Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System

Quantitative control of subcellular protein localization with a photochromic dimerizer

Artificial control of intracellular protein dynamics with high precision provides deep insight into complicated biomolecular networks. Optogenetics and caged compound-based chemically induced dimerization (CID) systems are emerging as tools for spatiotemporally regulating intracellular protein dynamics. However, both technologies face several challenges for accurate control such as the duration of activation, deactivation rate and repetition cycles. Herein, we report a photochromic CID system that uses the photoisomerization of a ligand so that both association and dissociation are controlled by light, enabling quick, repetitive and quantitative regulation of the target protein localization upon illumination with violet and green light. We also demonstrate the usability of the photochromic CID system as a potential tool to finely manipulate intracellular protein dynamics during multicolor fluorescence imaging to study diverse cellular processes. We use this system to manipulate PTEN-induced kinase 1 (PINK1)-Parkin-mediated mitophagy, showing that PINK1 recruitment to the mitochondria can promote Parkin recruitment to proceed with mitophagy.

Unlocking Amides: A General Method for the Self-Immolative Release of Amide-Containing Molecules

The controlled liberation of molecules from a constructed framework is a subject of profound interest across various chemical fields. It allows for the masking of a molecule's properties and precise deployment upon a single controllable release event. While numerous methodologies have been developed for amines, alcohols, and thiols, approaches for utilising amides as payload-release handles are still in their early stages of development, despite the prevalence of amides in therapeutic compounds and materials. Herein, is presented a comprehensive strategy for the controlled and selective release of a diverse range of amides with stable linkers. The versatility of this approach is demonstrated by its successful application in the targeted release of various amide-containing drugs in their natural form via the use of commonly used trigger motifs, such as dipeptides or glycosides. As a proof of concept, the FDA-approved antibiotic linezolid has been successfully converted into a prodrug form and released selectively only in the presence of the trigger event. Significantly, in its prodrug state, no activity against Mycobacterium tuberculosis was exhibited. Linezolid's full potential was achieved only upon controlled release, where an equipotent efficacy to the free linezolid control was demonstrated, thus emphasising the immense potential of this method.

Photoactivatable Nanobody Conjugate Dimerizer Temporally Resolves Tiam1-Rac1 Signaling Axis

The precise spatiotemporal dynamics of protein activities play a crucial role in cell signaling pathways. To control cellular functions in a spatiotemporal manner, a powerful method called photoactivatable chemically induced dimerization (pCID) is used. In this study, photoactivatable nanobody conjugate inducers of dimerization (PANCIDs) is introduced, which combine pCID with nanobody technology. A PANCID consists of a nanobody module that directly binds to an antigenic target, a photocaged small molecule ligand, and a cyclic decaarginine (cR10 *) cell-penetrating peptide (CPP) for efficient nonendocytic intracellular delivery. Therefore, PANCID photodimerizers also benefit from nanobodies, such as their high affinities (in the nm or pm range), specificities, and ability to modulate endogenous proteins. Additionally it is demonstrated that the nanobody moiety can be easily replaced with alternative ones, expanding the potential applications. By using PANCIDs, the dynamics of the Tiam1-Rac1 signaling cascade is investigated and made an interesting finding. It is found that Rac1 and Tiam1 exhibit distinct behaviors in this axis, acting as time-resolved "molecular oscillators" that transit between different functions in the signaling cascade when activated either slowly or rapidly.

Spatiotemporally Controlled Photolabeling of Genetically Unmodified Proteins in Live Cells

Selective labeling of the protein of interest (POI) in genetically unmodified live cells is crucial for understanding protein functions and kinetics in their natural habitat. In particular, spatiotemporally controlled installation of the labels on a POI under light control without affecting their original activity is in high demand but is a tremendous challenge. Here, we describe a novel ligand-directed photoclick strategy for spatiotemporally controlled labeling of endogenous proteins in live cells. It was realized with a designer labeling reagent skillfully integrating the photochemistries of 2-nitrophenylpropyloxycarbonyl and 3-hydroxymethyl-2-naphthol with an affinity ligand. Highly electrophilic ortho-naphthoquinone methide was photochemically released and underwent a proximity coupling reaction with nucleophilic amino acid residues on the POI in live cells. With fluorescein as a marker, this photoclick strategy enables time-resolved labeling of carbonic anhydrase subtypes localized either on the cell membrane or in the cytoplasm and a discriminable visualization of their metabolic kinetics. Given the versatility underlined by facilely tethering other functional entities (e.g., biotin, a peptide short chain) via acylation or (in cell) Huisgen cycloaddition, this affinity-driven photoclick chemistry opens up enormous opportunities for discovering dynamic functions and mechanistic interrogation of endogenous proteins in live cells.

