Posttranslational modifications of protein cysteine thiols play a significant role in redox regulation and the pathogenesis of human diseases. Herein, we report the characterization of the cellular redox landscape in terms of quantitative, site-specific occupancies of both S-glutathionylation (SSG) and total reversible thiol oxidation (total oxidation) in RAW 264.7 macrophage cells under basal conditions. The occupancies of thiol modifications for ~4000 cysteine sites were quantified, revealing a mean site occupancy of 4.0% for SSG and 11.9% for total oxidation, respectively. Correlations between site occupancies and structural features such as pKa, relative residue surface accessibility, and hydrophobicity were observed. Proteome-wide site occupancy analysis revealed that the average occupancies of SSG and total oxidation in specific cellular compartments correlate well with the expected redox potentials of respective organelles in macrophages, consistent with the notion of redox compartmentalization. The lowest average occupancies were observed in more reducing organelles such as the mitochondria (non-membrane) and nucleus, while the highest average occupancies were found in more oxidizing organelles such as endoplasmic reticulum (ER) and lysosome. Furthermore, a pattern of subcellular susceptibility to redox changes was observed under oxidative stress induced by exposure to engineered metal oxide nanoparticles. Peroxisome, ER, and mitochondria (membrane) are the organelles which exhibit the most significant redox changes; while mitochondria (non-membrane) and Golgi were observed as the organelles being most resistant to oxidative stress. Finally, it was observed that Cys residues at enzymatic active sites generally had a higher level of occupancy compared to non-active Cys residues within the same proteins, suggesting site occupancy as a potential indicator of protein functional sites. The raw data are available via ProteomeXchange with identifier PXD019913.

Sarcopenia and exercise intolerance are major contributors to reduced quality of life in the elderly for which there are few effective treatments. We tested whether enhancing mitochondrial function and reducing mitochondrial oxidant production with SS-31 (elamipretide) could restore redox balance and improve skeletal muscle function in aged mice. Young (5 mo) and aged (26 mo) female C57BL/6Nia mice were treated for 8-weeks with 3 mg/kg/day SS-31. Mitochondrial function was assessed in vivo using 31P and optical spectroscopy. SS-31 reversed age-related decline in maximum mitochondrial ATP production (ATPmax) and coupling of oxidative phosphorylation (P/O). Despite the increased in vivo mitochondrial capacity, mitochondrial protein expression was either unchanged or reduced in the treated aged mice and respiration in permeabilized gastrocnemius (GAS) fibers was not different between the aged and aged+SS-31 mice. Treatment with SS-31 also restored redox homeostasis in the aged skeletal muscle. The glutathione redox status was more reduced and thiol redox proteomics indicated a robust reversal of cysteine S-glutathionylation post-translational modifications across the skeletal muscle proteome. The gastrocnemius in the age+SS-31 mice was more fatigue resistant with significantly greater mass compared to aged controls. This contributed to a significant increase in treadmill endurance compared to both pretreatment and untreated control values. These results demonstrate that the shift of redox homeostasis due to mitochondrial oxidant production in aged muscle is a key factor in energetic defects and exercise intolerance. Treatment with SS-31 restores redox homeostasis, improves mitochondrial quality, and increases exercise tolerance without an increase in mitochondrial content. Since elamipretide is currently in clinical trials these results indicate it may have direct translational value for improving exercise tolerance and quality of life in the elderly.

Protein S-glutathionylation is an important reversible post-translational modification implicated in redox signaling. Oxidative modifications to protein thiols can alter the activity of metabolic enzymes, transcription factors, kinases, phosphatases, and the function of contractile proteins. However, the extent to which muscle contraction induces oxidative modifications in redox sensitive thiols is not known. The purpose of this study was to determine the targets of S-glutathionylation redox signaling following fatiguing contractions. Anesthetized adult male CB6F1 (BALB/cBy × C57BL/6) mice were subjected to acute fatiguing contractions for 15 min using in vivo stimulations. The right (stimulated) and left (unstimulated) gastrocnemius muscleswere collected 60 min after the last stimulation and processed for redox proteomics assay of S-glutathionylation. Using selective reduction with a glutaredoxin enzyme cocktail and resin-assisted enrichment technique, we quantified the levels of site-specific protein S-glutathionylation at rest and following fatiguing contractions. Redox proteomics revealed over 2200 sites of S-glutathionylation modifications, of which 1290 were significantly increased after fatiguing contractions. Muscle contraction leads to the greatest increase in S-glutathionylation in the mitochondria (1.03%) and the smallest increase in the nucleus (0.47%). Regulatory cysteines were significantly S-glutathionylated on mitochondrial complex I and II, GAPDH, MDH1, ACO2, and mitochondrial complex V among others. Similarly, S-glutathionylation of RYR1, SERCA1, titin, and troponin I2 are known to regulate muscle contractility and were significantly S-glutathionylated after just 15 min of fatiguing contractions. The largest fold changes (> 1.6) in the S-glutathionylated proteome after fatigue occurred on signaling proteins such as 14-3-3 protein gamma and MAP2K4, as well as proteins like SERCA1, and NDUV2 of mitochondrial complex I, at previously unknown glutathionylation sites. These findings highlight the important role of redox control over muscle physiology, metabolism, and the exercise adaptive response. This study lays the groundwork for future investigation into the altered exercise adaptation associated with chronic conditions, such as sarcopenia.

