Tripping up Trp: Modification of protein tryptophan residues by reactive oxygen species, modes of detection, and biological consequences

Dioxygenation of tryptophan residues by superoxide and myeloperoxidase

When neutrophils ingest pathogens into phagosomes, they generate large amounts of the superoxide radical through the reduction of molecular oxygen. Superoxide is essential for effective antimicrobial defense, but the precise role it plays in bacterial killing is unknown. Within phagosomes, superoxide reacts with the heme enzyme myeloperoxidase (MPO) and is converted to hydrogen peroxide, then subsequently to the bactericidal oxidant hypochlorous acid. But other reactions of superoxide with MPO may also contribute to host defense. Here, we demonstrate that MPO uses superoxide to dioxygenate tryptophan residues within model peptides via two hypochlorous acid-independent pathways. Using mass spectrometry, we show that formation of N-formylkynurenine is the favored reaction. This reaction is consistent with a direct transfer of dioxygen from an intermediate of MPO, where superoxide is bound to the active site heme iron (compound III). In addition, hydroperoxides are formed when superoxide adds to tryptophan radicals, which are produced during the peroxidase cycle of MPO. Proteomic analysis revealed that tryptophan dioxygenation occurs on the abundant neutrophil protein calprotectin and lactoferrin during phagocytosis of Staphylococcus aureus, indicating that this is a physiologically relevant modification. Our study enhances the understanding of superoxide chemistry in the phagosome. It also suggests that tryptophan dioxygenation by MPO and superoxide may occur during infection and inflammation.

Micellar Solvent Accessibility of Esterified Polyoxyethylene Chains as Crucial Element of Polysorbate Oxidation: A Density Functional Theory, Molecular Dynamics Simulation and Liquid Chromatography/Mass Spectrometry Investigation

Given that the amphiphilicity of polysorbates represents a key factor in the protection of proteins from particle formation, the loss of this property through degradative processes is a significant concern. Therefore, the present study sought to identify the factors that contribute to the oxidative cleavage of the polysorbate (PS) molecule and to ascertain the preferred sites of degradation. In order to gain insight into the radical susceptibility of the individual polysorbate segments and their accessibility to water, conceptual density functional theory calculations and molecular dynamics simulations were performed. The behavior of monoesters and diesters was examined in both monomer form and within the context of micelles. The theoretical results were corroborated by experimental findings, wherein polysorbate 20 was subjected to 50 ppb Fe2+ and 100,000 lx·h of visible light, and subsequently stored at 25 °C/60% r.h. or 40 °C/75% r.h. for a period of 3 months. Molecular dynamics simulations demonstrated that unesterified polyoxyethylene(POE) chains within a polysorbate 20 molecule exhibited the greatest water accessibility, indicating their heightened susceptibility to oxidation. Nevertheless, the oxidative cleavage of esterified polyoxyethylene chains of a polysorbate 20 molecule is highly detrimental to the protective effect on protein particle formation. This occurs presumably at the oxyethylene (OE) units in the vicinity of the sorbitan ring, leaving a nonamphiphilic molecule in the worst case. Consequently, the critical degradation sites were identified, resulting in the formation of degradation products that indicate a loss of amphiphilicity in PS.

Integrating time since deposition estimation of bloodstains into a DNA profiling workflow: A novel approach using fluorescence spectroscopy

