Detection, identification, and quantification of oxidative protein modifications

Quantitative readout of methionine residue solvent accessibility in E. coli cells using radiolytic hydroxyl radical labeling and mass spectrometry

Reactive oxygen species play a crucial role in cellular processes, but their effects on protein structure and function in vivo remain challenging to study. Here, we present an approach using synchrotron-based X-ray footprinting methods to probe protein structure, via quantitative LC-coupled mass spectrometry of methionine oxidation (MSOx) in live E. coli. A label-free proteomic analysis identified 2104 proteins from E. coli, with 465 proteins exhibiting MSOx modifications distributed across multiple cellular compartments. Changes in MSOx modification with increasing X-ray dose revealed a correlation between rates of modification and solvent-accessible surface area in vivo for selected proteins responsive to exposure, providing a direct probe of protein structure and its conformational plasticity in the cell. The approach developed here offers a unique in-cell quantitative readout of methionine oxidation and solvent accessibility through radiolytic hydroxyl radical labeling. With this method, the landscape of methionine oxidation in E. coli can be mapped, providing insights into protein behavior under oxidative stress. It represents a first step in developing radiolysis and E. coli as platforms for in vivo protein structure assessment. The potential applications in drug discovery, protein engineering, and systems biology of protein conformations are considerable.

Oxidation products of proteins in plasma of newborns reflect damage inflicted by O2 supplementation and correlate with gestational age

Treatment of neonates, and especially preterm newborns, with supplementary O2, can result in oxidative stress and both short- and long-term health complications. Oxidation products formed on proteins, which are the principal targets of reactive species in plasma, can be used to assess damage arising from O2 therapy. We hypothesized that this may be particularly relevant for preterm neonates. Oxidation products formed on proteins in the plasma of term and preterm newborns were quantified to assess their possible use as biomarkers. Plasma samples from 114 term and preterm neonates with and without O2 supplementation (fraction of inspired oxygen, FiO2 > 21 % and 21 %, respectively) were analyzed. Total protein content and protein carbonyls were determined spectrophotometrically, whilst specific oxidation products from Tyr, Trp and Met were quantified using liquid chromatography coupled to mass detection (LC-MS). Kynurenine (Kyn), N-formylkynurenine (NFKyn), dihydroxydiphenylalanine (DOPA), 3-nitrotyrosine (3-NTyr), methionine sulfoxide (MetSO) and di-tyrosine (di-Tyr) were assessed in their protein-bound form. Alcohols, hydroperoxides and dimers of Trp were also investigated. Carbonyl groups, as well as 3-NTyr and MetSO, showed statistical differences between term and preterm neonates. However, only MetSO was sensitive to O2 supplementation in both term and preterm subjects. The plasma levels of these products showed an inverse association with gestational age. The advantages and limitations of these products as biomarkers of protein oxidation, and the experimental procedures needed to quantify these accurately, should be considered when designing future clinical investigations.

Research progress on the mechanism of curcumin anti-oxidative stress based on signaling pathway

Oxidative stress refers to an imbalance between oxidative capacity and antioxidant capacity, leading to oxidative damage to proteins, lipids, and DNA, which can result in cell senescence or death. It is closely associated with the occurrence and development of various diseases, including cardiovascular diseases, nephropathy, malignant tumors, neurodegenerative diseases, hypertension, diabetes, and inflammatory diseases. Curcumin is a natural polyphenol compound of β-diketone, which has a wide range of pharmacological activities such as anti-inflammatory, antibacterial, anti-oxidative stress, anti-tumor, anti-fibrosis, and hypolipidemic, demonstrating broad research and development value. It has a wide range of biological targets and can bind to various endogenous biomolecules. Additionally, it maintains the redox balance primarily by scavenging ROS, enhancing the activity of antioxidant enzymes, inhibiting lipid peroxidation, and chelating metal ions. This paper systematically describes the antioxidative stress mechanisms of curcumin from the perspective of signaling pathways, focusing on the Keap1-Nrf2/ARE, NF-κB, NOX, MAPK and other pathways. The study also discusses potential pathway targets and the complex crosstalk among these pathways, aiming to provide insights for further research on curcumin's antioxidant mechanisms and its clinical applications.

Quantitative analysis of the proteome and protein oxidative modifications in primary human coronary artery endothelial cells and associated extracellular matrix

Vascular endothelial cells (ECs) play a key role in physiology by controlling arterial contraction and relaxation, and molecular transport. EC dysfunction is associated with multiple pathologies. Here, we characterize the cellular and extracellular matrix (ECM) proteomes of primary human coronary artery ECs, from multiple donors, and oxidation/nitration products formed on these during cell culture, using liquid chromatography-mass spectrometry. In total ∼9900 proteins were identified in cells from 3 donors, with ∼7000 proteins per donor. Of these ∼5300 were consistently identified, indicating some heterogeneity across the donors, with age a possible cause. Multiple endogenous oxidation products were detected on both ECM and cellular proteins (and particularly endoplasmic reticulum species). In contrast, nitration was mostly detected on cell proteins and particularly cytoskeletal proteins, consistent with intracellular generation of nitrating agents, possibly from endothelial nitric oxide synthase (eNOS) or peroxidase enzymes. The modifications are ascribed to both physiological enzymatic activity (hydroxylation at proline/lysine; predominantly on ECM proteins and especially collagens) and the formation of reactive species (oxidation at tryptophan/tyrosine/histidine; nitration at tryptophan/tyrosine). The identified sites are present on a limited number of peptides (104 oxidized; 23 nitrated) from a modest number of proteins. A small number of proteins were detected with multiple modifications, consistent with these being selective and specific targets. Several nitrated peptides were consistently detected across all donors, and also in human smooth muscle cells suggesting that these are major targets in the vascular proteome. These data provide a 'background' proteome dataset for studies of endothelial dysfunction in disease.

To activate a G protein-coupled receptor permanently with cell surface photodynamic action in the gastrointestinal tract

Different from reversible agonist-stimulated receptor activation, singlet oxygen oxidation activates permanently G protein-coupled receptor (GPCR) cholecystokinin 1 (CCK1R) in type II photodynamic action, with soluble photosensitizer dyes (sulphonated aluminum phthalocyanine, λmax 675 nm) or genetically encoded protein photosensitizers (KillerRed λmax 585 nm; mini singlet oxygen generator λmax 450 nm), together with a pulse of light (37 mW/cm2, 1-2 minutes). Three lines of evidence shed light on the mechanism of GPCR activated by singlet oxygen (GPCR-ABSO): (1) CCK1R is quantitatively converted from dimer to monomer; (2) Transmembrane domain 3, a pharmacophore for permanent photodynamic CCK1R activation, can be transplanted to non-susceptible M3 acetylcholine receptor; and (3) Larger size of disordered region in intracellular loop 3 correlates with higher sensitivity to photodynamic CCK1R activation. GPCR-ABSO will add to the arsenal of engineered designer GPCR such as receptors activated solely by synthetic ligands and designer receptors exclusively activated by designer drugs, but show some clear advantages: Enhanced selectivity (double selectivity of localized photosensitizer and light illumination), long-lasting activation with no need for repeated drug administration, antagonist-binding site remains intact when needed, ease to apply to multiple GPCR. This type of permanent photodynamic activation may be applied to functional proteins other than GPCR.