In this work, new lignin-based flame retardant LHDs were successfully synthesized through the reaction between lignin, 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) and hexamethylene diisocyanate (HDI). The chemical structure of LHD was characterized by FTIR, 1H NMR, 31P NMR. The thermal stability of LHD was studied by TGA. The results showed that the residual carbon content of L15HD (15% of lignin in LHD) at 600 °C reached 16.55%, indicating that this prepared flame retardant can be a type of good char forming agent. LHDs were then applied to prepare flame-retardant lignin-based polyurethane (FLPU). Lignin-based polyurethane (LPU) was synthesized by the reaction between lignin, polyethylene glycol 200 (PEG 200) and hexamethylene diisocyanate (HDI). The limiting oxygen index (LOI) value of the FLPU reached 30.2% when the addition content of L15HD (15% lignin in LHD) in L20PU (20% lignin in LPU) was 25%, exhibiting excellent flame-retardant properties. Scanning electron microscopy (SEM) analysis of the FLPU char residual showed that there was a continuous dense outer carbon layer on the residue surface, and the inner carbon layer had many expansion bubbles, indicating the LHDs have an excellent flame retardant effect for PU. In addition, FLPU presented better hardness and adhesion than PU. The hardness of FL15-25L20PU (lignin content in LPU was 20%, and added content of L15HD in LPU was 25%) reached 4H, and its adhesion was 0. These excellent properties illustrated that the LHDs are ideal flame retardants and reinforcing agents for LPU because of the co-curing and strong interface between LHD and LPU.

Protein thiols play a crucial role in redox signaling, in the regulation of enzymatic activity and protein function, and in maintaining redox homeostasis in living systems. The unique chemical reactivity of the thiol group makes protein cysteines susceptible to reactions with reactive oxygen and nitrogen species that form various reversible and irreversible post-translational modifications (PTMs). The reversible PTMs in particular are major components of redox signaling and are involved in the regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in both healthy and disease states has been increasingly recognized. Herein, we review recent advances in quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including general considerations of sample processing, chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for specific biological applications. Although technical limitations remain, redox proteomics is paving the way to a better understanding of redox signaling and regulation in both healthy and disease states.

It is well known that the reactive oxygen species NO can trigger cell death in plants and other organisms, but the underlying molecular mechanisms are not well understood. Here we provide evidence that NO may trigger cell death in tomato (Solanum lycopersicum) by inhibiting the activity of phosphoinositide-dependent kinase 1 (SlPDK1), a conserved negative regulator of cell death in yeasts, mammals, and plants, via S-nitrosylation. Biotin-switch assays indicated that SlPDK1 is a target of S-nitrosylation. Moreover, the kinase activity of SlPDK1 was inhibited by S-nitrosoglutathione in a concentration-dependent manner, indicating that SlPDK1 activity is abrogated by S-nitrosylation. The S-nitrosoglutathione–induced inhibition was reversible in the presence of a reducing agent but additively enhanced by hydrogen peroxide (H2O2). Our LC-MS/MS analyses further indicated that SlPDK1 is primarily S-nitrosylated on a cysteine residue at position 128 (Cys128), and substitution of Cys128 with serine completely abolished SlPDK1 kinase activity, suggesting that S-nitrosylation of Cys128 is responsible for SlPDK1 inhibition. In summary, our results establish a potential link between NO-triggered cell death and inhibition of the kinase activity of tomato PDK1.