Determining the time since deposition (TSD) of bloodstains is important to establish a timeline of bloodshed, while DNA profiling addresses identity (source attribution). Traditionally treated as separate processes, this study integrates TSD estimation into routine DNA profiling by analyzing typically discarded cell lysate (eluates) from spin-column-based DNA extractions. Fluorescence spectroscopy was used to analyze eluates from bloodstains deposited up to 99 weeks. Two excitation-emission matrices (EEMs) were acquired for each sample and deconvoluted using parallel factor analysis (PARAFAC) to identify individual fluorophores. For example, tryptophan demonstrated a time-dependent decrease in fluorescence. Additionally, we observed an accumulation of fluorescent oxidation products (FOX) and advanced glycation end products (AGEs) over TSD. An untargeted metabolomics high-performance liquid chromatography-mass spectrometry workflow was applied to assist with fluorophore identification. Chemometric models were used to estimate TSD from EEM fluorescence data. Boruta feature selection coupled with random forest regression outperformed all other models and achieved high accuracy, with an R2 of 0.993 and root mean square error of prediction (RMSEP) of 2.83 weeks for the full 99-week period, and an R2 of 0.987 and RMSEP of 2.06 weeks for the 1-year timeframe. Comparisons were also made between anticoagulant-free (AC-free) and anticoagulant-treated (AC-treated) bloodstains deposited up to 3 months. We noted differences in fluorescence based on AC treatment, with AC-free blood exhibiting higher FOX and lower AGE fluorescence than AC-treated blood. Our findings demonstrate the effectiveness and feasibility of integrating TSD estimation into routine forensic DNA extractions while maintaining high prediction accuracies.

"Illuminated Glycoporphyrins": A photodynamic approach for Candida albicans inactivation

The continuous increase in the incidence of invasive mycoses, particularly those caused by Candida albicans, is a relevant health issue worldwide due to the lack of effective antifungals and the constant emergence of resistant strains. One of the most promising therapies to treat infections caused by resistant microorganisms is photodynamic inactivation (PDI). The development of novel photosensitizers (PSs) with suitable properties is a key factor to consider when optimizing this therapy. In this work, we designed, synthesized, and characterized four glycoporphyrins functionalized with S-galactose (acetylated and deacetylated) and varying the number of tertiary amino groups as precursors of cationic centers, which can be activated by protonation at physiological pH. The amino and glycosyl groups were introduced to enhance interaction with the microbial cell wall, increase hydrophilicity, and evaluate their combined effect on PS efficiency in photoinactivation. All derivatives presented the characteristic absorption and emission properties of the porphyrin macrocycle. Moreover, the glycoporphyrins were capable of generating singlet oxygen and superoxide anion radical. The photophysical and photodynamic properties were not affected by the different substitution patterns on the porphyrin core. PDI treatments of C. albicans cultures, treated with 5 μM of the PS and irradiated for 30 min, produced cellular inactivation of ∼3.5 log for glycoporphyrins with cationic centers. Furthermore, PDI of C. albicans mediated by glycoporphyrins was potentiated by the addition of KI. Under these conditions, a significant enhancement in cellular death was observed, achieving complete eradication of the treated cell suspensions. Moreover, glycoporphyrins containing pH-activable groups, combined with KI, showed outstanding efficacy against C. albicans pseudohyphae. These in vitro findings underscore the significant impact of substitution patterns on antimicrobial action. To our knowledge, this study marks the first application of glycosylated porphyrin derivatives containing pH-activatable cationic groups in the photoinactivation of C. albicans, paving the way for the development of novel derivatives with potential applications as effective antifungal PSs.

Trp31 Residue of Trx-1 Is Essential for Maintaining Antioxidant Activity and Cellular Redox Defense Against Oxidative Stress