Design of Benzyl-triazolopyrimidine-Based NADPH Oxidase Inhibitors Leads to the Discovery of a Potent Dual Covalent NOX2/MAOB Inhibitor

NADPH oxidases (NOXs) are enzymes dedicated to reactive oxygen species (ROS) production and are implicated in cancer, neuroinflammation, and neurodegenerative diseases. VAS2870 is a covalent inhibitor of mainly NOX2 and NOX5. It alkylates a conserved active-site cysteine, blocking productive substrate binding. To enhance potency and selectivity toward NOXs, we conducted some chemical modifications, leading to the discovery of compound 9a that preferentially inhibits NOX2 with an IC50 of 0.155 μM, and only upon its preactivation. We found that 9a, bearing a pargyline moiety, is also able to selectively inhibit MAOB over MAOA (465-fold) with an IC50 of 0.182 μM, being the first-in-class dual NOX2/MAOB covalent inhibitor. Tested in the BV2 microglia neuroinflammation model, 9a decreased ROS production and downregulated proinflammatory cytokines as iNOS, IL-1β, and IL-6 expression more efficiently than the single target inhibitors (rasagiline for MAOB and VAS2870 for NOXs) but also, more importantly, than their combination.

Salivary effector SfPDI modulates plant defense responses to enhance foraging efficiency of Spodoptera frugiperda

Research on the interactions between herbivorous insects and plants, facilitated by insect secretions, has increasingly emphasized species with chewing mandibles over time. However, the molecular mechanisms underlying the interaction between Spodoptera frugiperda and plants remain poorly understood. In this study, we identified a protein disulfide isomerase (SfPDI) from the salivary glands of S. frugiperda that regulates the interaction between S. frugiperda and plants. We found that SfPDI is highly expressed in the salivary glands of S. frugiperda and is secreted into plants as a secretory protein. The RNAi revealed that SfPDI contributes to the growth and development of S. frugiperda on host plants, while its overexpression in tobacco induces necrosis in tobacco leaves and triggers a burst of reactive oxygen species (ROS). Differentially expressed genes suggested that SfPDI may suppresses the expression of plant JA by positively regulating MYC2 and TIFYs and negatively regulating WRKYs. Notably, SfPDI may modulate these high expression of receptors (NB-LRR, GL-RLK, and RLK) lead to hypersensitive response (HR) cell death and the accumulation of lignification of plant. This study provides a foundation for further exploring insect-plant interaction mechanisms and a theoretical basis for developing insect-resistant germplasm and environmentally friendly pest control strategies.

Discrete Hybrid Vanadium-oxo Cluster as a Targeted Tool for Selective Protein Oxidative Modifications and Cleavage

Understanding the impact of oxidative modification on protein structure and functions is essential for developing therapeutic strategies to combat macromolecular damage and cell death. However, selectively inducing oxidative modifications in proteins under physiological conditions remains challenging. Herein we demonstrate that [V6O13{(OCH2)3CCH2OH}2]2- (V6-OH) hybrid metal-oxo cluster can be used for selective protein oxidative cleavage and modifications. We present the first example of a protein-bound hybrid vanadate cluster, where its interactions with protein surfaces and the redox activity of vanadium enable selective oxidative modifications. Single Crystal X-ray Diffraction (SC-XRD) of the V6-OH and hen egg white lysozyme (HEWL) complex revealed that the binding is dictated both by the inorganic core and the organic ligands attached to it. Selective oxidation or cleavage of HEWL occurs under physiological conditions by producing reactive oxygen species (ROS) in presence of ascorbate (Asc) as a reducing agent. The outcome of the oxidative reaction can be tuned by varying the concentration of V6-OH to result either in selective oxidation of the amino acid side chains or peptide bond cleavage. LC-MS and crystallography revealed that oxidative modifications were mainly concentrated near the cluster binding sites, providing spatial control of ROS production. This study advances our understanding of vanadium's role in biological systems and demonstrates the potential of hybrid metal-oxo clusters in protein modification.

Polyphenol autoxidation and prooxidative activity induce protein oxidation and protein-polyphenol adduct formation in model systems

Polyphenols are well-known for their antioxidant properties, but their prooxidative activity remain less understood. This study quantitatively examined the formation of hydrogen peroxide (H2O2) during the autooxidation of nine different polyphenols in model systems, investigating how it impacts protein oxidation and protein-polyphenol covalent adduct formation. Polyphenols (4 mM) generated H2O2 in the range of 0.2-242 μM, depending on type of polyphenol, incubation time, temperature, and pH, but no clear relationship between polyphenol structure and H2O2 production was observed. The presence of free amino acids and proteins (bovine serum albumin and β-lactoglobulin) inhibited H2O2 formation, with Cys completely scavenging H2O2. Met was highly susceptible to oxidation with a 25-75% loss, forming methionine sulfoxide through a two-electron oxidation pathway. Trp and Tyr were oxidized to produce dioxindolyl-ʟ-alanine, kynurenine, 3,4-dihydroxyphenylalanine, N'-formylkynurenine, and 5-hydroxytryptophan in the nmol/mol-mmol/mol amino acid range. Furthermore, autoxidation of polyphenols resulted in >177 distinct amino acid/protein-polyphenol adducts as identified using LC-Orbitrap-MS/MS analysis.

Unravelling the Structure of One-Electron Oxidation Products of Model Peptide Backbones Containing Methionine by IRMPD Spectroscopy: The Effect of the Neighbouring Groups

A series of Methionine (Met) derivatives, where either the amino group and/or the carboxylic acid group is blocked by acetyl and/or methyl ester functionalities, has been investigated by Collision Induced Dissociation-tandem mass spectrometry (CID-MS2) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. The CID-MS2 experiments were performed using a Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization (ESI) source. The IRMPD spectra were recorded employing a Paul type ion-trap coupled with the free-electron laser (FEL) FELIX in the fingerprint region from 600 to 2000 cm-1. We show that the oxidation of the methionine residue with protected terminal groups induces the formation of a sulfoxide function. However, compared to the IRMPD spectrum of protonated methionine and methionine sulfoxide, significant spectral differences are observed in the spectra of model protected peptide backbones containing methionine. DFT calculations show that protonation occurs on the sulfoxide group in the gas phase for these model peptide backbones containing methionine, shifting the diagnostic signature of the sulfoxide group from 1000 to 862 cm-1.