Protein S-glutathionylation (P-SSG) is a reversible redox modification known to alter the activity of transcription factors, kinases, and contractile proteins as well as protect critical cysteine residues from irreversible oxidation. Exercise elicits an acute oxidative stress that is reported to result in beneficial adaptive responses, a process known as redox signaling. We hypothesized that redox signaling will occur through P-SSG of regulatory cysteines following fatiguing muscle contractions. To test this hypothesis, we performed acute fatiguing contractions using an in vivo stimulation protocol on anesthetized CB6F1 (BALB/cBy x C57BL/6) mice. Muscle force production was monitored by a force transducer throughout the 15 minutes of fatiguing stimulations. The right (stimulated) and left (unstimulated) gastrocnemius were collected 60 minutes after the last stimulation and processed for redox proteomics using resin-assisted thiol enrichment and selective reduction. Redox proteomics revealed over 1,500 P-SSG modifications that were significantly increased by fatiguing contractions. Mitochondrial proteins were among the most sensitive to glutathionylation. Ingenuity Pathway Analysis revealed mitochondrial dysfunction, calcium signaling, cytoskeleton signaling, and oxidative stress response in the top ten affected pathways. Critical cysteines on beta-actin, troponin I, ryanodine receptor 1, SERCA1, ATP synthase subunit alpha and NADH dehydrogenase flavoprotein 1 were among those significantly glutathionylated that have previously been reported to alter protein and muscle function. These modifications of redox sensitive proteins implicate rapid regulation of metabolism, excitation/contraction coupling, kinase activity, and contractile protein function, and protection from irreversible oxidation. Together, these data suggest a direct role of ROS in acute exercise signaling and map the redox sensitive proteome in mouse muscle. This study lays the groundwork for future investigation into the redox signaling of altered exercise adaptation associated with chronic conditions, such as sarcopenia, the age-related loss of muscle mass and function.

Reversible oxidative modifications of protein thiols represent a fundamental mechanism of redox signaling by modulating enzyme activities and protein functions in a variety of cellular activities, such as signaling, metabolism, gene expression, and apoptosis. The stoichiometry (or occupancy) of oxidative modifications on specific cysteine residue is important for understanding the functional role of the modification; however, this aspect of quantification has been underexplored. Herein we report the stoichiometric quantification of both S-glutathionylation (SSG) and total oxidation in macrophages at the basal physiological conditions by applying resin-assisted quantitative redox proteomics. The stoichiometry information of SSG and total oxidation on a total of ~4,100 Cys sites was quantified. The basal average oxidation level of protein thiols was ~12%, which is consistent with the overall reducing status in vivo. The average percentage of SSG in total oxidation was 32.0% at basal, supporting that SSG is one major type of thiol modifications. Interesting, we observed that the redox potential of a cellular organelle was well correlated with the level of oxidation in the organelle. For example, endoplasmic reticulum and lysosome have much higher oxidation levels than those from reducing organelles, such as nucleus and mitochondrion. In contrast, the reducing organelles have an average higher percentage of SSG in total oxidation, suggesting SSG is the dominant modification and plays an important regulatory role in these organelles. Moreover, the integration of stoichiometric and dynamic data reveals potential evidence of inhibitory and activation sites via redox modifications

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.

A patterned gold nanoparticle microarray, functionalized with a nanoscale silicate coating, has been developed for on-chip, high-throughput mass spectrometric analyses of biomolecules with minimal sample preparation and reagent costs. Fabrication was realized by the combination of layer-by-layer functionalization of the nanoparticles with suitable polyelectrolytes, followed by fluidic patterning of the glass microarray support and calcination for permanent fixation of the nano-coating. Performance of the microarray was evaluated for surface-assisted laser-desorption/ionization mass spectrometry (SALDI-MS), where the nano-silicate coating was found to enhance SALDI efficiency, resulting in comparable performance to some common organic matrices for small and medium sized molecules. Performance contributing factors of this material have been discussed; heat confinement and interband transition/plasmonic resonance may play important roles. Taking the accessibility of fabrication, performance, and reusability of this substrate together, the material developed here provides a new tool for multiplexed and chip-based mass spectrometric analysis.

The development of a functional disulfide, FmSSPy-A (Fm = 9-fluorenylmethyl; Py = pyridinyl), is reported. It can effectively convert small molecule and protein thiols (-SH) to form -S-SFm adducts under mild conditions. This method allows for a H2S-free and biomimetic protocol to generate highly reactive persulfides (in their anionic forms). The high nucleophilicity of persulfides toward a number of thiol-blocking reagents is also demonstrated. The method holds promise for further understanding the chemical biology of persulfides and S-sulfhydration.

