An introduction to methods for analyzing thiols and disulfides: Reactions, reagents, and practical considerations

Exploring the unmapped cysteine redox proteoform landscape

Cysteine redox proteoforms define the diverse molecular states that proteins with cysteine residues can adopt. A protein with one cysteine residue must adopt one of two binary proteoforms: reduced or oxidized. Their numbers scale: a protein with 10 cysteine residues must assume one of 1,024 proteoforms. Although they play pivotal biological roles, the vast cysteine redox proteoform landscape comprising vast numbers of theoretical proteoforms remains largely uncharted. Progress is hampered by a general underappreciation of cysteine redox proteoforms, their intricate complexity, and the formidable challenges that they pose to existing methods. The present review advances cysteine redox proteoform theory, scrutinizes methodological barriers, and elaborates innovative technologies for detecting unique residue-defined cysteine redox proteoforms. For example, chemistry-enabled hybrid approaches combining the strengths of top-down mass spectrometry (TD-MS) and bottom-up mass spectrometry (BU-MS) for systematically cataloguing cysteine redox proteoforms are delineated. These methods provide the technological means to map uncharted redox terrain. To unravel hidden redox regulatory mechanisms, discover new biomarkers, and pinpoint therapeutic targets by mining the theoretical cysteine redox proteoform space, a community-wide initiative termed the "Human Cysteine Redox Proteoform Project" is proposed. Exploring the cysteine redox proteoform landscape could transform current understanding of redox biology.

Ten "Cheat Codes" for Measuring Oxidative Stress in Humans

Formidable and often seemingly insurmountable conceptual, technical, and methodological challenges hamper the measurement of oxidative stress in humans. For instance, fraught and flawed methods, such as the thiobarbituric acid reactive substances assay kits for lipid peroxidation, rate-limit progress. To advance translational redox research, we present ten comprehensive "cheat codes" for measuring oxidative stress in humans. The cheat codes include analytical approaches to assess reactive oxygen species, antioxidants, oxidative damage, and redox regulation. They provide essential conceptual, technical, and methodological information inclusive of curated "do" and "don't" guidelines. Given the biochemical complexity of oxidative stress, we present a research question-grounded decision tree guide for selecting the most appropriate cheat code(s) to implement in a prospective human experiment. Worked examples demonstrate the benefits of the decision tree-based cheat code selection tool. The ten cheat codes define an invaluable resource for measuring oxidative stress in humans.

Accurate redox state indication by in situ derivatization with N-ethylmaleimide - Profiling of transsulfuration and glutathione pathway metabolites by UPLC-MS/MS

BACKGROUND

Reduced and oxidized glutathione play an important role for the intracellular detoxification of reactive oxygen species. The iron-dependent formation of such reactive oxygen species in conjunction with the inhibition of the redox-balancing enzyme glutathione peroxidase 4 underlie an imbalance in the cellular redox state, thereby resulting in a non-apoptotic form of cell death, defined as ferroptosis, which is relevant in several pathologies.

METHODS

Here we present a rapid ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based method providing the accurate quantification of 12 glutathione pathway metabolites after in situ derivatization with N-Ethylmaleimide (NEM). The method was validated regards linearity, recovery and accuracy as well as precision. The assay includes glutathione and its oxidized form glutathione disulfide. Furthermore, the related precursors cysteine, cystine, glutamic acid, γ-glutamylcysteine and cysteinylglycine, biomarkers of protein crosslinking such as cystathionine and lanthionine, as well as metabolites of the transsulfuration pathway, methionine, homocysteine and serine are simultaneously determined.

RESULTS

Twelve glutathione pathway metabolites were simultaneously analyzed in four different human cell line extracts within a total LC run time of 5.5 min. Interday coefficients of variation (1.7 % to 12.0 %), the mean observed accuracy (100.0 % ± 5.2 %), linear quantification ranges over three orders of magnitude for all analytes and sufficient metabolite stability after NEM-derivatization demonstrate method reliability. Immediate derivatization with NEM at cell harvesting prevents autooxidation of glutathione, ensures accurate results for the GSH/GSSG redox ratio and thereby allows interpretation of cellular redox state.

CONCLUSION

The described UPLC-MS/MS method provides a sensitive and selective tool for a fast and simultaneous analysis of glutathione pathway metabolites, its direct precursors and related compounds. Assay performance characteristics demonstrate the suitability of the method for applications in different cell cultures. Therefore, by providing glutathione related functional metabolic readouts, the method enables investigations in mechanisms of ferroptosis and alterations in oxidative stress levels in several pathophysiologies.

A new era of cysteine proteomics - Technological advances in thiol biology

Cysteines are amenable to a diverse set of modifications that exhibit critical regulatory functions over the proteome and thereby control a wide range of cellular processes. Proteomic technologies have emerged as a powerful strategy to interrogate cysteine modifications across the proteome. Recent advancements in enrichment strategies, multiplexing capabilities and increased analytical sensitivity have enabled deeper quantitative cysteine profiling, capturing a substantial proportion of the cysteine proteome. This is complemented by a rapidly growing repertoire of analytical strategies illuminating the diverse landscape of cysteine modifications. Cysteine chemoproteomics technologies have evolved into a powerful strategy to facilitate the development of covalent drugs, opening unprecedented opportunities to target the extensive undrugged proteome. Herein we review recent technological and scientific advances that shape the cysteine proteomics field.

