Nuclear bodies protect phase separated proteins from degradation in stressed proteome.

RNA-binding proteins (RBPs) containing intrinsically disordered domains undergo liquid-liquid phase separation to form nuclear bodies under stress conditions. This process is also connected to the misfolding and aggregation of RBPs, which are associated with a series of neurodegenerative diseases. However, it remains elusive how folding states of RBPs changes upon the formation and maturation of nuclear bodies. Here, we describe SNAP-tag based imaging methods to visualize the folding states of RBPs in live cells via time-resolved quantitative microscopic analyses of their micropolarity and microviscosity. Using these imaging methods in conjunction with immunofluorescence imaging, we demonstrate that RBPs, represented by TDP-43, initially enters the PML nuclear bodies in its native state upon transient proteostasis stress, albeit it begins to misfolded during prolonged stress. Furthermore, we show that heat shock protein 70 co-enters the PML nuclear bodies to prevent the degradation of TDP-43 from the proteotoxic stress, thus revealing a previously unappreciated protective role of the PML nuclear bodies in the prevention of stress-induced degradation of TDP-43. In summary, our imaging methods described in the manuscript, for the first time, reveal the folding states of RBPs, which were previously challenging to study with conventional methods in nuclear bodies of live cells. This study uncovers the mechanistic correlations between the folding states of a protein and functions of nuclear bodies, in particular PML bodies. We envision that the imaging methods can be generally applied to elucidating the structural aspects of other proteins that exhibit granular structures under biological stimulus.

Fluorogenic detection of protein aggregates in live cells using the AggTag method.

Protein aggregation is a process that occurs through the self-assembly of misfolded proteins to form soluble oligomers and insoluble aggregates. While there has been significant interest in protein aggregation for neurodegenerative diseases, progress in this field of research has been limited by the lack of effective methods to detect and interrogate these species in live cells. To resolve this issue, we have developed a new imaging method named the AggTag to report on protein aggregation in live cells with fluorescence microscopy. The AggTag method utilizes a genetic fusion of a protein of interest (POI) to a protein tag to conjugate with the AggTag probe, which contains a fluorophore that turns on its fluorescence upon interaction with protein aggregates. Unlike the conventional methods, this method enables one to detect soluble misfolded oligomers that were previously invisible. Furthermore, the AggTag method has been applied for the simultaneous detection of co-aggregation between two different POIs by a dual-color and orthogonal tagging system. This chapter aims to provide step-by-step procedures of the AggTag method for researchers who intend to study aggregation of POIs in mammalian cell lines.

A General Strategy to Enhance Donor-Acceptor Molecules Using Solvent-Excluding Substituents.

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 ß-carbonyl-based polar substituent. The results reveal a mechanism wherein the ß-carbonyl substituent creates a structural buffer between the donor and the surrounding solvent. Through computational and experimental analyses, it is demonstrated that the ß-carbonyl simultaneously attenuates two distinct solvent-dependent quenching mechanisms. Using the ß-carbonyl substituent, improvements in the photophysical properties of commonly used D-A fluorophores and their enhanced performance in biological imaging are shown.

A Fluorogenic AggTag Method Based on Halo- and SNAP-Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells.

Protein aggregation involves the assembly of partially misfolded proteins into oligomeric and higher-order structures that have been associated with several neurodegenerative diseases. However, numerous questions relating to protein aggregation remain unanswered due to the lack of available tools for visualization of these species in living cells. We recently developed a fluorogenic method named aggregation tag (AggTag), and presented the AggTag probe P1, based on a Halo-tag ligand, to report on the aggregation of a protein of interest (POI) in live cells. However, the Halo-tag-based AggTag method only detects the aggregation of one specific POI at a time. In this study, we have expanded the AggTag method by using SNAP-tag technology to enable fluorogenic and biorthogonal detection of the aggregation of two different POIs simultaneously in live cells. A new AggTag probe-P2, based on a SNAP-tag ligand bearing a green solvatochromic fluorophore-was synthesized for this purpose. Using confocal imaging and chemical crosslinking experiments, we confirmed that P2 can also report both on soluble oligomers and on insoluble aggregates of a POI fused with SNAP-tag in live cells. Ultimately, we showed that the orthogonal fluorescence of P1 and P2 allows for simultaneous visualization of two different pathogenic protein aggregates in the same cell.

A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede.

Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M-1 s-1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.

Development of new peptide-based receptor of fluorescent probe with femtomolar affinity for Cu(+) and detection of Cu(+) in Golgi apparatus.

