Profiling Protein Sâ Sulfination with Maleimideâ Linked Probes

Cysteine residues are susceptible to oxidation to form Sâ sulfinyl (Râ SO2H) and Sâ sulfonyl (Râ SO3H) postâ translational modifications. Here we present a simple bioconjugation strategy to label Sâ sulfinated proteins by using reporterâ linked maleimides. After alkylation of free thiols with iodoacetamide, Sâ sulfinated cysteines react with maleimide to form a sulfone Michael adduct that remains stable under acidic conditions. Using this sequential alkylation strategy, we demonstrate differential Sâ sulfination across mouse tissue homogenates, as well as enhanced Sâ sulfination following pharmacological induction of endoplasmic reticulum stress, lipopolysaccharide stimulation, and inhibitors of the electron transport chain. Overall, this study reveals a broadened profile of maleimide reactivity across cysteine modifications, and outlines a simple method for profiling the physiological role of cysteine Sâ sulfination in disease.Maleimide, but not iodoacetamide, reacts with aryl and alkyl sulfinic acid standards and Sâ sulfinated proteins to give a sulfonylâ succinimide adduct that is stable under acidic conditions. This sequential alkylation strategy can be used for selective sulfinic acid labeling in biological samples. This study reveals a broadened profile of maleimide reactivity across cysteine modifications in proteins.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/1/cbic201700137_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/2/cbic201700137.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138861/3/cbic201700137-sup-0001-misc_information.pd

Global Analysis of Palmitoylated Proteins in Toxoplasma gondii

SummaryPost-translational modifications (PTMs) such as palmitoylation are critical for the lytic cycle of the protozoan parasite Toxoplasma gondii. While palmitoylation is involved in invasion, motility, and cell morphology, the proteins that utilize this PTM remain largely unknown. Using a chemical proteomic approach, we report a comprehensive analysis of palmitoylated proteins in T. gondii, identifying a total of 282 proteins, including cytosolic, membrane-associated, and transmembrane proteins. From this large set of palmitoylated targets, we validate palmitoylation of proteins involved in motility (myosin light chain 1, myosin A), cell morphology (PhIL1), and host cell invasion (apical membrane antigen 1, AMA1). Further studies reveal that blocking AMA1 palmitoylation enhances the release of AMA1 and other invasion-related proteins from apical secretory organelles, suggesting a previously unrecognized role for AMA1. These findings suggest that palmitoylation is ubiquitous throughout the T. gondii proteome and reveal insights into the biology of this important human pathogen

DIA-SIFT: A Precursor and Product Ion Filter for Accurate Stable Isotope Data-Independent Acquisition Proteomics

Quantitative mass spectrometry-based protein profiling is widely used to measure protein levels across different treatments or disease states, yet current mass spectrometry acquisition methods present distinct limitations. While data-independent acquisition (DIA) bypasses the stochastic nature of data-dependent acquisition (DDA), fragment spectra derived from DIA are often complex and challenging to deconvolve. In-line ion mobility separation (IMS) adds an additional dimension to increase peak capacity for more efficient product ion assignment. As a similar strategy to sequential window acquisition methods (SWATH), IMS-enabled DIA methods rival DDA methods for protein annotation. Here we evaluate IMS-DIA quantitative accuracy using stable isotope labeling by amino acids in cell culture (SILAC). Since SILAC analysis doubles the sample complexity, we find that IMS-DIA analysis is not sufficiently accurate for sensitive quantitation. However, SILAC precursor pairs share common retention and drift times, and both species cofragment to yield multiple quantifiable isotopic <i>y</i>-ion peak pairs. Since <i>y</i>-ion SILAC ratios are intrinsic for each quantified precursor, combined MS1 and <i>y</i>-ion ratio analysis significantly increases the total number of measurements. With increased sampling, we present DIA-SIFT (<i>S</i>ILAC <i>I</i>ntrinsic <i>F</i>iltering <i>T</i>ool), a simple statistical algorithm to identify and eliminate poorly quantified MS1 and/or MS2 events. DIA-SIFT combines both MS1 and <i>y</i>-ion ratios, removes outliers, and provides more accurate and precise quantitation (<15% CV) without removing any proteins from the final analysis. Overall, pooled MS1 and MS2 quantitation increases sampling in IMS-DIA SILAC analyses for accurate and precise quantitation

HDAC8 Substrates Identified by Genetically Encoded Active Site Photocrosslinking

The histone deacetylase family comprises 18 enzymes that catalyze deacetylation of acetylated lysine residues; however, the specificity and substrate profile of each isozyme remains largely unknown. Due to transient enzyme–substrate interactions, conventional co-immunoprecipitation methods frequently fail to identify enzyme-specific substrates. Additionally, compensatory mechanisms often limit the ability of knockdown or chemical inhibition studies to achieve significant fold changes observed by acetylation proteomics methods. Furthermore, measured alterations do not guarantee a direct link between enzyme and substrate. Here we present a chemical crosslinking strategy that incorporates a photoreactive, non-natural amino acid, <i>p</i>-benzoyl-l-phenylalanine, into various positions of the structurally characterized isozyme histone deacetylase 8 (HDAC8). After covalent capture, co-immunoprecipitation, and mass spectrometric analysis, we identified a subset of HDAC8 substrates from human cell lysates, which were further validated for catalytic turnover. Overall, this chemical crosslinking approach identified novel HDAC8-specific substrates with high catalytic efficiency, thus presenting a general strategy for unbiased deacetylase substrate discovery