A Facile and Green Approach for the Preparation of Amine-Functionalized Poly(ethylene glycol) by Reducing Poly(ethylene glycol) Azide with Dithiothreitol

A facile and green approach for the preparation of PEGn-NH2s from PEGn-N3s in water with DTT as the reduction reagent has been developed, avoiding the introduction of metal ions and difficulties in purification compared to the traditional synthesis process of PEGn-NH2s. A series of high-purity linear and multiarm PEGn-NH2s with different molecular weights were synthesized, demonstrating the versatility of this method. Additionally, HS-PEG45-NH2 with high fidelity of thiol and amine was easily prepared through the one-step two functional group conversion of N3-PEG45-S-S-PEG45-N3, and the PEG-based NH2-PEG@AuNPs were also prepared. This technology will promote the application of PEGn-NH2s in the fields of medicine and biomaterials.

Quantitative analysis of the glutathione pathway cellular metabolites by targeted liquid chromatography-tandem mass spectrometry

Glutathione, its biosynthesis intermediates, and other thiol metabolites are of central relevance for the redox homeostasis of cells. Their analysis is critical due to the facile interconversion of redox pairs during sampling, sample preparation, and data acquisition, in particular in the electrospray ionization interface. In this work, we propose a fast-targeted liquid chromatography-tandem mass spectrometry method to accurately analyze 14 metabolites from the glutathione pathway. N-Ethylmaleimide reagent is added with the extraction solvent and instantly stabilizes the thiol-redox state by derivatization. Liquid chromatographic separation of the analytes was performed on a sub-2 μm superficially porous hydrophilic interaction liquid chromatography column with sulfobetaine chemistry. Tandem mass spectrometry with triple-quadrupole mass spectrometry in multiple-reaction monitoring acquisition mode allowed sensitive detection of the targeted metabolites with limits of quantification in the range of 5-25 nM. Run times of 3 min enable a high throughput analysis of cellular samples. For calibration, a 13 C-labelled cell extract was used as an internal standard. The method was validated and the concentrations of glutathione and its biosynthesis intermediates were determined in HeLa cells.

Reverse Thiol Trapping Approach to Assess the Thiol Status of Metal-Binding Mitochondrial Proteins

Thiol-disulfide interconversions are pivotal in the intricate chemistry of biological systems. They play a vital role in governing cellular redox potential and shielding against oxidative harm. These interconversions can also act as molecular switches within an expanding array of redox-regulated proteins, facilitating dynamic and responsive processes. Furthermore, metal-binding proteins often use thiols for coordination. Reverse thiol trapping is a valuable analytical tool to study the redox state of cysteines in biological systems. By selectively capturing and stabilizing free thiol species with an alkylating agent, reverse thiol trapping allows for their subsequent identification and quantification. Various methods can be employed to analyze the trapped thiol adducts, including electrophoresis-based methods, mass spectrometry, nuclear magnetic resonance spectroscopy, and chromatographic techniques. In this chapter, we will focus on describing a simple and sensitive method to sequentially block thiols in their cellular state with a cell-permeant agent (iodoacetamide), and following reduction and denaturation of the samples, trap the native disulfides with a second blocker that shifts the apparent molecular weight of the protein. The oxidation status of proteins for which suitable antibodies are available can then be analyzed by immunoblotting. We present examples of mitochondrial proteins that use cysteine thiols to coordinate metal factors such as iron-sulfur clusters, zinc, and copper.

Thiol and thioether-based metal-organic frameworks: synthesis, structure, and multifaceted applications

Metal-organic frameworks (MOFs) are unique hybrid porous materials formed by combining metal ions or clusters with organic ligands. Thiol and thioether-based MOFs belong to a specific category of MOFs where one or many thiols or thioether groups are present in organic linkers. Depending on the linkers, thiol-thioether MOFs can be divided into three categories: (i) MOFs where both thiol or thioether groups are part of the carboxylic acid ligands, (ii) MOFs where only thiol or thioether groups are present in the organic linker, and (iii) MOFs where both thiol or thioether groups are part of azolate-containing linkers. MOFs containing thiol-thioether-based acid ligands are synthesized through two primary approaches; one is by utilizing thiol and thioether-based carboxylic acid ligands where the bonding pattern of ligands with metal ions plays a vital role in MOF formation (HSAB principle). MOFs synthesized by this approach can be structurally differentiated into two categories: structures without common structural motifs and structures with common structural motifs (related to UiO-66, UiO-67, UiO-68, MIL-53, NU-1100, etc.). The second approach to synthesize thiol and thioether-based MOFs is indirect methods, where thiol or thioether functionality is introduced in MOFs by techniques like post-synthetic modifications (PSM), post-synthetic exchange (PSE) and by forming composite materials. Generally, MOFs containing only thiol-thioether-based ligands are synthesized by interfacial assisted synthesis, forming two-dimensional sheet frameworks, and show significantly high conductivity. A limited study has been done on MOFs containing thiol-thioether-based azolate ligands where both nitrogen- and sulfur-containing functionality are present in the MOF frameworks. These materials exhibit intriguing properties stemming from the interplay between metal centres, organic ligands, and sulfur functionality. As a result, they offer great potential for multifaceted applications, ranging from catalysis, sensing, and conductivity, to adsorption. This perspective is organised through an introduction, schematic representations, and tabular data of the reported thiol and thioether MOFs and concluded with future directions.

Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design

In biological or abiotic systems, rhythms occur, owing to the coupling between positive and negative feedback loops in a reaction network. Using the Semenov-Whitesides oscillatory network for thioester hydrolysis as a prototype, we experimentally and theoretically analyzed the role of fast and slow inhibitors in oscillatory reaction networks. In the presence of positive feedback, a single fast inhibitor generates a time delay, resulting in two saddle-node bifurcations and bistability in a continuously stirred tank reactor. A slow inhibitor produces a node-focus bifurcation, resulting in damped oscillations. With both fast and slow inhibitors present, the node-focus bifurcation repeatedly modulates the saddle-node bifurcations, producing stable periodic oscillations. These fast and slow inhibitions result in a pair of time delays between steeply ascending and descending dynamics, which originate from the positive and negative feedbacks, respectively. This pattern can be identified in many chemical relaxation oscillators and oscillatory models, e.g., the bromate-sulfite pH oscillatory system, the Belousov-Zhabotinsky reaction, the trypsin oscillatory system, and the Boissonade-De Kepper model. This study provides a novel understanding of chemical and biochemical rhythms and suggests an approach to designing such behavior.