Engineered nanoparticles (ENPs) are increasingly utilized for commercial and medical applications; thus, understanding their potential adverse effects is an important societal issue. Herein, we investigated protein S-glutathionylation (SSG) as an underlying regulatory mechanism by which ENPs may alter macrophage innate immune functions, using a quantitative redox proteomics approach for site-specific measurement of SSG modifications. Three high-volume production ENPs (SiO2, Fe3O4, and CoO) were selected as representatives which induce low, moderate, and high propensity, respectively, to stimulate cellular reactive oxygen species (ROS) and disrupt macrophage function. The SSG modifications identified highlighted a broad set of redox sensitive proteins and specific Cys residues which correlated well with the overall level of cellular redox stress and impairment of macrophage phagocytic function (CoO > Fe3O4 ≫ SiO2). Moreover, our data revealed pathway-specific differences in susceptibility to SSG between ENPs which induce moderate versus high levels of ROS. Pathways regulating protein translation and protein stability indicative of ER stress responses and proteins involved in phagocytosis were among the most sensitive to SSG in response to ENPs that induce subcytoxic levels of redox stress. At higher levels of redox stress, the pattern of SSG modifications displayed reduced specificity and a broader set pathways involving classical stress responses and mitochondrial energetics (e.g., glycolysis) associated with apoptotic mechanisms. An important role for SSG in regulation of macrophage innate immune function was also confirmed by RNA silencing of glutaredoxin, a major enzyme which reverses SSG modifications. Our results provide unique insights into the protein signatures and pathways that serve as ROS sensors and may facilitate cellular adaption to ENPs, versus intracellular targets of ENP-induced oxidative stress that are linked to irreversible cell outcomes.

Mitochondrial oxidative stress is a common feature of skeletal myopathies across multiple conditions; however, the mechanism by which it contributes to skeletal muscle dysfunction remains controversial. Oxidative damage to proteins, lipids, and DNA has received the most attention, yet an important role for reversible redox post-translational modifications (PTMs) in pathophysiology is emerging. The possibility that these PTMs can exert dynamic control of muscle function implicates them as a mechanism contributing to skeletal muscle dysfunction in chronic disease. Herein, we discuss the significance of thiol-based redox dependent modifications to mitochondrial, myofibrillar and excitation-contraction (EC) coupling proteins with an emphasis on how these changes could alter skeletal muscle performance under chronically stressed conditions. A major barrier to a better mechanistic understanding of the role of reversible redox PTMs in muscle function is the technical challenges associated with accurately measuring the changes of site-specific redox PTMs. Here we will critically review current approaches with an emphasis on sample preparation artifacts, quantitation, and specificity. Despite these challenges, the ability to accurately quantify reversible redox PTMs is critical to understanding the mechanisms by which mitochondrial oxidative stress contributes to skeletal muscle dysfunction in chronic diseases.

Identifying the direct protein targets of a bioactive small molecule gives insight into the compound’s mechanism of action, its efficacy, and possible toxicity. Target identification is becoming an increasingly important part of the drugdevelopment process. However, given the transient and heterogeneous nature of interactions between small molecules and proteins, this step is often difficult, greatly slowing the development of new therapeutics. For this reason, new methods to rapidly identify the direct protein targets of bioactive small molecules are of great importance. Enrichment strategies coupled with quantitative mass spectrometry have shown great promise in target identification. Here we will present our progress toward developing an engineered enzymatic tagging method that enables specific labeling and enrichment of protein targets from complex lysates. This method couples the binding of a small molecule to a proximity-based labeling event. Labeled target proteins are enriched and subsequently identified using quantitative LC-MS/MS. We will discuss several variations of this method, and highlight our progress towards applying proximity labeling to small-molecule target identification and validation. B.2 Modelling Atherosclerosis: Molecular Changes in the Ascending Aorta of Cholesterol-fed Rabbits Jingshu Xu, Mia Jüllig, Martin J. Middleditch, Garth J.S. Cooper School of Biological Sciences, University of Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, New Zealand; Department of Pharmacology, Medical Sciences Division, University of Oxford, Oxford, UK; Centre for Advanced Discovery and Experimental Therapeutics, NIHR Manchester Biomedical Research Centre, the University of Manchester, Manchester, UK

Localized surface plasmon resonance (LSPR) represents a sensitive and versatile method for detection of biomolecules in a label-free fashion, but identification of bound analytes can be challenging with LSPR alone, especially for samples in a complex medium. We report the fabrication of an optically active, plasmonic film of gold nanoparticles by using a self-assembly and calcination process, which offers orthogonal measurements enabling multifaceted characterization on the same surface with LSPR and surface-assisted laser desorption/ionization mass spectrometry. This proof-of-concept study involves plasmonic characterization of the fabricated nanofilm, real-time monitoring of vesicle-surface interactions toward formation of fluid lipid bilayer, and mass spectrometric analysis of peptides and cytochrome c digest. This multifunction-enabling surface material can yield complementary analytical information, providing new tools for comprehensive analysis of biomolecular samples.

Protein-protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, we have developed a new in vivo cross-linking mass spectrometry platform that couples a novel membrane-permeable, enrichable, and MS-cleavable cross-linker with multistage tandem mass spectrometry. This strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells and thus enables the determination of protein interaction interfaces. The utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and the targeted protein complex level. Our work represents a general approach for studying in vivo PPIs and provides a solid foundation for future studies toward the complete mapping of PPI networks in living systems.