Thioredoxin-1 (Trx-1) is an important redox protein found in almost all prokaryotic and eukaryotic cells, which has a highly conserved active site sequence: Trp-Cys-Gly-Pro-Cys. To investigate whether the Trp31 residue is essential for the antioxidant activity of human Trx-1 (hTrx-1), we mutated Trx-1 by replacing Trp31 with Ala31 (31Ala) or deleting Trp31 residue (31Del). We introduced 31Ala and 31Del mutations into prokaryotic cells for hTrx-1 protein expression, protein purification and evaluation of antioxidant activity. The results showed that neither the replacing mutation to Ala31 nor the deletion of Trp31 residue affected the efficient expression of hTrx-1 protein in prokaryotic cells, indicating that neither form of Trp31 mutation would disrupt the folded structure of the Trx-1 protein. Comparison of the antioxidant activity of purified hTrx-1 proteins of wild-type, 31Ala and 31Del forms revealed that both mutant forms significantly decreased the antioxidant capacity of hTrx-1. Further investigations on eukaryotic cells showed that H2O2 treatment caused massive cell death in EA.Hy926 human endothelial cells with 31Ala and 31Del mutations compared to wild-type cells, which was associated with increased ROS production and downregulation of antioxidant Nrf2 and HO-1 expression in the mutant cells. These results suggested that mutations in the Trp31 residue of hTrx-1 remarkably disrupted cellular redox defense against oxidative stress. The antioxidant activity of hTrx-1 relies on the thiol-disulfide exchange reaction, in which the content of thiol groups forming disulfide bonds in hTrx-1 is critical. We found that the content of free thiol groups specifically participating in disulfide bond formation was significantly lower in Trp31 mutant hTrx-1 than in wild-type hTrx-1; that was speculated to affect the formation of disulfide bonds between Cys32 and Cys35 by virtual analysis, thus abolishing the antioxidant activity of hTrx-1 in cleaving oxidized groups and defending against oxidative stress. The present study provided valuable insights towards understanding the importance of Trp31 residue of hTrx-1 in maintaining the correct conformation of the Trx fold structure, the antioxidant functionality of hTrx-1 and the cellular redox defense capability against oxidative stress.

Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Luminescent Lanthanide Infinite Coordination Polymers for Ratiometric Sensing Applications

Ratiometric lanthanide coordination polymers (Ln-CPs) are advanced materials that combine the unique optical properties of lanthanide ions (e.g., Eu3+, Tb3+, Ce3+) with the structural flexibility and tunability of coordination polymers. These materials are widely used in biological and chemical sensing, environmental monitoring, and medical diagnostics due to their narrow-band emission, long fluorescence lifetimes, and excellent resistance to photobleaching. This review focuses on the composition, sensing mechanisms, and applications of ratiometric Ln-CPs. The ratiometric fluorescence mechanism relies on two distinct emission bands, which provides a self-calibrating, reliable, and precise method for detection. The relative intensity ratio between these bands varies with the concentration of the target analyte, enabling real-time monitoring and minimizing environmental interference. This ratiometric approach is particularly suitable for detecting trace analytes and for use in complex environments where factors like background noise, temperature fluctuations, and light intensity variations may affect the results. Finally, we outline future research directions for improving the design and synthesis of ratiometric Ln-CPs, such as incorporating long-lifetime reference luminescent molecules, exploring near-infrared emission systems, and developing up-conversion or two-photon luminescent materials. Progress in these areas could significantly broaden the scope of ratiometric Ln-CP applications, especially in biosensing, environmental monitoring, and other advanced fields.

Effect of Boiling Treatment on Linoleic Acid-Induced Oxidation of Myofibrillar Protein in Grass Carp

The aim of this study was to investigate the promotion of linoleic acid (OLA)-induced myofibrillar protein (MP) oxidation by boiling treatment. The effect of the boiling treatment on grass carp MP oxidation induced by OLA was investigated. The total sulfhydryl content, fluorescence intensity, and amino acid content were reduced with the increasing OLA concentration after the boiling treatment, while the boiled oxidized MP's carbonyl content (4.76 ± 0.14 nmol/mg) was 2.14 times higher than that of the native MP (2.22 ± 0.02 nmol/mg) at an OLA concentration of 10 mM. Additionally, the secondary structure of MP became more disordered, shifting from an α-helix to random coils and β-turns. When the concentration of OLA was higher than 5 mM, both the surface hydrophobicity and water holding capacity (WHC) decreased with the increasing OLA concentration. Furthermore, the boiling treatment led to a reduction in immobile water and an increase in free water content in the MP gel. These findings establish a theoretical basis for regulating MP oxidation to improve fish quality during boiling.

