Methods for high throughput discovery of fluoroprobes that recognize tau fibril polymorphs.

Aggregation of microtubule-associated protein tau (MAPT/tau) into conformationally distinct fibrils underpins neurodegenerative tauopathies. Fluorescent probes (fluoroprobes), such as thioflavin T (ThT), have been essential tools for studying tau aggregation; however, most of them do not discriminate between amyloid fibril conformations (polymorphs). This gap is due, in part, to a lack of high-throughput methods for screening large, diverse chemical collections. Here, we leverage advances in protein adaptive differential scanning fluorimetry (paDSF) to screen the Aurora collection of 300+ fluorescent dyes against multiple synthetic tau fibril polymorphs. This screen, coupled with orthogonal secondary assays, revealed pan-fibril binding chemotypes, as well as fluoroprobes selective for subsets of fibrils. One fluoroprobe recognized tau pathology in ex vivo brain slices from Alzheimer's disease patients. We propose that these scaffolds represent entry points for development of selective fibril ligands and, more broadly, that high throughput, fluorescence-based dye screening is a platform for their discovery.

Exploration of the binding determinants of protein phosphatase 5 (PP5) reveals a chaperone-independent activation mechanism.

The protein phosphatase 5 (PP5) is normally recruited to its substrates by the molecular chaperones, heat shock protein 70 (Hsp70) and heat shock protein 90 (Hsp90). This interaction requires the tetratricopeptide repeat (TPR) domain of PP5, which binds to an EEVD motif at the extreme C termini of cytosolic Hsp70 and Hsp90 isoforms. In addition to bringing PP5 into proximity with chaperone-bound substrates, this interaction also relieves autoinhibition in PP5's catalytic domain, promoting its phosphatase activity. To better understand the molecular determinants of this process, we screened a large, pentapeptide library for binding to PP5. This screen identified the amino acid preferences at each position, which we validated by showing that the optimal sequences bind 4- to 7-fold tighter than the natural EEVD motifs and stimulate PP5's enzymatic activity. The enhanced affinity for PP5's TPR domain was confirmed using a protein-adaptive differential scanning fluorimetry assay. Using this increased knowledge of structure-activity relationships, we re-examined affinity proteomics results to look for potential EEVD-like motifs in the C termini of known PP5-binding partners. This search identified elongator acetyltransferase complex subunit 1 (IKBKAP) as a putative partner, and indeed, we found that its C-terminal sequence, LSLLD, binds directly to PP5's TPR domain in vitro. Consistent with this idea, mutation of elongator acetyltransferase complex subunit 1's terminal aspartate was sufficient to interrupt the interaction with PP5 in vitro and in cells. Together, these findings reveal the sequence preferences of PP5's TPR domain and expand the scope of PP5's functions to include chaperone-independent complexes.

Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes.

Differential scanning fluorimetry (DSF) is a technique that reports protein thermal stability via the selective recognition of unfolded states by fluorogenic dyes. However, DSF applications remain limited by protein incompatibilities with existing DSF dyes. Here we overcome this obstacle with the development of a protein-adaptive DSF platform (paDSF) that combines a dye library 'Aurora' with a streamlined procedure to identify protein-dye pairs on demand. paDSF was successfully applied to 94% (66 of 70) of proteins, tripling the previous compatibility and delivering assays for 66 functionally and biochemically diverse proteins, including 10 from severe acute respiratory syndrome coronavirus 2. We find that paDSF can be used to monitor biological processes that were previously inaccessible, demonstrated for the interdomain allostery of O-GlcNAc transferase. The chemical diversity and varied selectivities of Aurora dyes suggest that paDSF functionality may be readily extended. paDSF is a generalizable tool to interrogate protein stability, dynamics and ligand binding.

Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry.

Flexible in vitro methods alter the course of biological discoveries. Differential Scanning Fluorimetry (DSF) is a particularly versatile technique which reports protein thermal unfolding via fluorogenic dye. However, applications of DSF are limited by widespread protein incompatibilities with the available DSF dyes. Here, we enable DSF applications for 66 of 70 tested proteins (94%) including 10 from the SARS-CoV2 virus using a chemically diverse dye library, Aurora, to identify compatible dye-protein pairs in high throughput. We find that this protein-adaptive DSF platform (paDSF) not only triples the previous protein compatibility, but also fundamentally extends the processes observable by DSF, including interdomain allostery in O-GlcNAc Transferase (OGT). paDSF enables routine measurement of protein stability, dynamics, and ligand binding.

Synthetic dyes: A mass spectrometry approach and applications.

Synthetic dyes are found in a wide variety of applications today, including but not limited to textiles, foods, and medicine. The analysis of these molecules is pertinent to several fields such as forensics, environmental monitoring, and quality control, all of which require the sensitivity and selectivity of analysis provided by mass spectrometry (MS). Recently, there has been an increase in the implementation of MS evaluation of synthetic dyes by various methods, with the majority of research thus far falling under electrospray ionization and moving toward direct ionization methods. This review covers an overview of the chemistry of synthetic dyes needed for the understanding of MS sample preparation and spectral results, current fields of application, ionization methods, and fragmentation trends and works that have been reported in recent years.

The characterization of disperse dyes in polyester fibers using DART mass spectrometry.

Textile fibers alone are highly prevalent in our environment, and not only are there a wide variety of fibers, but generally, consumer textiles are colored. Given the variety of crime locations where dyes are encountered and the potential circumstances, a rapid, preparation free analysis of samples is highly beneficial. This study has characterized a collection of commercially available textiles dyes by verifying the chemical structure, collecting reference spectra, and developing a method to analyze dyed fibers via Direct Analysis in Real-Time (DART) mass spectrometry. A methodology for direct analysis of pieces of fabric and single thread samples of polyester fibers dyed with disperse dyes was developed. The presence of 31 target dyes on fibers whose structures were previously established via high-resolution mass spectrometry was confirmed. Dyed fabrics containing mixtures of dyes in varying concentrations were also evaluated to determine whether each dye in the composition could be detected. The DART-MS methodology was sensitive and positively characterized disperse dyes in polyester fibers, allowing for blind identification of mixtures with the assistance of a high-resolution mass spectrometry database.

Characterization of synthetic dyes for environmental and forensic assessments: A chromatography and mass spectrometry approach.

Dyes have become common substances since they are employed in mostly all objects surrounding our daily activities such as clothing and upholstery. Based on the usage and disposal of these objects, the transfer of the dyes to other media such as soil and water increases their prevalence in our environment. However, this prevalence could help to solve crimes and pollution problems if detection techniques are proper. For that reason, the detection and characterization of dyes in complex matrices is important to determine the possible events leading to their deposition (natural degradation, attempts of removal, possible match with evidence, among others). Currently, there are several chromatographic and mass spectrometric approaches used for the identification of these organic molecules and their derivatives with high specificity and accuracy. This review presents current chromatographic and mass spectrometric methods that are used for the detection and characterization of disperse, acid, basic, and reactive dyes, and their derivatives.