Relationship Between Brain Insulin Resistance, Carbohydrate Consumption, and Protein Carbonyls, and the Link Between Peripheral Insulin Resistance, Fat Consumption, and Malondialdehyde

The consumption of a high-fat (HFD) or high-carbohydrate/low-fat (LFD) diet is related to insulin resistance; however, central and peripheral alterations can occur independently. In this study, the timeline of insulin resistance was determined while taking into consideration the role of diet in oxidative damage. Background/Objectives: The aim of this study was to ascertain whether a HFD or LFD induces peripheral insulin resistance (PIR) before brain insulin resistance (BIR), and whether the timing of these alterations correlates with heightened oxidative damage markers in plasma, adipose tissue, and the cerebral cortex. Methodology and Results: Three-month-old C57BL/6 male mice were fed with a HFD, LFD, or standard diet for 1, 2, or 3 months. Glucose and insulin tolerance tests were performed to determine PIR, and the hypothalamic thermogenic response to insulin was used to determine their BIR status. For oxidative damage, the levels of malondialdehyde (MDA) and the protein carbonyl group (PCO) and the enzymatic activity of glutathione peroxidase (GSH-Px) were evaluated in plasma, white adipose tissue, brown adipose tissue, and the cerebral cortex. PIR occurred at 3 months of the HFD, but MDA levels in the white adipose tissue increased at 2 months. BIR occurred at 1 and 2 months of the LFD, but the enzymatic activity of GSH-Px was lower at 1 month and the amount of the PCO increased at 2 months. Conclusions: The intake of a HFD or LFD of different durations can influence the establishment of PIR or BIR, and oxidative damage in the fat tissue and cerebral cortex can play an important role.

Reactive oxygen species-mediated signal transduction and utilization strategies in microalgae

Reactive oxygen species (ROS) are crucial in stress perception, the integration of environmental signals, and the activation of downstream response networks. This review emphasizes ROS-mediated signaling pathways in microalgae and presents an overview of strategies for leveraging ROS. Eight distinct signaling pathways mediated by ROS in microalgae have been summarized, including the calcium signaling pathway, the target of rapamycin signaling pathway, the mitogen-activated protein kinase signaling pathway, the cyclic adenosine monophosphate/protein kinase A signaling pathway, the ubiquitin/protease pathway, the ROS-regulated transcription factors and enzymes, the endoplasmic reticulum stress, and the retrograde ROS signaling. Moreover, this review outlines three strategies for utilizing ROS: two-stage cultivation, combined stress with phytohormones, and strain engineering. The physicochemical properties of various ROS, together with their redox reactions with downstream targets, have been elucidated to reveal the role of ROS in signal transduction processes while delineating the ROS-mediated signal transduction network within microalgae.

Molecular characterization, transcriptional profiling, and antioxidant activity assessment of nucleoredoxin (NXN) as a novel member of thioredoxin from red-lip mullet (Planiliza haematocheilus)

Nucleoredoxin (NXN) is a prominent oxidoreductase enzyme, classified under the thioredoxin family, and plays a pivotal role in regulating cellular redox homeostasis. Although the functional characterization of NXN has been extensively studied in mammals, its role in fish remains relatively unexplored. In this study, the NXN gene from Planiliza haematocheilus (PhNXN) was molecularly and functionally characterized using in silico tools, expression analyses, and in vitro assays. The predicted protein sequence of PhNXN contained 418 amino acids with an anticipated molecular mass of 47.53 kDa. It comprised a highly conserved 188CPPC191 catalytic motif in the central NXN domain and two thioredoxin-like domains enriched with conserved Cys residues. PhNXN protein was primarily localized in the cytoplasm and nucleus of the cells. The spatial and temporal expression analyses of PhNXN mRNA showed the highest expression level in the brain under normal physiological conditions, while a significant modulation was detected in the blood and head kidney following immunostimulation with polyinosinic: polycytidylic acid, lipopolysaccharides, and Lactococcus garvieae. Recombinant PhNXN protein exhibited DPPH radical scavenging, thiol-dependent disulfide reduction, and cupric ion reduction activities. Additionally, PhNXN overexpression significantly suppressed oxidative stress-induced cell death, heavy metal cation-induced reactive oxygen species production, and viral hemorrhagic septicemia virus-induced cellular apoptosis in fish cells. Furthermore, PhNXN overexpression in RAW 264.7 cells demonstrated notable nitric oxide scavenging activity, M2-type polarization, and anti-inflammatory effect. Collectively, the overall findings of the study highlight the antioxidant and immunological functions of PhNXN in red-lip mullet.

Human health risk assessment by exposure to contaminants from an urban reservoir: a pilot study in the Madin Dam (México)

Water contamination greatly impacts human health. The Metropolitan Area of the Valley of Mexico (MAVM) is one of the most densely inhabited and polluted places globally, with a significant problem being the rising water demand. The research aims to assess the impact of metals such as iron, aluminum, lead, cadmium, and total chromium, among others, in the water of the Madin Dam, a key reservoir in the area's water supply. The assessment concentrated on individuals who were in good health and had been exposed to these pollutants. It analyzed factors such as levels of oxidized proteins; changes in the function of antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase); and their genetic expression, the occurrence of micronuclei, and the amount of DNA methylation. The findings were linked to the metals present in the MAVM drinking water, and the risk was evaluated. The research included four groups: two associated with the Madin Dam, consisting of persons living nearby or using water from the reservoir, and two acting as a control. The study highlighted a significant link between long-term exposure to pollutants in drinking water and elevated levels of oxidized proteins, increased micronuclei frequency, changes in antioxidant enzyme activity and gene expression, and a higher percentage of 5-methylcytosine. The risk assessment showed that people who use drinking water and/or consume fish from Madin Dam have a potential higher risk associated with metal contamination.

Exploring Strategies to Prevent and Treat Ovarian Cancer in Terms of Oxidative Stress and Antioxidants

Oxidative stress is a state of imbalance between the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) and the antioxidant defence system in the body. Oxidative stress may be associated with a variety of diseases, such as ovarian cancer, diabetes mellitus, and neurodegeneration. The generation of oxidative stress in ovarian cancer, one of the common and refractory malignancies among gynaecological tumours, may be associated with several factors. On the one hand, the increased metabolism of ovarian cancer cells can lead to the increased production of ROS, and on the other hand, the impaired antioxidant defence system of ovarian cancer cells is not able to effectively scavenge the excessive ROS. In addition, chemotherapy and radiotherapy may elevate the oxidative stress in ovarian cancer cells. Oxidative stress can cause oxidative damage, promote the development of ovarian cancer, and even result in drug resistance. Therefore, studying oxidative stress in ovarian cancer is important for the prevention and treatment of ovarian cancer. Antioxidants, important markers of oxidative stress, might serve as one of the strategies for preventing and treating ovarian cancer. In this review, we will discuss the complex relationship between oxidative stress and ovarian cancer, as well as the role and therapeutic potential of antioxidants in ovarian cancer, thus guiding future research and clinical interventions.

Protein oxidation: The effect of different preservation methods or phenolic additives during chilled and frozen storage of meat/meat products

Lipid and protein oxidation have significant effects on the shelf-life and nutritional value of meat and meat products. While lipid oxidation has been extensively studied, it has been recognized that proteins are also susceptible to oxidation. However, the precise mechanisms of oxygen-induced amino acid and protein modifications in the food matrix remain unclear. This review comprehensively explores the impact of various preservation techniques, including high hydrostatic pressure (HHP), irradiation (IR), and modified atmosphere packaging (MAP), on protein oxidation during chilled or frozen storage of meat products. While these techniques have shown promising results in extending shelf-life, their effects on protein oxidation are dose-dependent and must be carefully controlled to maintain product quality. Preservation techniques involving the use of phenolic additives have demonstrated synergistic effects in mitigating protein oxidation during storage. Notably, natural phenolic additives have shown comparable efficacy compared to artificial antioxidants. Additionally, incorporating phenolic additives into bio-edible films has shown promise in combating protein oxidation.