Distinct accumulation patterns, translocation efficiencies, and impacts of nano-fertilizer and nano-pesticide in wheat through foliar versus soil application

The use of nano-chemicals in agriculture has been shown to enhance crop production through soil additions or foliar sprays. However, the accumulation pattern, translocation efficiency, mode of action of nanomaterials (NMs) via different application methods remain unclear. In this study, wheat was treated with CuO-NPs/CeO2-NPs (50 and 100 nm) for 21 days using soil and foliar application separately. Foliar spray resulted in higher accumulation and more efficient translocation of NMs compared to soil addition. Smaller NMs exhibited higher accumulation and transfer capabilities under the same application method. The accumulation of CuO-NPs was approximately 20 times greater than that of CeO2-NPs, particularly under the soil addition treatment. Scanning electron microscopy analysis demonstrated that NMs could directly enter wheat leaves via stomata during foliar application. Wheat growth was inhibited by roughly 15 % following CuO-NPs exposure, whereas no significant effects on growth were observed with CeO2-NPs. By integrating nontargeted metabolomics analysis with targeted physiological characteristics assessments, it was revealed that CuO-NPs mainly disturbed nitrogen metabolism pathways and induced oxidative damage. In contrast, CeO2-NPs enhanced carbohydrates related biological processes such as starch and sucrose metabolism, glycolysis, and TCA cycle, which are crucial for carbon metabolism. These findings suggest that the type of nanomaterial is a crucial factor to consider when evaluating their foliar or soil application in agriculture.

Functionality of Reactive Oxygen Species (ROS) in Plants: Toxicity and Control in Poaceae Crops Exposed to Abiotic Stress

Agriculture and changing environmental conditions are closely related, as weather changes could adversely affect living organisms or regions of crop cultivation. Changing environmental conditions trigger different abiotic stresses, which ultimately cause the accumulation of reactive oxygen species (ROS) in plants. Common ROS production sites are the chloroplast, endoplasmic reticulum, plasma membrane, mitochondria, peroxisomes, etc. The imbalance in ROS production and ROS detoxification in plant cells leads to oxidative damage to biomolecules such as lipids, nucleic acids, and proteins. At low concentrations, ROS initiates signaling events related to development and adaptations to abiotic stress in plants by inducing signal transduction pathways. In plants, a stress signal is perceived by various receptors that induce a signal transduction pathway that activates numerous signaling networks, which disrupt gene expression, impair the diversity of kinase/phosphatase signaling cascades that manage the stress response in the plant, and result in changes in physiological responses under various stresses. ROS production also regulates ABA-dependent and ABA-independent pathways to mitigate drought stress. This review focuses on the common subcellular location of manufacturing, complex signaling mechanisms, and networks of ROS, with an emphasis on cellular effects and enzymatic and non-enzymatic antioxidant scavenging mechanisms of ROS in Poaceae crops against drought stress and how the manipulation of ROS regulates stress tolerance in plants. Understanding ROS systems in plants could help to create innovative strategies to evolve paths of cell protection against the negative effects of excessive ROS in attempts to improve crop productivity in adverse environments.

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.'

Development of a high throughput oxidation profiling strategy for monoclonal antibody products

Oxidation is one of the most common degradation pathways of biopharmaceutics, potentially leading to altered product stability, pharmacokinetics, reduced biological activity and/or an increased immunogenicity. However, it is often insufficiently assessed in early development stages, leaving potential molecule liabilities undiscovered. Aim of the present work was the development of a high throughput oxidation profiling strategy, applicable throughout various stages of biopharmaceutical development. The study demonstrates that the combination of multiple stress assays, including peroxide-based, visible light, and metal-catalyzed oxidation (MCO), enables a comprehensive understanding of a mAb's oxidation susceptibility. The most effective parameters to evaluate oxidation in a high-throughput screening workflow are aggregation, tryptophan oxidation and changes in the hydrophobicity profile of the Fc and Fab subunit measured via Size Exclusion Chromatography, Intrinsic Tryptophan Fluorescence Emission spectroscopy and Reversed-Phase Chromatography subunit analysis, respectively. This oxidation profiling approach is valuable tool to systematically characterize the oxidation susceptibility under relevant conditions, time effective and with minimal sample consumption.