Comparison of Reactive Sites in 2(1H)-Quinolone Derivatives for the Detection of Biologically Important Sulfur Compounds

Novel fluorescent probes based on 2(1H)-quinolone skeleton containing a malonate group (Q1-Q3) were synthesized and proposed for biothiols detection. Their chemical reactivity toward thiols was compared to the reactivity of derivative having a dicyanovinyl group (Q4) as a reactive site. The detailed photophysical properties of these compounds were assessed through the determination of absorption and fluorescence spectra, fluorescence quantum yield, and fluorescence lifetime. In the presence of biothiols, an increase in the fluorescence intensity of compounds Q1-Q3 and a hypsochromic shift in their emission bands were observed. In contrast, the compound with the dicyanovinyl group (Q4) in the presence of biothiols and cyanide ion showed the quenching of fluorescence, while a fluorescence "turn on" effect was observed toward reactive sulfur species.

Performance benchmarking microplate-immunoassays for quantifying target-specific cysteine oxidation reveals their potential for understanding redox-regulation and oxidative stress

The antibody-linked oxi-state assay (ALISA) for quantifying target-specific cysteine oxidation can benefit specialist and non-specialist users. Specialists can benefit from time-efficient analysis and high-throughput target and/or sample n-plex capacities. The simple and accessible "off-the-shelf" nature of ALISA brings the benefits of oxidative damage assays to non-specialists studying redox-regulation. Until performance benchmarking establishes confidence in the "unseen" microplate results, ALISA is unlikely to be widely adopted. Here, we implemented pre-set pass/fail criteria to benchmark ALISA by evaluating immunoassay performance in diverse contexts. ELISA-mode ALISA assays were accurate, reliable, and sensitive. For example, the average inter-assay CV for detecting 20%- and 40%-oxidised PRDX2 or GAPDH standards was 4.6% (range: 3.6-7.4%). ALISA displayed target-specificity. Immunodepleting the target decreased the signal by ∼75%. Single-antibody formatted ALISA failed to quantify the matrix-facing alpha subunit of the mitochondrial ATP synthase. However, RedoxiFluor quantified the alpha subunit displaying exceptional performance in the single-antibody format. ALISA discovered that (1) monocyte-to-macrophage differentiation amplified PRDX2-oxidation in THP-1 cells and (2) exercise increased GAPDH-specific oxidation in human erythrocytes. The "unseen" microplate data were "seen-to-be-believed" via orthogonal visually displayed immunoassays like the dimer method. Finally, we established target (n = 3) and sample (n = 100) n-plex capacities in ∼4 h with 50-70 min hands-on time. Our work showcases the potential of ALISA to advance our understanding of redox-regulation and oxidative stress.

Characterization of four thermogelled egg yolk varieties based on moisture and protein content

There are obvious differences between egg yolks of different varieties. Additionally, boiled eggs, which are widely liked and consumed globally, are nutrient rich. However, they absorb water in the esophagus during swallowing, and this result in an uncomfortable sensation. Here, we determined the moisture content and distribution as well as the protein contents and properties of 4 varieties of thermogelled egg yolks. Among the varieties, Green Shelled thermogelled egg yolk showed the highest protein content and solubility. Additionally, the ionic, hydrogen, and disulfide bonds corresponding to Rhode Island Red thermogelled egg yolk samples were the weakest, while the hydrophobic interaction force corresponding to the Hetian Dahei (HD) egg yolk samples was the weakest. Further, the distribution of the moisture contents of the 4 varieties was significantly different (P < 0.05). HD egg yolk showed the highest moisture content, and its bound and immobile moisture contents were significantly higher than those of the other 3 varieties. Egg yolk moisture content also affected free amino acid content, which was the highest for HD egg yolk. Therefore, owing to its high moisture content, HD egg yolk was conducive for chewing and swallowing and given its high free amino acid content, it also had a more suitable taste and flavor. The results of this study provide a theoretical basis for the application of egg yolks in food processing.

A New Method for the Determination of Total Content of Vitamin C, Ascorbic and Dehydroascorbic Acid, in Food Products with the Voltammetric Technique with the Use of Tris(2-carboxyethyl)phosphine as a Reducing Reagent

The objective of the study was to develop a new method for the determination of the total content of vitamin C and dehydroascorbic acid in food, based on the technique of differential pulse voltammetry with the use of a boron-doped diamond electrode modified with mercury film. A comparison was made between the results obtained with the developed method and a proposed reference method based on high-performance liquid chromatography with spectrophotometric detection. The reduction of dehydroascorbic acid was performed with the use of tris(2-carboxyethyl)phosphine. The interference caused by the presence of tris(2-carboxyethyl)phosphine during the voltammetric determination of ascorbic acid was effectively eliminated through a reaction with N-ethylmaleimide. The conducted validation of the voltammetric method indicated that correct results of analysis of the total content of vitamin C and ascorbic acid were obtained. Analysis of the content of dehydroascorbic acid was imprecise due to the application of the differential method. The results of the analyses and the determined validation parameters of the developed method are characterised by a high degree of conformance with the results obtained with the chromatographic reference method, which indicates the equivalence of the two methods.