Hidden route of protein damage through oxygen-confined photooxidation

Oxidative modifications can disrupt protein folds and functions, and are strongly associated with human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), which primarily attack the protein surface. Yet, it remains unclear whether and how internal protein folds capable of trapping oxygen (O2) contribute to oxidative damage. Here, we report a hidden pathway of protein damage, which we refer to as O2-confined photooxidation. In this process, O2 is captured in protein cavities and subsequently converted into multiple ROS, primarily mediated by tryptophan residues under blue light irradiation. The generated ROS then attack the protein interior through constrained diffusion, causing protein damage. The effects of this photooxidative reaction appear to be extensive, impacting a wide range of cellular proteins, as supported by whole-cell proteomic analysis. This photooxidative mechanism may represent a latent oxidation pathway in human tissues directly exposed to visible light, such as skin and eyes.

Facts, Dogmas, and Unknowns About Mitochondrial Reactive Oxygen Species in Cancer

Cancer metabolism is sustained both by enhanced aerobic glycolysis, characteristic of the Warburg phenotype, and oxidative metabolism. Cell survival and proliferation depends on a dynamic equilibrium between mitochondrial function and glycolysis, which is heterogeneous between tumors and even within the same tumor. During oxidative phosphorylation, electrons from NADH and FADH2 originated in the tricarboxylic acid cycle flow through complexes of the electron transport chain. Single electron leaks at specific complexes of the electron transport chain generate reactive oxygen species (ROS). ROS are a concentration-dependent double-edged sword that plays multifaceted roles in cancer metabolism. ROS serve either as signaling molecules favoring cellular homeostasis and proliferation or damage DNA, protein and lipids, causing cell death. Several aspects of ROS biology still remain unsolved. Among the unknowns are the actual levels at which ROS become cytotoxic and if toxicity depends on specific ROS species or if it is caused by a cumulative effect of all of them. In this review, we describe mechanisms of mitochondrial ROS production, detoxification, ROS-induced cytotoxicity, and the use of antioxidants in cancer treatment. We also provide updated information about critical questions on the biology of ROS on cancer metabolism and discuss dogmas that lack adequate experimental demonstration. Overall, this review brings a comprehensive perspective of ROS as drivers of cancer progression, inducers of cell death, and the potential use of antioxidants as anticancer therapy.

Role of Polyphosphate as an Inorganic Chaperone to Prevent Protein Aggregation Under Copper Stress in Saccharolobus solfataricus

Polyphosphates are biopolymers composed of phosphate monomers linked by high-energy phosphoanhydride bonds. They are present across all life domains, serving as a source of energy, metal chelators, and playing a crucial role in stress defense. In Escherichia coli, polyphosphates also function as inorganic molecular chaperones. The present study aims to investigate whether polyphosphate serves a similar chaperone function in archaea, using Saccharolobus solfataricus as a model organism. To this end, polyphosphate was extracted and quantified, the ADP/ATP ratio was determined, insoluble protein extracts were analyzed at different time points after copper exposure, and qPCR was performed to measure the expression of stress-related genes. PolyP was extracted after exposing the archaeon S. solfataricus to different copper concentrations. We determined that polyP degradation is directly correlated with metal concentration. At the minimum inhibitory concentration (MIC) of 2 mM Cu2+, polyP degradation stabilized 2 h after exposure and showed no recovery even after 24 h. The ADP/ATP ratio was measured and showed differences in the presence or absence of polyP. The analysis of proteins precipitated under copper stress showed a higher proportion of insoluble proteins at an elevated metal concentration. On the other hand, increased protein precipitation was detected in the absence of polyP. Gene expression analysis via qPCR was conducted to assess the expression of genes involved in chaperone and chaperonin production, copper resistance, oxidative stress response, and phosphate metabolism under prolonged copper exposure, both in the presence and absence of polyP. The results indicated an upregulation of all the chaperonins measured in the presence of polyP. Interestingly, just some of these genes were upregulated in polyP's absence. Despite copper stress, there was no upregulation of superoxide dismutase in our conditions. These results highlight the role of polyP in the copper stress response in S. solfataricus, particularly to prevent protein precipitation, likely due to its function as an inorganic chaperone. Additionally, the observed protein precipitation could be attributable to interactions between copper and some amino acids on the protein structures rather than oxidative stress induced by copper exposure, as previously described in E. coli. Our present findings provide new insights into the protective role of polyP as an inorganic chaperone in S. solfataricus and emphasize its importance in maintaining cellular homeostasis under metal stress conditions.

Lactobionic acid modified cobalt coordination polymer-coated peroxymonosulfate nanoparticles generate sulfate/hydroxy dual-radicals for targeted cancer therapy

Free radical therapy, based on the sulfate radical derived from peroxymonosulfate, has recently been explored as a potential cancer treatment. However, while it is promising, its successful application is restricted by several limitations including the uncontrollable generation of free radicals and the instability in aqueous medium. Herein, we prepared LCP nanoparticles by using PMS as a core, the Co-coordination polymer (Co-CP) as a coating layer, and lactobionic acid as a targeting ligand for hepatoma carcinoma cells. LCP could be activated by cobalt ions released from Co-CP, and successfully induced apoptosis and ferroptosis via the inhibition of glutathione peroxidase 4 and caused the accumulation of lipid peroxidation to enhance the efficacy of free radical therapy.

Reactive oxygen species and oxidative stress in acute pancreatitis: Pathogenesis and new therapeutic interventions

Acute pancreatitis (AP) is a common acute gastrointestinal disorder affecting approximately 20% of patients with systemic inflammatory responses that may cause pancreatic and peripancreatic fat necrosis. This condition often progresses to multiple organ failure, significantly increasing morbidity and mortality. Oxidative stress, characterized by an imbalance between the body's reactive oxygen species (ROS) and antioxidants, activates the inflammatory signaling pathways. Although the pathogenesis of AP is not fully understood, ROS are increasingly recognized as critical in the disease's progression and development. Modulating the oxidative stress pathway has shown efficacy in mitigating the progression of AP. Despite numerous basic studies examining this pathway, comprehensive reviews of recent research remain sparse. This systematic review offers an in-depth examination of the critical role of oxidative stress in the pathogenesis and progression of AP and evaluates the therapeutic potential of antioxidant interventions in its management.

Polyphenols for stroke therapy: the role of oxidative stress regulation

Stroke is associated with a high incidence and disability rate, which seriously endangers human health. Oxidative stress (OS) plays a crucial role in the underlying pathologic progression of cerebral damage in stroke. Emerging experimental studies suggest that polyphenols have antioxidant potential and express protective effects after different types of strokes, but no breakthrough has been achieved in clinical studies. Nanomaterials, due to small characteristic sizes, can be used to deliver drugs, and have shown excellent performance in the treatment of various diseases. The drug delivery capability of nanomaterials has significant implications for the clinical translation and application of polyphenols. This comprehensive review introduces the mechanism of oxidative stress in stroke, and also summarizes the antioxidant effects of polyphenols on reactive oxygen species generation and oxidative stress after stroke. Also, the application characteristics and research progress of nanomaterials in the treatment of stroke with antioxidants are presented.