Porphyrin-BODIPY Dyad: Enhancing Photodynamic Inactivation via Antenna Effect

A porphyrin-BODIPY dyad (P-BDP) was obtained through covalent bonding, featuring a two-segment design comprising a light-harvesting antenna system connected to an energy acceptor unit. The absorption spectrum of P-BDP resulted from an overlap of the individual spectra of its constituent parts, with the fluorescence emission of the BODIPY unit experiencing significant quenching (96 %) due to the presence of the porphyrin unit. Spectroscopic, computational, and redox investigations revealed a competition between photoinduced energy and electron transfer processes. The dyad demonstrated the capability to sensitize both singlet molecular oxygen and superoxide radical anions. Additionally, P-BDP effectively induced the photooxidation of L-tryptophan. In suspensions of Staphylococcus aureus cells, the dyad led to a reduction of over 3.5 log (99.99 %) in cell survival following 30 min of irradiation with green light. Photodynamic inactivation caused by P-BDP was also extended to the individual bacterium level, focusing on bacterial cells adhered to a surface. This dyad successfully achieved the total elimination of the bacteria upon 20 min of irradiation. Therefore, P-BDP presents an interesting photosensitizing structure that takes advantage of the light-harvesting antenna properties of the BODIPY unit combined with porphyrin, offering potential to enhance photoinactivation of bacteria.

Orthogonal Translation for Site-Specific Installation of Post-translational Modifications

Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.

An artificial metalloenzyme that can oxidize water photocatalytically: design, synthesis, and characterization

In nature, light-driven water oxidation (WO) catalysis is performed by photosystem II via the delicate interplay of different cofactors positioned in its protein scaffold. Artificial systems for homogeneous photocatalytic WO are based on small molecules that often have limited solubility in aqueous solutions. In this work, we alleviated this issue and present a cobalt-based WO-catalyst containing artificial metalloenzyme (ArM) that is active in light-driven, homogeneous WO catalysis in neutral-pH aqueous solutions. A haem-containing electron transfer protein, cytochrome B5 (CB5), served to host a first-row transition-metal-based WO catalyst, CoSalen (CoIISalen, where H2Salen = N,N'-bis(salicylidene)ethylenediamine), thus producing an ArM capable of driving photocatalytic WO. The CoSalen ArM formed a water-soluble pre-catalyst in the presence of [Ru(bpy)3](ClO4)2 as photosensitizer and Na2S2O8 as the sacrificial electron acceptor, with photocatalytic activity similar to that of free CoSalen. During photocatalysis, the CoSalen-protein interactions were destabilized, and the protein partially unfolded. Rather than forming tens of nanometer sized CoOx nanoparticles as free CoSalen does under photocatalytic WO conditions, the CB5 : CoSalen ArM showed limited protein cross-linking and remained soluble. We conclude that a weak, dynamic interaction between a soluble cobalt species and apoCB5 was formed, which generated a catalytically active adduct during photocatalysis. A detailed analysis was performed on protein stability and decomposition processes during the harsh oxidizing reaction conditions of WO, which will serve for the future design of WO ArMs with improved activity and stability.

Oxidative cyclization reagents reveal tryptophan cation-π interactions

Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.

Oxidative Post-translational Protein Modifications upon Ischemia/Reperfusion Injury

While reperfusion, or restoration of coronary blood flow in acute myocardial infarction, is a requisite for myocardial salvage, it can paradoxically induce a specific damage known as ischemia/reperfusion (I/R) injury. Our understanding of the precise pathophysiological molecular alterations leading to I/R remains limited. In this study, we conducted a comprehensive and unbiased time-course analysis of post-translational modifications (PTMs) in the post-reperfused myocardium of two different animal models (pig and mouse) and evaluated the effect of two different cardioprotective therapies (ischemic preconditioning and neutrophil depletion). In pigs, a first wave of irreversible oxidative damage was observed at the earliest reperfusion time (20 min), impacting proteins essential for cardiac contraction. A second wave, characterized by irreversible oxidation on different residues and reversible Cys oxidation, occurred at late stages (6-12 h), affecting mitochondrial, sarcomere, and inflammation-related proteins. Ischemic preconditioning mitigated the I/R damage caused by the late oxidative wave. In the mouse model, the two-phase pattern of oxidative damage was replicated, and neutrophil depletion mitigated the late wave of I/R-related damage by preventing both Cys reversible oxidation and irreversible oxidation. Altogether, these data identify protein PTMs occurring late after reperfusion as an actionable therapeutic target to reduce the impact of I/R injury.