Hydrogen-Deuterium Addition and Exchange in N-Ethylmaleimide Reaction with Glutathione Detected by NMR Spectroscopy

Glutathione (GSH) is an important and ubiquitous thiol compound abundantly present in virtually every living cell. It is a powerful antioxidant critically required to protect cells from oxidative damage and free radical injury. Its quantification in ex vivo analysis remains a major challenge because it spontaneously oxidizes to form glutathione disulfide. N-Ethylmaleimide (NEM) is a well-known Michael acceptor, which reacts rapidly and irreversibly with thiol and prevents disulfide bond formation. Based on thiol conjugation to NEM, recently, the concentration of GSH was determined in human blood using NMR spectroscopy [Anal. Chem, 2021, 93(44): 14844-14850]. It was found that hydrogen-deuterium addition and exchange occur during the thiol-maleimide reaction as well as NMR analysis, generating a series of poorly explored diastereomers/isotopomers. Here, we establish a general NMR approach to identify the thiosuccinimide diastereomers/isotopomers derived from the thiol-maleimide reaction. The thiol-Michael addition reaction was conducted for GSH and another thiol compound, cysteine, separately, using D2O and H2O. The conjugates were characterized by 1H/13C 1D/2D NMR under different solvent, buffer, and pH conditions. The Michael addition combined with the H/D exchange formed twelve unique diastereomers/isotopomers. NMR measurements allowed the distinct assignment of all structures in solutions and quantification of H/D addition and exchange. Interestingly, the deuterium exchange rate was dependent on structure, pH, and buffer. The elucidation of the thiol-maleimide reaction and H/D exchange mechanism can potentially impact areas including metabolomics, small molecule synthesis, and bioconjugation chemistry.

Advances and Trends in Omics Technology Development

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

Basal oxidation of conserved cysteines modulates cardiac titin stiffness and dynamics

Titin, as the main protein responsible for the passive stiffness of the sarcomere, plays a key role in diastolic function and is a determinant factor in the etiology of heart disease. Titin stiffness depends on unfolding and folding transitions of immunoglobulin-like (Ig) domains of the I-band, and recent studies have shown that oxidative modifications of cryptic cysteines belonging to these Ig domains modulate their mechanical properties in vitro. However, the relevance of this mode of titin mechanical modulation in vivo remains largely unknown. Here, we describe the high evolutionary conservation of titin mechanical cysteines and show that they are remarkably oxidized in murine cardiac tissue. Mass spectrometry analyses indicate a similar landscape of basal oxidation in murine and human myocardium. Monte Carlo simulations illustrate how disulfides and S-thiolations on these cysteines increase the dynamics of the protein at physiological forces, while enabling load- and isoform-dependent regulation of titin stiffness. Our results demonstrate the role of conserved cysteines in the modulation of titin mechanical properties in vivo and point to potential redox-based pathomechanisms in heart disease.

Development of a highly sensitive Prussian-blue-based enzymatic biosensor for L-carnitine employing the thiol/disulfide exchange reaction

This is the first report of conducting proof-of-concept study for amperometric acetyltransferase-based L-carnitine sensor by employing the thiol/disulfide exchange reaction. The carnitine acetyltransferase (CrAT) catalyzes the reaction between acetyl-CoA and L-carnitine to produce CoA which is difficult to detect directly by electrochemical methods owing to steric hindrance and electrostatic effect of CoA. The thiol/disulfide exchange reaction between CoA and cystamine was mediated in the enzymatic reaction to produce electrochemically detectable low molecular weight of cationic cysteamine. The sensor exhibited high sensitivity and selectivity for L-carnitine in the concentration range 0.28-50 µM with a limit of detection of 0.28 µM. This is a promising strategy for L-carnitine sensing in point-of-care testing applications.

Introducing Thioredoxin-Related Transmembrane Proteins: Emerging Roles of Human TMX and Clinical Implications

Significance: The presence of a large number of thioredoxin superfamily members suggests a complex mechanism of redox-based regulation in mammalian cells. However, whether these members are functionally redundant or play separate and distinct roles in each cellular compartment remains to be elucidated. Recent Advances: In the mammalian endoplasmic reticulum (ER), ∼20 thioredoxin-like proteins have been identified. Most ER oxidoreductases are soluble proteins located in the luminal compartment, whereas a small family of five thioredoxin-related transmembrane proteins (TMX) also reside in the ER membrane and play crucial roles with specialized functions. Critical Issues: In addition to the predicted function of ER protein quality control, several independent studies have suggested the diverse roles of TMX family proteins in the regulation of cellular processes, including calcium homeostasis, bioenergetics, and thiol-disulfide exchange in the extracellular space. Moreover, recent studies have provided evidence of their involvement in the pathogenesis of various diseases. Future Directions: Extensive research is required to unravel the physiological roles of TMX family proteins. Given that membrane-associated proteins are prime targets for drug discovery in a variety of human diseases, expanding our knowledge on the mechanistic details of TMX action on the cell membrane will provide the molecular basis for developing novel diagnostic and therapeutic approaches as a potent molecular target in a clinical setting. Antioxid. Redox Signal. 36, 984-1000.