A glutamine metabolic switch supports erythropoiesis

Metabolic requirements vary during development, and our understanding of how metabolic activity influences cell specialization is incomplete. Here, we describe a switch from glutamine catabolism to synthesis required for erythroid cell maturation. Glutamine synthetase (GS), one of the oldest functioning genes in evolution, is activated during erythroid maturation to detoxify ammonium generated from heme biosynthesis, which is up-regulated to support hemoglobin production. Loss of GS in mouse erythroid precursors caused ammonium accumulation and oxidative stress, impairing erythroid maturation and recovery from anemia. In β-thalassemia, GS activity is inhibited by protein oxidation, leading to glutamate and ammonium accumulation, whereas enhancing GS activity alleviates the metabolic and pathological defects. Our findings identify an evolutionarily conserved metabolic adaptation that could potentially be leveraged to treat common red blood cell disorders.

Influence of photobiomodulation and radiofrequency on the healing of pressure lesions in mice

The objective of this study was to ascertain the impact of photobiomodulation and radiofrequency on the healing of pressure injuries in mice. A total of 70 animals were randomly assigned to seven experimental groups. A pressure injury was induced in the dorsal region of the mice by the application of two magnets. The photobiomodulation treatment was administered at a dosage of 3.6 J per session. In the radiofrequency group, the treatment time was four minutes and the power was 22 watts. The analyses included the lesion area, infrared thermography, and the collection of material for cytokine, histological, and histochemical analyses following euthanasia. In the macroscopic analyses, the 660 nm photobiomodulation group demonstrated superior outcomes in comparison to the control group. With regard to the microscopic analyses, the greatest difference between the groups was observed when TNF-α was evaluated in the photobiomodulation group. It can be observed that the groups irradiated by electrophysical means (i.e., a combination of radiofrequency with PBM 830 nm-660 nm) exhibited a positive influence on the repair process, with the greatest impact observed in the group irradiated by a combination of radiofrequency and 660 nm photobiomodulation.

Redox regulation of proteostasis

Oxidants produced through endogenous metabolism or encountered in the environment react directly with reactive sites in biological macromolecules. Many proteins, in particular, are susceptible to oxidative damage, which can lead to their altered structure and function. Such structural and functional changes trigger a cascade of events that influence key components of the proteostasis network. Here, we highlight recent advances in our understanding of how cells respond to the challenges of protein folding and metabolic alterations that occur during oxidative stress. Immediately after an oxidative insult, cells selectively block the translation of most new proteins and shift molecular chaperones from folding to a holding role to prevent wholesale protein aggregation. At the same time, adaptive responses in gene expression are induced, allowing for increased expression of antioxidant enzymes, enzymes that carry out the reduction of oxidized proteins, and molecular chaperones, all of which serve to mitigate oxidative damage and rebalance proteostasis. Likewise, concomitant activation of protein clearance mechanisms, namely proteasomal degradation and particular autophagic pathways, promotes the degradation of irreparably damaged proteins. As oxidative stress is associated with inflammation, aging, and numerous age-related disorders, the molecular events described herein are therefore major determinants of health and disease.

Focused starvation of tumor cells using glucose oxidase: A comprehensive review

Starvation therapy targets the high metabolic demand of tumor cells. It primarily leans over the consumption of intracellular glucose and simultaneous blockade of alternative metabolic pathways. The strategy involves the use of glucose oxidase (GOx) for catalyzing the conversion of glucose into gluconic acid and hydrogen peroxide. Under these conditions, metabolic re-programming of tumor cells enables the utilization of substrates such as amino acids, fatty acids and lipids. This can be overcome by co-administration of chemo-, photo- and immuno-therapeutics together with glucose oxidase. Targeted delivery of glucose oxidase at tumor site can be enabled with the use of nanoformulations. In this review, we highlight that the outcomes of starvation therapy can be improved using rationally developed nano-formulations. It is possible to load synergistically acting bioactives in these formulations and deliver in site-specific manner and hence achieve the elimination of tumors cells with greater efficacy.

Half-Curcumin-Based Chemiluminescence Probes and Their Applications in Detecting Quasi-Stable Oxidized Proteins

Numerous methods have been reported for detecting ROS/RNS in vitro and in vivo; however, detecting methods for the secondary products of the reactive oxygen species (ROS)/reactive nitrogen species (RNS) reactions, particularly quasi-stable oxidized products, have been much less explored. In this report, we observed that half-curcumins could generate chemiluminescence (CL). In contrast to other chemiluminescence scaffolds, the distinguishing feature of a half-curcumin is the formation of a carbanion intermediate of its acetylacetone moiety, opening unique avenues for applications. In this study, we designed a series of half-curcumins CRANAD-Xs and found that CRANAD-164 could be used to detect quasi-stable oxidized proteins (QSOP) in vivo and in patient serum samples. We illustrated that CRANAD-164 could be used to monitor the responses of taurine, an amino acid with newly reported anti-aging capacity, in an inflammatory mouse model. Remarkably, we further demonstrated that the QSOP levels were much higher in the disease serum samples, including Alzheimer's disease (AD), compared to the samples from healthy controls. Moreover, our results revealed that the sera chemiluminescence intensities were higher in aged healthy controls compared to young healthy subjects, suggesting that CRANAD-164 can be used to monitor the increase of QSOP during aging.

Redox system and ROS-related disorders in peroxisomes

Peroxisomes are essential organelles that help mitigate the oxidative damage caused by reactive oxygen species (ROS) through their antioxidant systems. They perform functions such as α-oxidation, β-oxidation, and the synthesis of cholesterol and ether phospholipids. During the breakdown of specific metabolites, peroxisomes generate ROS as byproducts, which can either be neutralized or contribute to oxidative stress. The relationship between peroxisomal metabolism and ROS-related disorders, including neurodegenerative diseases and cancers, has been studied for decades; however, the exact mechanisms remain unclear. Our review will provide recent insights into the peroxisomal redox system and its association with oxidative stress-related diseases.