HDAC8 Substrates Identified by Genetically Encoded Active Site Photocrosslinking

The histone deacetylase family comprises 18 enzymes that catalyze deacetylation of acetylated lysine residues; however, the specificity and substrate profile of each isozyme remains largely unknown. Due to transient enzyme–substrate interactions, conventional co-immunoprecipitation methods frequently fail to identify enzyme-specific substrates. Additionally, compensatory mechanisms often limit the ability of knockdown or chemical inhibition studies to achieve significant fold changes observed by acetylation proteomics methods. Furthermore, measured alterations do not guarantee a direct link between enzyme and substrate. Here we present a chemical crosslinking strategy that incorporates a photoreactive, non-natural amino acid, <i>p</i>-benzoyl-l-phenylalanine, into various positions of the structurally characterized isozyme histone deacetylase 8 (HDAC8). After covalent capture, co-immunoprecipitation, and mass spectrometric analysis, we identified a subset of HDAC8 substrates from human cell lysates, which were further validated for catalytic turnover. Overall, this chemical crosslinking approach identified novel HDAC8-specific substrates with high catalytic efficiency, thus presenting a general strategy for unbiased deacetylase substrate discovery

Affinity-Based Selectivity Profiling of an In-Class Selective Competitive Inhibitor of Acyl Protein Thioesterase 2

Activity-based protein profiling (ABPP) has revolutionized the discovery and optimization of active-site ligands across distinct enzyme families, providing a robust platform for in-class selectivity profiling. Nonetheless, this approach is less straightforward for profiling reversible inhibitors and does not access proteins outside the ABPP probe’s target profile. While the active-site competitive acyl protein thioesterase 2 inhibitor ML349 (<i>K</i>_i = 120 nM) is highly selective within the serine hydrolase enzyme family, it could still interact with other cellular targets. Here we present a chemoproteomic workflow to enrich and profile candidate ML349-binding proteins. In human cell lysates, biotinylated-ML349 enriches a recurring set of proteins, including metabolite kinases and flavin-dependent oxidoreductases that are potentially enhanced by avidity-driven multimeric interactions. Confirmatory assays by native mass spectrometry and fluorescence polarization quickly rank-ordered these weak off-targets, providing justification to explore ligand interactions and stoichiometry beyond ABPP

Variable-Velocity Traveling-Wave Ion Mobility Separation Enhancing Peak Capacity for Data-Independent Acquisition Proteomics

High mass accuracy, data-dependent acquisition is the current standard method in mass spectrometry-based peptide annotation and quantification. In high complexity samples, limited instrument scan speeds often result in under-sampling. In contrast, all-ion data-independent acquisition methods bypass precursor selection, alternating high and low collision energies to analyze product and precursor ions across wide mass ranges. Despite capturing data for all events, peptide annotation is limited by inadequate alignment algorithms or overlapping ions. Ion mobility separation can add an orthogonal analytical dimension, reducing ion interference to improve reproducibility, peak capacity, and peptide identifications to rival modern hybrid quadrupole orbitrap systems. Despite the advantages of ion mobility separation in complex proteomics analyses, there has been no quantitative measure of ion mobility resolution in a complex proteomic sample. Here, we present TWIMExtract, a data extraction tool to export defined slices of liquid chromatography/ion mobility/mass spectrometry (LC-IM-MS) data, providing a route to quantify ion mobility resolution from a commercial traveling-wave ion mobility time-of-flight mass spectrometer. Using standard traveling-wave ion mobility parameters (600 m/s, 40 V), 90% of the annotated peptides occupied just 23% of the ion mobility drift space, yet inclusion of ion mobility nearly doubled the overall peak capacity. Relative to fixed velocity traveling-wave ion mobility settings, ramping the traveling-wave velocity increased drift space occupancy, amplifying resolution by 16%, peak capacity by nearly 50%, and peptide/protein identifications by 40%. Overall, variable-velocity traveling-wave ion mobility-mass spectrometry significantly enhances proteomics analysis in all-ion fragmentation acquisition

Harnessing Redox Cross-Reactivity To Profile Distinct Cysteine Modifications

Cysteine <i>S</i>-nitrosation and <i>S</i>-sulfination are naturally occurring post-translational modifications (PTMs) on proteins induced by physiological signals and redox stress. Here we demonstrate that sulfinic acids and nitrosothiols react to form a stable thiosulfonate bond, and leverage this reactivity using sulfinate-linked probes to enrich and annotate hundreds of endogenous <i>S</i>-nitrosated proteins. In physiological buffers, sulfinic acids do not react with iodoacetamide or disulfides, enabling selective alkylation of free thiols and site-specific analysis of <i>S</i>-nitrosation. In parallel, <i>S</i>-nitrosothiol-linked probes enable enrichment and detection of endogenous <i>S</i>-sulfinated proteins, confirming that a single sulfinic acid can react with a nitrosothiol to form a thiosulfonate linkage. Using this approach, we find that hydrogen peroxide addition increases <i>S</i>-sulfination of human DJ-1 (PARK7) at Cys106, whereas Cys46 and Cys53 are fully oxidized to sulfonic acids. Comparative gel-based analysis of different mouse tissues reveals distinct profiles for both <i>S</i>-nitrosation and <i>S</i>-sulfination. Quantitative proteomic analysis demonstrates that both <i>S</i>-nitrosation and <i>S</i>-sulfination are widespread, yet exhibit enhanced occupancy on select proteins, including thioredoxin, peroxiredoxins, and other validated redox active proteins. Overall, we present a direct, bidirectional method to profile select redox cysteine modifications based on the unique nucleophilicity of sulfinic acids