Arylazopyrazole-Based Photoswitchable Inhibitors Selective for Escherichia coli Dihydrofolate Reductase

Selective inhibitors of Escherichia coli dihydrofolate reductase (eDHFR) are crucial chemical biology tools that have widespread clinical applications. We developed a set of eDHFR-selective photoswitchable inhibitors by derivatizing the structure of our previously reported methotrexate (MTX) azolog, azoMTX. Substitution of the skeletal p-phenylene group of azoMTX with bulky bis-alkylated arylazopyrazole moieties significantly increased its selectivity toward eDHFR over human DHFR. Owing to the physical properties of arylazopyrazoles, the new ligands exhibited nearly complete Z-to-E photoconversion and high thermostability of Z-isomers. In addition, real-time photoreversible control of eDHFR activity was achieved by alternatively switching the illumination light wavelengths.

A photoactivatable self-localizing ligand with improved photosensitivity for chemo-optogenetic control of protein localization in living cells

Light-mediated control of protein localization in living cells is a powerful approach for manipulating and probing complex biological systems. By incorporating a classical 6-nitroveratryloxycarbonyl (NVOC) caging group into the inner plasma membrane (PM)-localizing trimethoprim ligand, we recently developed a photoactivatable self-localizing ligand (paSL) that can rapidly recruit engineered Escherichia coli dihydrofolate reductase-fusion proteins from the cytoplasm to the PM upon violet (ca. 400 nm)-light illumination. However, because the photosensitivity of the NVOC-caged paSL is low to moderate, photouncaging experiments require high light intensity, which may not be ideal for many cell applications. Herein, we present a new 7-diethylaminocoumarin (DEAC)-caged paSL with improved photosensitivity. DEAC-caged paSL induced efficient protein recruitment upon violet-light irradiation, even at the low intensity under which NVOC-caged paSL does not respond. DEAC-caged paSL was insensitive to excitation light used to image green fluorescent proteins (GFPs), and it was applicable for simultaneous optical stimulation of Gαq signaling and fluorescence imaging of subsequent Ca²⁺ oscillations using a GFP-based Ca²⁺ biosensor in living cells.

Programmable motion control and trajectory manipulation of microparticles through tri-directional symmetrical acoustic tweezers

Acoustic tweezers based on travelling surface acoustic waves (TSAWs) have the potential for contactless trajectory manipulation and motion-parameter regulation of microparticles in biological and microfluidic applications. Here, we present a novel design of a tri-directional symmetrical acoustic tweezers device that enables the precise manipulation of linear, clockwise, and anticlockwise trajectories of microparticles. By switching the excitation combinations of interdigital electrodes (IDTs), various shape patterns of acoustic pressure fields can be formed to capture and steer microparticles accurately according to pre-defined trajectories. Numerical simulations and experimental tests were conducted in this study. By adjusting the input electric signals and the fluid's viscosity, the device is able to manipulate microparticles of various forms as well as brine shrimp egg cells with the accurate modulation of motion parameters. The results show that the proposed programmable design possesses low-cost, compact, non-contact, and high biocompatibility benefits, with the capacity to accurately manage microparticles in a range of motion trajectories, independent of their physical and/or chemical characteristics. Thus, our design has strong potential applications in chemical composition analysis, drug delivery, and cell assembly.

Real-Time Spatial and Temporal Analysis of the Translocation of the Apoptosis-Inducing Factor in Cells

Translocation of the apoptosis-inducing factor (AIF) from the mitochondria to the nucleus is crucial for AIF-mediated apoptosis. However, the lack of methods for real-time spatial and temporal analysis of translocation of functional AIF is a large hurdle to gain a detailed understanding of this process. In this study, a genetic code expansion technique was developed to overcome this hurdle. Specifically, this technique was utilized to construct ANAP-AIF containing a small fluorescent amino acid (ANAP) at a specific site in cells. Additionally, we developed efficient fluorescence resonance energy-transfer systems consisting of ANAP-AIF and either yellow fluorescent protein (YFP)-fused cyclophilin A (CypA) or Hsp70, respective positive and negative regulators for AIF translocation to the nucleus. We found that apoptosis inducers, including apoptozole, 2-phenylethynesulfonamide (PES), myricetin, Bam7, reactivating p53 and inducing tumor apoptosis (RITA), brefeldin A, and carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP) promote translocation of mitochondrial AIF to the cytosol after 4 h incubation, reaching a maximum after 6-7 h. However, these substances did not enhance AIF translocation to the nucleus through the interaction of AIF with Hsp70 in the cytosol. On the other hand, treatment with apoptosis inducers, such as paclitaxel, silibinin, doxorubicin, actinomycin D, and camptothecin caused AIF translocation to the nucleus after 4 h incubation through AIF binding to CypA, reaching saturation after 6-7 h. It was also found that Hsp70 and CypA regulate AIF translocation in a mutually exclusive manner because they do not interact with AIF simultaneously in cells undergoing apoptosis. The results demonstrate clearly that ANAP-incorporated proteins are powerful to obtain a more in-depth understanding of protein translocation.