Oxidation of polysorbates - An underestimated degradation pathway?

To ensure the stability of biologicals over their entire shelf-life, non-ionic surface-active compounds (surfactants) are added to protect biologics from denaturation and particle formation. In this context, polysorbate 20 and 80 are the most used detergents. Despite their benefits of low toxicity and high biocompatibility, specific factors are influencing the intrinsic stability of polysorbates, leading to degradation, loss in efficacy, or even particle formation. Polysorbate degradation can be categorized into chemical or enzymatic hydrolysis and oxidation. Under pharmaceutical relevant conditions, hydrolysis is commonly originated from host cell proteins, whereas oxidative degradation may be caused by multiple factors such as light, presence of residual metal traces, peroxides, or temperature, which can be introduced upon manufacturing or could be already present in the raw materials. In this review, we provide an overview of the current knowledge on polysorbates with a focus on oxidative degradation. Subsequently, degradation products and key characteristics of oxidative-mediated polysorbate degradation in respect of different types and grades are summarized, followed by an extensive comparison between polysorbate 20 and 80. A better understanding of the radical-induced oxidative PS degradation pathway could support specific mitigation strategies. Finally, buffer conditions, various stressors, as well as appropriate mitigation strategies, reagents, and alternative stabilizers are discussed. Prior manufacturing, careful consideration and a meticulous risk-benefit analysis are highly recommended in terms of polysorbate qualities, buffers, storage conditions, as well as mitigation strategies.

Oxidation Products of Tryptophan and Proline in Adipokinetic Hormones-Artifacts or Post-Translational Modifications?

BACKGROUND

Adipokinetic hormones (AKHs) regulate important physiological processes in insects. AKHs are short peptides with blocked termini and Trp in position 8. Often, proline occupies position 6. Few post-translational modifications have been found, including hydroxyproline ([Hyp6]) and kynurenine. Our recent data suggest that the Hyp- and Kyn-containing AKHs occur more often than originally thought and we here investigate if they are natural or artifactual.

METHODS

From crude extracts of the corpora cardiaca (CC) of various insect species, AKHs were analyzed using liquid chromatography coupled to high-resolution mass spectrometry (LC-MS). Synthetic [Hyp6]-AKHs were tested in an in vivo metabolic assay. Freshly dissected Periplaneta americana and Blaberus atropos CCs (with precautions taken against oxidation) were analyzed. B. atropos CC were placed into a depolarizing saline and the released AKHs were measured.

RESULTS

Hyp was detected in several decapeptides from cockroaches. The modified form accompanied the AKH at concentrations below 7%. The [Hyp6]-AKHs of B. atropos were present in fresh CC preparations and were shown to be releasable from the CC ex vivo. Synthetic [Hyp6]-containing peptides tested positively in a hypertrehalosemic bioassay. Hydroxyprolination was also detected for Manto-CC from the termite Kalotermes flavicollis and for Tetsu-AKH of the grasshopper, Tetrix subulata. Oxidized Trp-containing forms of Nicve-AKH were found in species of the burying beetle genus Nicrophorus.

CONCLUSIONS

Trp oxidation is known to occur easily during sample handling and is likely the reason for the present findings. For hydroxyprolination, however, the experimental evidence suggests endogenous processes.