Modulation of pulsed electric field induced oxidative processes in protein solutions by pro- and antioxidants sensed by biochemiluminescence

Technologies based on pulsed electric field (PEF) are increasingly pervasive in medical and industrial applications. However, the detailed understanding of how PEF acts on biosamples including proteins at the molecular level is missing. There are indications that PEF might act on biomolecules via electrogenerated reactive oxygen species (ROS). However, it is unclear how this action is modulated by the pro- and antioxidants, which are naturally present components of biosamples. This knowledge gap is often due to insufficient sensitivity of the conventionally utilized detection assays. To overcome this limitation, here we employed an endogenous (bio)chemiluminescence sensing platform, which enables sensitive detection of PEF-generated ROS and oxidative processes in proteins, to inspect effects of pro-and antioxidants. Taking bovine serum albumin (BSA) as a model protein, we found that the chemiluminescence signal arising from its solution is greatly enhanced in the presence ofH 2 O 2 as a prooxidant, especially during PEF treatment. In contrast, the chemiluminescence signal decreases in the presence of antioxidant enzymes (catalase, superoxide dismutase), indicating the involvement of bothH 2 O 2 and electrogenerated superoxide anion in oxidation-reporting chemiluminescence signal before, during, and after PEF treatment. We also performed additional biochemical and biophysical assays, which confirmed that BSA underwent structural changes afterH 2 O 2 treatment, with PEF having only a minor effect. We proposed a scheme describing the reactions leading from interfacial charge transfer at the anode by which ROS are generated to the actual photon emission. Results of our work help to elucidate the mechanisms of action of PEF on proteins via electrogenerated reactive oxygen species and open up new avenues for the application of PEF technology. The developed chemiluminescence technique enables label-free, in-situ and non-destructive sensing of interactions between ROS and proteins. The technique may be applied to study oxidative damage of other classes of biomolecules such as lipids, nucleic acids or carbohydrates.

The Zea mays PeptideAtlas: A New Maize Community Resource

This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds and many sample types and experimental conditions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq, and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of proteins in the most recent B73 nuclear genome annotation. Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other B73 genome annotations will improve maize genome annotation. We also illustrate the high-confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, and K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical, and biological metadata. This new PeptideAtlas is integrated in MaizeGDB with a peptide track in JBrowse.

Alginate oligosaccharide supplementation improves boar semen quality under heat stress

Heat stress is a serious problem that affects animal husbandry by reducing growth and reproductive performance of animals. Adding plant extracts to the diet is an effective way to help overcome this problem. Alginate oligosaccharide (AOS) is a natural non-toxic antioxidant with multiple biological activities. This study analyzed the potential mechanism of AOS in alleviating heat stress and improving semen quality in boars through a combination of multiple omics tools. The results indicated that AOS could significantly increase sperm motility (P < 0.001) and sperm concentration (P < 0.05). At the same time, AOS improved the antioxidant capacity of blood and semen, and increased blood testosterone (P < 0.05) level. AOS could improve the metabolites in sperm, change the composition of gut microbiota, increase the relative abundance of beneficial bacteria such as Pseudomonas (P < 0.01), Escherichia-Shigella (P < 0.05), Bifidobacterium (P < 0.01), reduce the relative abundance of harmful bacteria such as Prevotella_9 (P < 0.05), Prevotellaceae_UCG-001 (P < 0.01), and increase the content of short chain fatty acids. Proteomic results showed that AOS increased proteins related to spermatogenesis, while decreasing heat shock protein 70 (P < 0.05) and heat shock protein 90 (P < 0.01). These results were verified using immunofluorescence staining technology. There was a good correlation among sperm quality, sperm metabolome, sperm proteome, and gut microbiota. In conclusion, AOS can be used as a feed additive to increase the semen quality of boars to enhance reproductive performance under heat stress.

Oxidative stress and aging: synergies for age related diseases

Aging is characterized by a progressive decline in physiological function and underlies several disabilities, including the increased sensitivity of cells and tissues to undergo pathological oxidative stress. In recent years, efforts have been made to better understand the relationship between age and oxidative stress and further develop therapeutic strategies to minimize the impact of both events on age-related diseases. In this work, we review the impact of the oxidant and antioxidant systems during aging and disease development and discuss the crosstalk of oxidative stress and other aging processes, with a focus on studies conducted in elderly populations.

Redox-dependent plasticity of oxMIF facilitates its interaction with CD74 and therapeutic antibodies

MIF is a ubiquitous protein involved in proinflammatory processes, which undergoes an oxidation-driven conformational change to oxidized (ox)MIF. We demonstrate that hypochlorous acid, produced by neutrophil-released myeloperoxidase (MPO) under inflammatory conditions, effectively oxidizes MIF into the oxMIF isoform, which is specifically recognized by the anti-oxMIF therapeutic antibody, ON104. NMR investigation of MIF oxidized by the MPO system revealed increased flexibility throughout the MIF structure, including at several catalytic and allosteric sites. Mass spectrometry of MPO-oxMIF revealed methionines as the primary site of oxidation, whereas Pro2 and Tyr99/100 remained almost unmodified. ELISA, SPR and cell-based assays demonstrated that structural changes caused by MPO-driven oxidation promoted binding of oxMIF to its receptor, CD74, which does not occur with native MIF. These data reveal the environment and modifications that facilitate interactions between MIF and its pro-inflammatory receptor, and a route for therapeutic intervention targeting the oxMIF isoform.

Fundamentals of redox regulation in biology

Oxidation-reduction (redox) reactions are central to the existence of life. Reactive species of oxygen, nitrogen and sulfur mediate redox control of a wide range of essential cellular processes. Yet, excessive levels of oxidants are associated with ageing and many diseases, including cardiological and neurodegenerative diseases, and cancer. Hence, maintaining the fine-tuned steady-state balance of reactive species production and removal is essential. Here, we discuss new insights into the dynamic maintenance of redox homeostasis (that is, redox homeodynamics) and the principles underlying biological redox organization, termed the 'redox code'. We survey how redox changes result in stress responses by hormesis mechanisms, and how the lifelong cumulative exposure to environmental agents, termed the 'exposome', is communicated to cells through redox signals. Better understanding of the molecular and cellular basis of redox biology will guide novel redox medicine approaches aimed at preventing and treating diseases associated with disturbed redox regulation.

Effects of stannous fluoride dentifrice on gingival health and oxidative stress markers: a prospective clinical trial

BACKGROUND

Periodontal disease results in oral dysbiosis, increasing plaque virulence and oxidative stress. Stannous fluoride (SnF2) binds lipopolysaccharides to reduce plaque virulence. This study prospectively assessed SnF2 effects on oxidative stress in adults with gingivitis.

METHODS

This was a 2-month, single-center, single-treatment clinical trial. Twenty "disease" (> 20 bleeding sites with ≥ 3 pockets 3 mm-4 mm deep) and 20 "healthy" (≤ 3 bleeding sites with pockets ≤ 2 mm deep) adults were enrolled. All participants were instructed to use SnF2 dentifrice twice daily for 2 months. An oral examination, Modified Gingival Index (MGI) examination and Gingival Bleeding Index (GBI) examination were conducted at baseline, 1 month and 2 months. Gingival crevicular fluid (GCF), saliva, oral lavage and supragingival plaque were collected at each visit to evaluate: Endotoxins, Protein Carbonyls, L-lactate dehydrogenase (LDH), Ferric reducing antioxidant power (FRAP), Oxidized low density lipoproteins (oxi-LDL), IL-6 and C-reactive protein (CRP). A subset-analysis examined participants considered at higher risk of cardiovascular disease. Change-from-baseline analyses within each group were of primary interest.