Staphylococcal Protein A with Engineered Cysteine: Comparison of Monomeric Content as a Critical Quality Attribute during Intracellular and Extracellular Expression

Background: The introduction of engineered cysteine in staphylococcal protein A (SPA-cys) for site-specific conjugation results in a substantial amount of dimerized SPA due to spontaneous oxidation during its production, leading to inaccessibility and thus rendering it unusable. Monomers are usually recovered from dimers by using reducing agents before conjugation in subsequent steps. However, this leads to low conjugation efficiency and increases overall cost and production time. This study aims to systematically compare and quantify the monomeric and dimeric content of SPA when produced through intracellular and extracellular routes in E. coli. Methods: Purified SPAs with and without cysteine from both intracellular and extracellular processes are compared for their monomeric content and efficiency to conjugate on solid support matrix with and without an additional pre-step of reduction. Results: The monomeric form of SPA-cys, which is a desired key quality attribute, is less than 50% when produced extracellularly. SPA-cys produced through the intracellular production process has high monomeric content (≥85%) and shows higher binding to solid support. Conclusion: The study demonstrates that the intracellular route for production of SPA-cys should be the preferred method, and the release assays for SPA-cys products should include the amount of monomeric content as one of the quality attributes. The abundance of monomeric content enhances the site-specific conjugation efficiency and density of SPA on the resin matrix.

RedoxiFluor: A microplate technique to quantify target-specific protein thiol redox state in relative percentage and molar terms

Unravelling how reactive oxygen species regulate fundamental biological processes is hampered by the lack of an accessible microplate technique to quantify target-specific protein thiol redox state in percentages and moles. To meet this unmet need, we present RedoxiFluor. RedoxiFluor uses two spectrally distinct thiol-reactive fluorescent conjugated reporters, a capture antibody, detector antibody and a standard curve to quantify target-specific protein thiol redox state in relative percentage and molar terms. RedoxiFluor can operate in global mode to assess the redox state of the bulk thiol proteome and can simultaneously assess the redox state of multiple targets in array mode. Extensive proof-of-principle experiments robustly validate the assay principle and the value of each RedoxiFluor mode in diverse biological contexts. In particular, array mode RedoxiFluor shows that the response of redox-regulated phosphatases to lipopolysaccharide (LPS) differs in human monocytes. Specifically, LPS increased PP2A-, SHP1-, PTP1B-, and CD45-specific reversible thiol oxidation without changing the redox state of calcineurin, PTEN, and SHP2. The relative percentage and molar terms are interpretationally useful and define the most complete and extensive microplate redox analysis achieved to date. RedoxiFluor is a new antibody technology with the power to quantify relative target-specific protein thiol redox state in percentages and moles relative to the bulk thiol proteome and selected other targets in a widely accessible, simple and easily implementable microplate format.

Applying selenocysteine-mediated expressed protein ligation to prepare the membrane enzyme selenoprotein S

The intrinsically disordered membrane-bound selenoprotein s (selenos) takes part in the protein quality control pathway, vesicle trafficking, and NF-kB signaling. The reactive selenocysteine (Sec) at the penultimate position is responsible for its enzymatic activity. We report the preparation of the soluble segment as well as the full-length selenos using expressed protein ligation. This chapter discusses the practical considerations of expressed protein ligation using selenopeptides and describes our optimized procedure for the semi-synthesis of selenos.

Generation of Protein-Phosphorodiamidate Morpholino Oligomer Conjugates for Efficient Cellular Delivery via Anthrax Protective Antigen

Phosphorodiamidate morpholino oligomers (PMOs) offer great promise as therapeutic agents for translation blocking or splice modulation due to their high stability and affinity for target sequences. However, in spite of their neutral charge as compared to natural oligonucleotides or phosphorothioate analogs, they still show little permeability for cellular membranes, highlighting the need for effective cytosolic delivery strategies. In addition, the implementation of strategies for efficient cellular targeting is highly desirable to minimize side effects and maximize the drug dose at its site of action. Anthrax toxin is a three-protein toxin of which the pore-forming protein anthrax protective antigen (PA) can be redirected to a receptor of choice and lethal factor (LF), one of the two substrate proteins, can be coupled to various cargoes for efficient cytosolic cargo delivery. In this protocol, we describe the steps to produce the proteins and protein conjugates required for cytosolic delivery of PMOs through the cation-selective pore generated by anthrax protective antigen. The method relies on the introduction of a unique cysteine at the C-terminal end of a truncated LF (aa 1-254), high-yield expression of the (truncated) toxin proteins in E. coli, functionalization of a PMO with a maleimide group and coupling of the maleimide-functionalized PMO to the unique cysteine on LF by maleimide-thiol conjugation chemistry. Through co-administration of PA with LF-PMO conjugates, an efficient cytosolic delivery of PMOs can be obtained.

Application of a New Dehydroascorbic Acid Reducing Agent in the Analysis of Vitamin C Content in Food

The analysis of total vitamin C content in food is most frequently performed by reducing dehydroascorbic acid to ascorbic acid, which is then assayed with the technique of high-performance liquid chromatography combined with spectrophotometric detection. Tris(2-carboxyethyl)phosphine is currently the only agent in use that efficiently reduces dehydroascorbic acid at pH < 2. Therefore, there is a continued need to search for new reducing agents that will display a high reactivity and stability in acidic solutions. The objective of the study was to verify the applicability of unithiol and tris(hydroxypropyl)phosphine for a reducing dehydroascorbic acid in an extraction medium with pH < 2. The conducted validation of the newly developed method of determining the total content of vitamin C using tris(hydroxypropyl)phosphine indicates its applicability for food analysis. The method allows obtaining equivalent results compared to the method based on the use of tris(2-carboxyethyl)phosphine. The low efficiency of dehydroascorbic acid reduction with the use of unithiol does not allow its application as a new reducing agent in vitamin C analysis.