Antioxidant Capacity of Free and Peptide Tryptophan Residues Determined by the ORAC (Oxygen Radical Absorbance Capacity) Assay Is Modulated by Radical-Radical Reactions and Oxidation Products

The ORAC (Oxygen Radical Absorbance Capacity) assay is commonly employed for determining the antioxidant capacity of bioactive peptides. To gain insights into the meaning of this index for peptides containing a single Trp, we studied the consumption of this residue and fluorescein (FLH, the probe of ORAC method), induced by radicals generated by AAPH (2,2'-Azo-bis(2-amidinopropane) dihydrochloride) thermolysis. ORAC values were rationalized from kinetics and computational calculations of bond dissociation energies (BDE) of the N-H bond (indole ring of Trp). Free Trp, di- and tri- peptides, and three larger peptides were studied. Solutions containing 70 nM FLH, 1-5 μM free Trp or peptides, and 10 mM AAPH were incubated at 37 °C in phosphate buffer. Kinetic studies showed that FLH minimally affected Trp consumption. However, a clear protection of FLH, characterized by pseudo-lag times, was evidenced, reflecting radical-radical reactions and FLH repairing. Peptides showed similar ORAC values (~1.9-2.8 Trolox equivalents), while BDE varied between 91.9 and 103.5 kcal. These results, added to the protection of FLH observed after total consumption of Trp, indicate a lack of discrimination of the assay for the chemical structure of peptides and the contribution of oxidation products to the index.

Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.

Reactive X (where X = O, N, S, C, Cl, Br, and I) species nanomedicine

Reactive oxygen, nitrogen, sulfur, carbonyl, chlorine, bromine, and iodine species (RXS, where X = O, N, S, C, Cl, Br, and I) have important roles in various normal physiological processes and act as essential regulators of cell metabolism; their inherent biological activities govern cell signaling, immune balance, and tissue homeostasis. However, an imbalance between RXS production and consumption will induce the occurrence and development of various diseases. Due to the considerable progress of nanomedicine, a variety of nanosystems that can regulate RXS has been rationally designed and engineered for restoring RXS balance to halt the pathological processes of different diseases. The invention of radical-regulating nanomaterials creates the possibility of intriguing projects for disease treatment and promotes advances in nanomedicine. In this comprehensive review, we summarize, discuss, and highlight very-recent advances in RXS-based nanomedicine for versatile disease treatments. This review particularly focuses on the types and pathological effects of these reactive species and explores the biological effects of RXS-based nanomaterials, accompanied by a discussion and the outlook of the challenges faced and future clinical translations of RXS nanomedicines.

Neuroanatomical zones of human traumatic brain injury reveal significant differences in protein profile and protein oxidation: Implications for secondary injury events

Traumatic brain injury (TBI) causes significant neurological deficits and long-term degenerative changes. Primary injury in TBI entails distinct neuroanatomical zones, i.e., contusion (Ct) and pericontusion (PC). Their dynamic expansion could contribute to unpredictable neurological deterioration in patients. Molecular characterization of these zones compared with away from contusion (AC) zone is invaluable for TBI management. Using proteomics-based approach, we were able to distinguish Ct, PC and AC zones in human TBI brains. Ct was associated with structural changes (blood-brain barrier (BBB) disruption, neuroinflammation, axonal injury, demyelination and ferroptosis), while PC was associated with initial events of secondary injury (glutamate excitotoxicity, glial activation, accumulation of cytoskeleton proteins, oxidative stress, endocytosis) and AC displayed mitochondrial dysfunction that could contribute to secondary injury events and trigger long-term degenerative changes. Phosphoproteome analysis in these zones revealed that certain differentially phosphorylated proteins synergistically contribute to the injury events along with the differentially expressed proteins. Non-synaptic mitochondria (ns-mito) was associated with relatively more differentially expressed proteins (DEPs) compared to synaptosomes (Syn), while the latter displayed increased protein oxidation including tryptophan (Trp) oxidation. Proteomic analysis of immunocaptured complex I (CI) from Syn revealed increased Trp oxidation in Ct > PC > AC (vs. control). Oxidized W272 in the ND1 subunit of CI, revealed local conformational changes in ND1 and the neighboring subunits, as indicated by molecular dynamics simulation (MDS). Taken together, neuroanatomical zones in TBI show distinct protein profile and protein oxidation representing different primary and secondary injury events with potential implications for TBI pathology and neurological status of the patients.