RESULTS

The disease group showed statistically significant reductions in GBI at Month 1 (67%) and Month 2 (85%) and in MGI at Month 1 (36%) and Month 2 (51%) versus baseline (p < 0.001). At baseline, the disease group showed greater LDH in GCF and oxi-LDL levels in saliva versus the healthy group (p ≤ 0.01). Total antioxidant capacity (FRAP) in saliva increased versus baseline for the disease group at Months 1 and 2 (p < 0.05), and levels for the disease group were greater than the healthy group at both timepoints (p < 0.05). SnF2 treatment reduced endotoxins (lavage) for both disease and healthy groups at Month 2 (p ≤ 0.021) versus baseline. There was a reduction in oxidative stress markers, namely protein carbonyl in saliva, at Months 1 and 2 (p < 0.001) for both groups and a reduction in cytokine IL-6 (lavage) in the disease group at Month 2 (p = 0.005). A subset analysis of participants at higher coronary disease risk showed reductions in endotoxins in lavage, oxi-LDL, and CRP in saliva at Month 2 (p ≤ 0.04).

CONCLUSION

SnF2 dentifrice use reversed gingival inflammation, suppressed endotoxins and reduced some harmful oxidant products in saliva and gingiva.

CLINICAL TRIAL REGISTRATION

Clinicaltrials.gov NCT05326373, registered on 13/04/2022.

Cysteine sulfenylation contributes to liver fibrosis via the regulation of EphB2-mediated signaling

Sulfenylation is a reversible oxidative posttranslational modification (PTM) of proteins on cysteine residues. Despite the dissection of various biological functions of cysteine sulfenylation, its roles in hepatic fibrosis remain elusive. Here, we report that EphB2, a receptor tyrosine kinase previously implicated in liver fibrosis, is regulated by cysteine sulfenylation during the fibrotic progression of liver. Specifically, EphB2 is sulfenylated at the residues of Cys636 and Cys862 in activated hepatic stellate cells (HSCs), leading to the elevation of tyrosine kinase activity and protein stability of EphB2 and stronger interactions with focal adhesion kinase for the activation of downstream mitogen-activated protein kinase signaling. The inhibitions of both EphB2 kinase activity and cysteine sulfenylation by idebenone (IDE), a marketed drug with potent antioxidant activity, can markedly suppress the activation of HSCs and ameliorate hepatic injury in two well-recognized mouse models of liver fibrosis. Collectively, this study reveals cysteine sulfenylation as a new type of PTM for EphB2 and sheds a light on the therapeutic potential of IDE for the treatment of liver fibrosis.

Elevated levels of iodide promote peroxidase-mediated protein iodination and inhibit protein chlorination

At inflammatory sites, immune cells generate oxidants including H₂O₂. Myeloperoxidase (MPO), released by activated leukocytes employs H₂O₂ and halide/pseudohalides to form hypohalous acids that mediate pathogen killing. Hypochlorous acid (HOCl) is a major species formed. Excessive or misplaced HOCl formation damages host tissues with this linked to multiple inflammatory diseases. Previously (Redox Biology, 2020, 28, 101331) we reported that iodide (I⁻) modulates MPO-mediated protein damage by decreasing HOCl generation with concomitant hypoiodous acid (HOI) formation. HOI may however impact on protein structure, so in this study we examined whether and how HOI, from peroxidase/H₂O₂/I⁻ systems ± Cl⁻, modifies proteins. Experiments employed MPO and lactoperoxidase (LPO) and multiple proteins (serum albumins, anastellin), with both chemical (intact protein and peptide mass mapping, LC-MS) and structural (SDS-PAGE) changes assessed. LC-MS analyses revealed dose-dependent iodination of anastellin and albumins by LPO/H2O2 with increasing I⁻. Incubation of BSA with MPO/H2O2/Cl⁻ revealed modest chlorination (Tyr286, Tyr475, ∼4 %) and Met modification. Lower levels of these species, and extensive iodination at specific Tyr and His residues (>20 % modification with ≥10 μM I⁻) were detected with increasing I⁻. Anastellin dimerization was inhibited by increasing I⁻, but less marked changes were observed with albumins. These data confirm that I⁻ competes with Cl⁻ for MPO and is an efficient HOCl scavenger. These processes decrease protein chlorination and oxidation, but result in extensive iodination. This is consistent with published data on the presence of iodinated Tyr on neutrophil proteins. The biological implications of protein iodination relative to chlorination require further clarification.

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.

Glial fibrillary acidic protein is pathologically modified in Alexander disease

Here, we describe pathological events potentially involved in the disease pathogenesis of Alexander disease (AxD). This is a primary genetic disorder of astrocyte caused by dominant gain-of-function mutations in the gene coding for an intermediate filament protein glial fibrillary acidic protein (GFAP). Pathologically, this disease is characterized by the upregulation of GFAP and its accumulation as Rosenthal fibers. Although the genetic basis linking GFAP mutations with Alexander disease has been firmly established, the initiating events that promote GFAP accumulation and the role of Rosenthal fibers (RFs) in the disease process remain unknown. Here, we investigate the hypothesis that disease-associated mutations promote GFAP aggregation through aberrant posttranslational modifications. We found high molecular weight GFAP species in the RFs of AxD brains, indicating abnormal GFAP crosslinking as a prominent pathological feature of this disease. In vitro and cell-based studies demonstrate that cystine-generating mutations promote GFAP crosslinking by cysteine-dependent oxidation, resulting in defective GFAP assembly and decreased filament solubility. Moreover, we found GFAP was ubiquitinated in RFs of AxD patients and rodent models, supporting this modification as a critical factor linked to GFAP aggregation. Finally, we found that arginine could increase the solubility of aggregation-prone mutant GFAP by decreasing its ubiquitination and aggregation. Our study suggests a series of pathogenic events leading to AxD, involving interplay between GFAP aggregation and abnormal modifications by GFAP ubiquitination and oxidation. More important, our findings provide a basis for investigating new strategies to treat AxD by targeting abnormal GFAP modifications.

Stability of Protein Pharmaceuticals: Recent Advances

There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'

Modification of extracellular matrix proteins by oxidants and electrophiles

The extracellular matrix (ECM) is critical to biological architecture and determines cellular properties, function and activity. In many situations it is highly abundant, with collagens and elastin being some of the most abundant proteins in mammals. The ECM comprises of multiple different protein species and sugar polymers, with both different isoforms and post-translational modifications (PTMs) providing a large variety of microenvironments that play a key role in determining tissue structure and health. A number of the PTMs (e.g. cross-links) present in the ECM are critical to integrity and function, whereas others are deleterious to both ECM structure and associated cells. Modifications induced by reactive oxidants and electrophiles have been reported to accumulate in some ECM with increasing age. This accumulation can be exacerbated by disease, and in particular those associated with acute or chronic inflammation, obesity and diabetes. This is likely to be due to higher fluxes of modifying agents in these conditions. In this focused review, the role and effects of oxidants and other electrophiles on ECM are discussed, with a particular focus on the artery wall and atherosclerotic cardiovascular disease. Modifications generated on ECM components are reviewed, together with the effects of these species on cellular properties including adhesion, proliferation, migration, viability, metabolic activity, gene expression and phenotype. Increasing data indicates that ECM modifications are both prevalent in human and mammalian tissues and play an important role in disease development and progression.