ALISA: A microplate assay to measure protein thiol redox state

Measuring protein thiol redox state is central to understanding redox signalling in health and disease. The lack of a microplate assay to measure target specific protein thiol redox state rate-limits progress on accessibility grounds: redox proteomics is inaccessible to most. Developing a microplate assay is important for accelerating discovery by widening access to protein thiol redox biology. Beyond accessibility, enabling high throughput time- and cost-efficient microplate analysis is important. To meet the pressing need for a microplate assay to measure protein thiol redox state, we present the Antibody-Linked Oxi-State Assay (ALISA). ALISA uses a covalently bound capture antibody to bind a thiol-reactive fluorescent conjugated maleimide (F-MAL) decorated target. The capture antibody-target complex is labelled with an amine-reactive fluorescent N-hydroxysuccinimide ester (F-NHS) to report total protein. The covalent bonds that immobilise the capture antibody to the epoxy group functionalised microplate enable one to selectively elute the target. Target specific redox state is ratiometrically calculated as: F-MAL (i.e., reversible thiol oxidation)/F-NHS (i.e., total protein). After validating the assay principle (i.e., increased target specific reversible thiol oxidation increases the ratio), we used ALISA to determine whether fertilisation-a fundamental biological process-changes Akt, a serine/threonine protein kinase, specific reversible thiol oxidation. Fertilisation significantly decreases Akt specific reversible thiol oxidation in Xenopus laevis 2-cell zygotes compared to unfertilised eggs. ALISA is an accessible microplate assay to advance knowledge of protein thiol redox biology in health and disease.

Redox proteomic study of Bacillus cereus thiol proteome during fermentative anaerobic growth

Background

Bacillus cereus is a notorious foodborne pathogen, which can grow under anoxic conditions. Anoxic growth is supported by endogenous redox metabolism, for which the thiol redox proteome serves as an interface. Here, we studied the cysteine (Cys) proteome dynamics of B. cereus ATCC 14579 cells grown under fermentative anoxic conditions. We used a quantitative thiol trapping method combined with proteomics profiling.

Results

In total, we identified 153 reactive Cys residues in 117 proteins participating in various cellular processes and metabolic pathways, including translation, carbohydrate metabolism, and stress response. Of these reactive Cys, 72 were detected as reduced Cys. The B. cereus Cys proteome evolved during growth both in terms of the number of reduced Cys and the Cys-containing proteins identified, reflecting its growth-phase-dependence. Interestingly, the reduced status of the B. cereus thiol proteome increased during growth, concomitantly to the decrease of extracellular oxidoreduction potential.

Conclusions

Taken together, our data show that the B. cereus Cys proteome during unstressed fermentative anaerobic growth is a dynamic entity and provide an important foundation for future redox proteomic studies in B. cereus and other organisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07962-y.

Intein-based Design Expands Diversity of Selenocysteine Reporters

The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.

Isotope-Coded Maleimide Affinity Tags for Proteomics Applications

Isotope-coded affinity tags (ICATs) are valuable tools for mass spectrometry-based quantitative proteomics, in particular, for comparison of protein (cysteine-residue) thiol oxidation state in normal, stressed, and diseased tissue. However, the iodoacetamido electrophile used in most commercial ICATs suffers from poor thiol-selectivity and modest rates of adduct formation, which can lead to spurious results. Hence, we designed and synthesized three ICATs containing thiol-selective N-alkylmaleimide electrophiles (isotope-coded maleimide affinity tags = ICMATs) and assessed these as mass spectrometry probes for ratiometric analysis of lysozyme and muscle proteomes. Two ICMAT pairs containing butylene/D₈-butylene linkers were effective MS probes, but not ideal for typical proteomics workflows, because peptides bearing these tags frequently did not coelute with HPLC. A switch to a phenylene/¹³C₆-phenylene linker solved this issue without compromising the efficiency of adduct formation.

Live monitoring of plant redox and energy physiology with genetically encoded biosensors

Genetically encoded biosensors pave the way for understanding plant redox dynamics and energy metabolism on cellular and subcellular levels.

Measuring Reactive Sulfur Species and Thiol Oxidation States: Challenges and Cautions in Relation to Alkylation-Based Protocols

Significance: Redox biology is gaining ground in research related to human physiology (metabolism, signaling), pathophysiology (cancer, cardiovascular disease, neurodegeneration), and toxicology (radiation- or xenobiotic-induced damage). A major hurdle in advancing redox medicine is the current lack of understanding the mechanisms underpinning the observed detrimental or beneficial in vivo effects. To gain deeper insights into the underlying molecular pathways of redox regulation, we need to appreciate the strengths and limitations of the currently available methods. Recent Advances: Reactive sulfur species (RSS), including cysteine derivatives of peptides and proteins along with small molecules such as hydrogen sulfide or inorganic polysulfides, are major players in redox biology. RSS-mediated regulation of protein functions is a widely studied mechanism in the field, and considerable efforts have been devoted to the development of selective detection methods. Critical Issues: A large number of available methods rely on an alkylation step to freeze the dynamism of consecutive oxidation and reduction events among RSS at a particular time point inside the cell. This process uses the assumption that alkylation blocks all redox events instantaneously. We argue that unfortunately this is often not the case, which could have serious impacts on detected sulfur species speciation and confound experimental results. Future Directions: Novel technologies and prudent optimization of existing methods to accurately characterize the dynamic redox status of the thiol proteome as well as detailed understanding of regulatory and signaling capacities of protein polysulfidation are crucial to open new routes toward therapeutic interventions.