Developing fluorescent probes for monitoring intracellular Cu(+) is important for human health and disease, whereas a few types of their receptors showing a limited range of binding affinities for Cu(+) have been reported. In the present study, we first report a novel peptide receptor of a fluorescent probe for the detection of Cu(+). Dansyl-labeled tripeptide probe (Dns-LLC) formed a 1:1 complex with Cu(+) and showed a turn-on fluorescent response to Cu(+) in aqueous buffered solutions. The dissociation constant of Dns-LLC for Cu(+) was determined to be 12 fM, showing that Dns-LLC had more potent binding affinity for Cu(+) than those of previously reported chemical probes for Cu(+). The binding mode study showed that the thiol group of the peptide receptor plays a critical role in potent binding with Cu(+) and the sulfonamide and amide groups of the probe might cooperate to form a complex with Cu(+). Dns-LLC detected Cu(+) selectively by a turn-on response among various biologically relevant metal ions, including Cu(2+) and Zn(2+). The selectivity of the peptide-based probe for Cu(+) was strongly dependent on the position of the cysteine residue in the peptide receptor part. The fluorescent peptide-based probe penetrated the living RKO cells and successfully detected Cu(+) in the Golgi apparatus in live cells by a turn-on response. Given the growing interest in imaging Cu(+) in live cells, a novel peptide receptor of Cu(+) will offer the potential for developing a variety of fluorescent probes for Cu(+) in the field of copper biochemistry.

Efficient ensemble system based on the copper binding motif for highly sensitive and selective detection of cyanide ions in 100% aqueous solutions by fluorescent and colorimetric changes.

A peptide-based ensemble for the detection of cyanide ions in 100% aqueous solutions was designed on the basis of the copper binding motif. 7-Nitro-2,1,3-benzoxadiazole-labeled tripeptide (NBD-SSH, NBD-SerSerHis) formed the ensemble with Cu(2+), leading to a change in the color of the solution from yellow to orange and a complete decrease of fluorescence emission. The ensemble (NBD-SSH-Cu(2+)) sensitively and selectively detected a low concentration of cyanide ions in 100% aqueous solutions by a colorimetric change as well as a fluorescent change. The addition of cyanide ions instantly removed Cu(2+) from the ensemble (NBD-SSH-Cu(2+)) in 100% aqueous solutions, resulting in a color change of the solution from orange to yellow and a "turn-on" fluorescent response. The detection limits for cyanide ions were lower than the maximum allowable level of cyanide ions in drinking water set by the World Health Organization. The peptide-based ensemble system is expected to be a potential and practical way for the detection of submicromolar concentrations of cyanide ions in 100% aqueous solutions.

The significance of hypersensitivity to autologous sweat and serum in cholinergic urticaria: cholinergic urticaria may have different subtypes.

BACKGROUND: The pathogenesis of cholinergic urticaria (ChU) has been unclear except for the involvement of acetylcholine. Attempts to classify ChU according to etiology have rarely been performed. OBJECTIVE: To evaluate the significance of responsiveness to autologous sweat and serum in ChU in relation to their clinical characteristics. METHODS: This study involved 18 patients diagnosed with ChU between January 2010 and April 2011 in the Catholic Medical Center-St. Paul's Hospital. History taking included symptom duration, association with atopy, decreased sweat secretions, seasonal variation, and response to treatment. Intradermal autologous serum skin test (ASST) and autologous sweat skin test (ASwST) and basophil histamine release test with sweat were done. RESULTS: Sweat hypersensitivity was proven by a positive ASwST and basophil histamine release test in only 37.5% of patients with ChU, and in none of the healthy controls. The weal size of ASwST correlated with percentage basophil histamine release. A positive response to autologous serum was displayed by 38.9% of patients, whereas 10% of healthy controls showed a positive ASST response. Intriguingly, patients with a positive ASwST had a negative ASST, and vice versa. Despite this, there was no difference in the clinical characteristics between positive ASST and positive ASwST groups. CONCLUSIONS: The frequency of hypersensitivity to autologous sweat and serum was significantly higher in patients with ChU, compared with healthy controls. This suggests that autoimmunity to an unknown serum factor as well as sweat hypersensitivity may be involved in the pathogenesis of ChU.

Ratiometric detection of nanomolar concentrations of heparin in serum and plasma samples using a fluorescent chemosensor based on peptides.

A peptidyl fluorescent chemosensor for heparin was synthesized by conjugating a pyrene fluorophore with the heparin-binding peptide. The fluorescent chemosensor (Py12; pyrene-RKRLQVQLSIRT) showed a highly sensitive ratiometric response to nanomolar concentrations of heparin in aqueous solutions at physiological pH by increasing excimer emission intensity at 500 nm with a concomitant decrease in monomer emission intensity at 400 nm. Py12 showed a sensitive ratiometric response to heparin over a wide pH range (1.5 ≤ pH ≤ 11.5) and exhibited high selectivity for heparin compared to other biological competitors, such as hyaluronic acid and chondroitin sulfate. Py12 sensitively and ratiometrically detected nanomolar concentrations of heparin in biologically relevant samples containing human serum and human plasma, respectively. The detection limit of Py12 was 34 pM (R(2) = 0.997) for heparin in an aqueous buffer solutions containing 5% human serum and 33 pM (R(2) = 0.994) for heparin in aqueous buffer solutions containing 5% human plasma. Py12 had sufficient sensitivity and selectivity for ratiometrically detecting a nanomolar concentration of heparin, indicating that the peptide-base chemosensor provides a potential tool for monitoring heparin levels in clinical plasma samples.