Redox signaling in cell fate: Beyond damage

This review explores the nuanced role of reactive oxygen species (ROS) in cell fate, challenging the traditional view that equates ROS with cellular damage. Through significant technological advancements in detecting localized redox states and identifying oxidized cysteines, a paradigm shift has emerged: from ROS as merely damaging agents to crucial players in redox signaling. We delve into the intricacies of redox mechanisms, which, although confined, exert profound influences on cellular physiological responses. Our analysis extends to both the positive and negative impacts of these mechanisms on cell death processes, including uncontrolled and programmed pathways. By unraveling these complex interactions, we argue against the oversimplified notion of a 'stress response', advocating for a more nuanced understanding of redox signaling. This review underscores the importance of localized redox states in determining cell fate, highlighting the sophistication and subtlety of ROS functions beyond mere damage.

Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers

Oxidation-reduction post-translational modifications (redox-PTMs) are chemical alterations to amino acids of proteins. Redox-PTMs participate in the regulation of protein conformation, localization and function, acting as signalling effectors that impact many essential biochemical processes in the cells. Crucially, the dysregulation of redox-PTMs of proteins has been implicated in the pathophysiology of numerous human diseases, including neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. This review aims to highlight the current gaps in knowledge in the field of redox-PTMs biology and to explore new methodological advances in proteomics and computational modelling that will pave the way for a better understanding of the role and therapeutic potential of redox-PTMs of proteins in neurodegenerative diseases. Here, we summarize the main types of redox-PTMs of proteins while providing examples of their occurrence in neurodegenerative diseases and an overview of the state-of-the-art methods used for their detection. We explore the potential of novel computational modelling approaches as essential tools to obtain insights into the precise role of redox-PTMs in regulating protein structure and function. We also discuss the complex crosstalk between various PTMs that occur in living cells. Finally, we argue that redox-PTMs of proteins could be used in the future as diagnosis and prognosis biomarkers for neurodegenerative diseases.

Gut microbiome, short-chain fatty acids, alpha-synuclein, neuroinflammation, and ROS/RNS: Relevance to Parkinson's disease and therapeutic implications

In this review, we explore how short-chain fatty acids (SCFAs) produced by the gut microbiome affect Parkinson's disease (PD) through their modulatory interactions with alpha-synuclein, neuroinflammation, and oxidative stress mediated by reactive oxygen and nitrogen species (ROS/RNS). In particular, SCFAs-such as acetate, propionate, and butyrate-are involved in gut-brain communication and can modulate alpha-synuclein aggregation, a hallmark of PD. The gut microbiome of patients with PD has lower levels of SCFAs than healthy individuals. Probiotics may be a potential strategy to restore SCFAs and alleviate PD symptoms, but the underlying mechanisms are not fully understood. Also in this review, we discuss how alpha-synuclein, present in the guts and brains of patients with PD, may induce neuroinflammation and oxidative stress via ROS/RNS. Alpha-synuclein is considered an early biomarker for PD and may link the gut-brain axis to the disease pathogenesis. Therefore, elucidating the role of SCFAs in the gut microbiome and their impact on alpha-synuclein-induced neuroinflammation in microglia and on ROS/RNS is crucial in PD pathogenesis and treatment.

The Intricate Balance between Life and Death: ROS, Cathepsins, and Their Interplay in Cell Death and Autophagy

Cellular survival hinges on a delicate balance between accumulating damages and repair mechanisms. In this intricate equilibrium, oxidants, currently considered physiological molecules, can compromise vital cellular components, ultimately triggering cell death. On the other hand, cells possess countermeasures, such as autophagy, which degrades and recycles damaged molecules and organelles, restoring homeostasis. Lysosomes and their enzymatic arsenal, including cathepsins, play critical roles in this balance, influencing the cell's fate toward either apoptosis and other mechanisms of regulated cell death or autophagy. However, the interplay between reactive oxygen species (ROS) and cathepsins in these life-or-death pathways transcends a simple cause-and-effect relationship. These elements directly and indirectly influence each other's activities, creating a complex web of interactions. This review delves into the inner workings of regulated cell death and autophagy, highlighting the pivotal role of ROS and cathepsins in these pathways and their intricate interplay.

Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.

ROS signaling in innate immunity via oxidative protein modifications

The innate immune response represents the first-line of defense against invading pathogens. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) have been implicated in various aspects of innate immune function, which involves respiratory bursts and inflammasome activation. These reactive species widely distributed within the cellular environment are short-lived intermediates that play a vital role in cellular signaling and proliferation and are likely to depend on their subcellular site of formation. NADPH oxidase complex of phagocytes is known to generate superoxide anion radical (O2 •-) that functions as a precursor for antimicrobial hydrogen peroxide (H2O2) production, and H2O2 is utilized by myeloperoxidase (MPO) to generate hypochlorous acid (HOCl) that mediates pathogen killing. H2O2 modulates the expression of redox-responsive transcriptional factors, namely NF-kB, NRF2, and HIF-1, thereby mediating redox-based epigenetic modification. Survival and function of immune cells are under redox control and depend on intracellular and extracellular levels of ROS/RNS. The current review focuses on redox factors involved in the activation of immune response and the role of ROS in oxidative modification of proteins in macrophage polarization and neutrophil function.

Exploring Extracellular Matrix Crosslinking as a Therapeutic Approach to Fibrosis

The extracellular matrix (ECM) provides structural support for tissues and regulatory signals for resident cells. ECM requires a careful balance between protein accumulation and degradation for homeostasis. Disruption of this balance can lead to pathological processes such as fibrosis in organs across the body. Post-translational crosslinking modifications to ECM proteins such as collagens alter ECM structure and function. Dysregulation of crosslinking enzymes as well as changes in crosslinking composition are prevalent in fibrosis. Because of the crucial roles these ECM crosslinking pathways play in disease, the enzymes that govern crosslinking events are being explored as therapeutic targets for fibrosis. Here, we review in depth the molecular mechanisms underlying ECM crosslinking, how ECM crosslinking contributes to fibrosis, and the therapeutic strategies being explored to target ECM crosslinking in fibrosis to restore normal tissue structure and function.

Formation of free acetaldehydes derived from lipid peroxidation in U937 monocyte-like cells

Acetaldehyde can be found in human cells as a byproduct of various metabolic pathways, including oxidative processes such as lipid peroxidation. This secondary product of lipid peroxidation plays a role in various pathological processes, leading to various types of civilization diseases. In this study, the formation of free acetaldehyde induced by oxygen-centred radicals was studied in monocyte-like cell line U937. Exposure of U937 cells to peroxyl/alkoxyl radicals induced by azocompound resulted in the formation of free acetaldehyde. Acetaldehyde is formed by the cleavage of fatty acids, which represents the breakdown of fatty acids into smaller fragments initiated by the cyclization of lipid peroxyl radical and β-scission of lipid alkoxyl radical. The cleavage of fatty acids alters the integrity of the plasma and nuclear membrane, leading to the loss of cell viability. Understanding the pathological processes of acetaldehyde formation is an active area of research with potential implications for preventing and treating various diseases associated with oxidative stress.