Analysis of Protein Oxidation in Food and Feed Products

Food and feed proteins are subject to oxidation reactions during production, processing, and storage. Several individual oxidized amino acids have been described in model systems and food; however, protein oxidation in food is still mostly assessed by the analysis of protein carbonylation. In the present review, the chemistry of protein oxidation and its implications for protein functionality, food flavor, and nutritional physiology are briefly summarized. Limitations of generic methods targeting redox-relevant functional groups and properties of typical reaction products, such as the determination of protein carbonyls and fluorescence spectroscopy, are presented. Methods for the quantitation of individual oxidation products of susceptible amino acids, such as cysteine, methionine, phenylalanine, tyrosine, and tryptophan, are reported. Special regard is paid to limitations resulting from the required hydrolysis procedures and unintended formation of the analytes during sample pretreatment. If available, results from food analysis obtained by different methods are compared. Suggestions and requirements for future works on protein oxidation in food and nutrition are given.

RP-HPLC method for simultaneous quantification of free and total thiol groups in native and heat aggregated whey proteins

Disulfide formation of whey proteins during heat treatment via thiol oxidation is important with regard to techno-functional properties. Due to the formation of other oxidation products than disulfides, the decrease in free thiol concentration is not proportional to the disulfide formation. Thus, in order to evaluate thiol reactivity and disulfide concentration both parameters are required. Currently applied methods focus mainly on the loss of free thiols using the spectrophotometric Ellman's assay. Next to that, we improved an existing RP-HPLC assay using the thiol reagent 4,4′-Dithiodipyridine (DTDP) to quantify free thiols as well as total (free thiols and disulfide bonds) thiols of native and heat-treated whey proteins. Thereby, the sample preparation technique, the sample handling, and the analysis technique were optimized. Thus, the paper provides a simple RP-HPLC method for quantification of thiol oxidation reactions to determine heat-induced changes in the structure of whey proteins. In addition, the method should be applicable to other protein systems due to the method validation by proteins of different amounts of free and total thiols in their structure.•

Simple RP-HPLC method for quantification of free and total thiols using 4,4′-Dithiodipyridine (DTDP).

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High recovery rates for free and total thiols.

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High stability within 24 h.

Redox signaling modulates Rho activity and tissue contractility in the Caenorhabditis elegans spermatheca

Actomyosin-based contractility in smooth muscle and nonmuscle cells is regulated by signaling through the small GTPase Rho and by calcium-activated pathways. We use the myoepithelial cells of the Caenorhabditis elegans spermatheca to study the mechanisms of coordinated myosin activation in vivo. Here, we show that redox signaling modulates RHO-1/Rho activity in this contractile tissue. Exogenously added as well as endogenously generated hydrogen peroxide decreases spermathecal contractility by inhibition of RHO-1, which depends on a conserved cysteine in its nucleotide binding site (C20). Further, we identify an endogenous gradient of H₂O₂ across the spermathecal tissue, which depends on the activity of cytosolic superoxide dismutase, SOD-1. Collectively, we show that SOD-1-mediated H₂O₂ production regulates the redox environment and fine tunes Rho activity across the spermatheca through oxidation of RHO-1 C20.

Introduction to approaches and tools for the evaluation of protein cysteine oxidation

Oxidative modifications of cysteine thiols in cellular proteins are pivotal to the way signal-stimulated reactive oxygen species are sensed and elicit appropriate or sometimes pathological responses, but the dynamic and often transitory nature of these modifications offer a challenge to the investigator trying to identify such sites and the responses they elicit. A number of reagents and workflows have been developed to identify proteins undergoing oxidation and to query the timing, extent and location of such modifications, as described in this minireview. While no approach is perfect to capture all the redox information in a functioning cell, best practices described herein can enable considerable insights into the "redox world" of cells and organisms.

Comparison of N-ethyl maleimide and N-(1-phenylethyl) maleimide for derivatization of biological thiols using liquid chromatography-mass spectrometry

The ratio between reduced and oxidized thiols, mainly glutathione and oxidized glutathione, is one of the biomarkers for the evaluation of oxidative stress. The accurate measurement of thiol concentrations is challenging because reduced thiols are easily oxidized during sample manipulation. Derivatization is commonly used to protect thiols from oxidation. The objective of this work was to systematically compare two cell-permeable derivatizing agents: N-ethyl maleimide (NEM) and (R)-(+)-N-(1-phenylethyl)maleimide (NPEM) in terms of derivatization efficiency, ionization enhancement, side product formation, reaction selectivity for thiols, pH dependence of the reaction, and derivative stability. All thiol measurements and the characterization of side products were performed using a biphenyl reversed phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Four thiols, cysteine (CYS), homocysteine, N-acetylcysteine (NAC), and glutathione (GSH), were used for the evaluation. Using 1:10 ratio of thiol:derivatizing agent, complete derivatization was obtained within 30 min for both agents tested with the exception of CYS-NEM, where 97% efficiency was obtained. The more hydrophobic NPEM provided better ionization of the thiols, with enhancement ranging from 2.1x for GSH to 5.7x for CYS in comparison to NEM. NPEM derivatization led to more extensive side reactions, such as double derivatization and ring opening, which hindered the accurate measurement of the thiol concentrations. Both NEM and NPEM also showed poor stability of CYS derivative due to its time-dependent conversion to cyclic cysteine-maleimide derivative. Both reagents also showed significant reactivity with amine-containing metabolites depending on the pH used during derivatization, but overall NEM was found to be more selective towards thiol group than NPEM. Taking into account all evaluation criteria, NEM was selected as a more suitable reagent for the thiol protection and derivatization, but strict control of pH 7.0 is recommended to minimize the side reactions. This work illustrates the importance of the characterization of side products and derivative stability during the evaluation of thiol derivatizing agents and contributes fundamental understanding to improve the accuracy of thiol determinations. The key sources of errors during maleimide derivatization include the derivatization of amine-containing metabolites, poor derivative stability of certain thiols (CYS and NAC), and the side reactions especially if ring opening of the reagent is not minimized. Graphical abstract.

Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein

To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.

Homogentisic acid affects human osteoblastic functionality by oxidative stress and alteration of the Wnt/β-catenin signaling pathway

Alkaptonuria (AKU) is a rare disease correlated with deficiency of the enzyme homogentisate 1,2 dioxygenase, which causes homogentisic acid (HGA) accumulation. HGA is subjected to oxidation/polymerization reactions, leading to the production of a peculiar melanin-like pigmentation (ochronosis) after chronic inflammation, which is considered as a triggering event for the generation of oxidative stress. Clinical manifestations of AKU are urine darkening, sclera pigmentation, early severe osteoarthropathy, and cardiovascular and renal complication. Despite major clinical manifestations of AKU being observed in the bones and skeleton, the molecular and functional parameters are so far unknown in AKU. In the present study, we used human osteoblasts supplemented with HGA as a AKU cellular model. We observed marked oxidative stress, and for the first time, we were able to correlate HGA deposition with an impairment in the Wnt/β-catenin signaling pathway, opening a range of possible therapeutic strategies for a disease still lacking a known cure.

Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation

Stimulation of plasma membrane receptor tyrosine kinases (RTKs), such as the epidermal growth factor receptor (EGFR), locally increases the abundance of reactive oxygen species (ROS). These ROS then oxidize cysteine residues in proteins to potentiate downstream signaling. Spatial confinement of ROS is an important regulatory mechanism of redox signaling that enables the stimulation of different RTKs to oxidize distinct sets of downstream proteins. To uncover additional mechanisms that specify cysteines that are redox regulated by EGF stimulation, we performed time-resolved quantification of the EGF-dependent oxidation of 4200 cysteine sites in A431 cells. Fifty-one percent of cysteines were statistically significantly oxidized by EGF stimulation. Furthermore, EGF induced three distinct spatiotemporal patterns of cysteine oxidation in functionally organized protein networks, consistent with the spatial confinement model. Unexpectedly, protein crystal structure analysis and molecular dynamics simulations indicated widespread redox regulation of cryptic cysteine residues that are solvent exposed only upon changes in protein conformation. Phosphorylation and increased flux of nucleotide substrates served as two distinct modes by which EGF specified the cryptic cysteine residues that became solvent exposed and redox regulated. Because proteins that are structurally regulated by different RTKs or cellular perturbations are largely unique, these findings suggest that solvent exposure and redox regulation of cryptic cysteine residues contextually delineate redox signaling networks.

Multiple Site-Specific Phosphorylation of IDPs Monitored by NMR

In line with their high accessibility, disordered proteins are exquisite targets of kinases. Eukaryotic organisms use the so-called intrinsically disordered proteins (IDPs) or intrinsically disordered regions of proteins (IDRs) as molecular switches carrying intracellular information tuned by reversible phosphorylation schemes. Solvent-exposed serines and threonines are abundant in IDPs, and, consistently, kinases often modify disordered regions of proteins at multiple sites. In this context, nuclear magnetic resonance (NMR) spectroscopy provides quantitative, residue-specific information that permits mapping of phosphosites and monitoring of their individual kinetics. Hence, NMR monitoring emerges as an in vitro approach, complementary to mass-spectrometry or immuno-blotting, to characterize IDP phosphorylation comprehensively. Here, we describe in detail generic protocols for carrying out NMR monitoring of IDP phosphorylation, and we provide a number of practical insights that improve handiness and reproducibility of this method.

Paradigm Shift in the Arena of Sample Preparation and Bioanalytical Approaches Involving Liquid Chromatography Mass Spectroscopic Technique

Sample preparation is a highly important and integral part of bioanalysis for cleaning up the complex biological matrices and thereby minimizing matrix effect. Matrix effect can jeopardize the precise quantification and adversely affect the reliability of liquid chromatography-mass spectrometry-based analytical results by alteration of analyte ionization. Matrix components result in suppression or enhancement of the intensity of analyte response. In spite of the high specificity and selectivity of tandem mass spectrometry, a relatively higher concentration of coeluted matrix elements present in biofluids may alter the efficiency of quantification of a bioanalytical method. Numerous literature reports different types of sample preparation techniques employed in bioanalysis. In this review, the strategies for selection of the appropriate sample clean-up technique in bioanalysis are discussed extensively. A paradigm shift in the arena of sample preparation and bioanalytical approaches involving the liquid chromatography-mass spectroscopic technique has been scrutinized. Current trends and possible future advancements in the field of biological sample extraction methods, including instrumental techniques are analyzed in detail.

Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes

The target of rapamycin (TOR) kinase is a master metabolic regulator with roles in nutritional sensing, protein translation, and autophagy. In Chlamydomonas reinhardtii, a unicellular green alga, TOR has been linked to the regulation of increased triacylglycerol (TAG) accumulation, suggesting that TOR or a downstream target(s) is responsible for the elusive “lipid switch” in control of increasing TAG accumulation under nutrient limitation. However, while TOR has been well characterized in mammalian systems, it is still poorly understood in photosynthetic systems, and little work has been done to show the role of oxidative signaling in TOR regulation. In this study, the TOR inhibitor AZD8055 was used to relate reversible thiol oxidation to the physiological changes seen under TOR inhibition, including increased TAG content. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 401 proteins were determined to have significant changes in oxidation following TOR inhibition. These oxidative changes mirrored characterized physiological modifications, supporting the role of reversible thiol oxidation in TOR regulation of TAG production, protein translation, carbohydrate catabolism, and photosynthesis through the use of reversible thiol oxidation. The delineation of redox-controlled proteins under TOR inhibition provides a framework for further characterization of the TOR pathway in photosynthetic eukaryotes.