mechanistic insights lay the foundation for guiding the targeted engineering of phiYFP and its derivatives for ratiometric imaging of cellular chloride with high selectivity. 

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3. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

   https://doi.org/10.7554/eLife.70236  

   Zagotta, William N; Sim, Brandon S; Nhim, Anthony K; Raza, Marium M; Evans, Eric GB; Venkatesh, Yarra; Jones, Chloe M; Mehl, Ryan A; Petersson, E James; Gordon, Sharona E (October 2021, eLife)

   With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions. 

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4. 1,2,3-Triazoles: Controlled Switches in Logic Gate Applications

   https://doi.org/10.3390/s23157000  

   Ghosh, Debanjana; Atkinson, Austin; Gibson, Jaclyn; Subbaiahgari, Harini; Ming, Weihua; Padgett, Clifford; Aiken, Karelle S.; Landge, Shainaz M. (August 2023, Sensors)

   A 1,2,3-triazole-based chemosensor is used for selective switching in logic gate operations through colorimetric and fluorometric response mechanisms. The molecular probe synthesized via “click chemistry” resulted in a non-fluorescent 1,4-diaryl-1,2,3-triazole with a phenol moiety (PTP). However, upon sensing fluoride, it TURNS ON the molecule’s fluorescence. The TURN-OFF order occurs through fluorescence quenching of the sensor when metal ions, e.g., Cu2+, and Zn2+, are added to the PTP-fluoride ensemble. A detailed characterization using Nuclear Magnetic Resonance (NMR) spectroscopy in a sequential titration study substantiated the photophysical characteristics of PTP through UV-Vis absorption and fluorescence profiles. A combination of fluorescence OFF-ON-OFF sequences provides evidence of 1,2,3-triazoles being controlled switches applicable to multimodal logic operations. The “INH” gate was constructed based on the fluorescence output of PTP when the inputs are F− and Zn2+. The “IMP” and “OR” gates were created on the colorimetric output responses using the probe’s absorption with multiple inputs (F− and Zn2+ or Cu2+). The PTP sensor is the best example of the “Write-Read-Erase-Read” mimic. 

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5. Dual‐Functional, Multi‐Targeting GNNQQNY‐AIE Conjugates as Amyloid Probes and Amyloid Modulators via Amyloid Cross‐Seeding Principle

   https://doi.org/10.1002/adfm.202208022  

   Tang, Yijing; Zhang, Dong; Gong, Xiong; Zheng, Jie (September 2022, Advanced Functional Materials)

   Abstract Amyloid protein aggregation is associated with many neurodegenerative diseases, including amyloid‐β (Aβ)in Alzheimer disease, human islet amyloid polypeptide (hIAPP) in type II diabetes, and human calcitonin (hCT) in medullary thyroid carcinoma. Significant efforts have been made to develop different diagnostic and prevention strategies for the early detection and intervention of these disease‐causative protein aggregates. However, conventional design wisdoms are mostly limited to the molecules with either single function (amyloid imaging or amyloid prevention) or single targeting protein (Aβ, hIAPP, or hCT). Here, a rational design strategy of an amyloid‐aggregation‐induced emission (AIE)‐active molecule is demonstrated by conjugating an amyloid fragment of GNNQQNY (G7) with an AIE fluorescent molecule of triphenylvinyl benzoic acid (namely, G7‐TBA), making G7‐TBA as multiple‐target, dual‐function, amyloid probes and amyloid modulators for detecting, monitoring, and altering amyloid aggregation of three different amyloid proteins (Aβ, hIAPP, and hCT). G7‐TBA probe shows conformationally specific binding affinities to amyloid aggregates, switching from an “off” state (low fluorescence) for amyloid monomers to an “on” state (high fluorescence) for β‐structure‐rich amyloid oligomers and fibrils in aqueous solution. Further surface immobilization of TBA probes on surface plasmon resonance surfaces allows to amplify detection sensitivity and binding affinity to amyloid aggregates formed at different aggregation stages. G7‐TBA as amyloid modulator enables acceleration of amyloid fibrillization and selectively protects cells from hIAPP‐induced toxicity. The distinct amyloid detection and modulation of G7‐TBA are essentially derived from the cross‐seeding between G7 and amyloid aggregation via β‐structure interaction, which by far exceed the binding affinity between commercial ThT and amyloid aggregates. Such design concepts of amyloid‐AIE conjugates can be further explored as multiple‐function and target probes and/or modulators for biomedical applications. 

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