LITE-1 mediates behavioral responses to X-rays in Caenorhabditis elegans

Rapid sensory detection of X-ray stimulation has been documented across a wide variety of species, but few studies have explored the underlying molecular mechanisms. Here we report the discovery of an acute behavioral avoidance response in wild type Caenorhabditis elegans to X-ray stimulation. The endogenous C. elegans UV-photoreceptor protein LITE-1 was found to mediate the locomotory avoidance response. Transgenic expression of LITE-1 in C. elegans muscle cells resulted in paralysis and egg ejection responses to X-ray stimulation, demonstrating that ectopic expression of LITE-1 can confer X-ray sensitivity to otherwise X-ray insensitive cells. This work represents the first demonstration of rapid X-ray based genetically targeted (X-genetic) manipulation of cellular electrical activity in intact behaving animals. Our findings suggest that LITE-1 has strong potential for use in this minimally invasive form of neuromodulation to transduce transcranial X-ray signals for precise manipulation of neural activity in mammals, bypassing the need for invasive surgical implants to deliver stimulation.

The inflammatory oxidant peroxynitrous acid modulates the structure and function of the recombinant human V3 isoform of the extracellular matrix proteoglycan versican

Continued oxidant production during chronic inflammation generates host tissue damage, with this being associated with pathologies including atherosclerosis. Atherosclerotic plaques contain modified proteins that may contribute to disease development, including plaque rupture, the major cause of heart attacks and strokes. Versican, a large extracellular matrix (ECM) chondroitin-sulfate proteoglycan, accumulates during atherogenesis, where it interacts with other ECM proteins, receptors and hyaluronan, and promotes inflammation. As activated leukocytes produce oxidants including peroxynitrite/peroxynitrous acid (ONOO^-/ONOOH) at sites of inflammation, we hypothesized that versican is an oxidant target, with this resulting in structural and functional changes that may exacerbate plaque development. The recombinant human V3 isoform of versican becomes aggregated on exposure to ONOO^-/ONOOH. Both reagent ONOO^-/ONOOH and SIN-1 (a thermal source of ONOO^-/ONOOH) modified Tyr, Trp and Met residues. ONOO^-/ONOOH mainly favors nitration of Tyr, whereas SIN-1 mostly induced hydroxylation of Tyr, and oxidation of Trp and Met. Peptide mass mapping indicated 26 sites with modifications (15 Tyr, 5 Trp, 6 Met), with the extent of modification quantified at 16. Multiple modifications, including the most extensively nitrated residue (Tyr¹⁶¹), are within the hyaluronan-binding region, and associated with decreased hyaluronan binding. ONOO^-/ONOOH modification also resulted in decreased cell adhesion and increased proliferation of human coronary artery smooth muscle cells. Evidence is also presented for colocalization of versican and 3-nitrotyrosine epitopes in advanced (type II-III) human atherosclerotic plaques. In conclusion, versican is readily modified by ONOO^-/ONOOH, resulting in chemical and structural modifications that affect protein function, including hyaluronan binding and cell interactions.

Mitochondrial Dysfunction, Altered Mitochondrial Oxygen, and Energy Metabolism Associated with the Pathogenesis of Schizophrenia

The significant complexity of the brain can lead to the development of serious neuropsychiatric disorders, including schizophrenia. A number of mechanisms are involved in the etiopathogenesis of schizophrenia, pointing to its complexity and opening a new perspective on studying this disorder. In this review of currently published studies, we focused on the contribution of mitochondria to the process, with an emphasis on oxidative damage, ROS, and energy metabolism. In addition, we point out the influence of redox imbalance, which can lead to the occurrence of oxidative stress with increased lipid peroxidation, linked to the formation of toxic aldehydes such as 4-hydroxynonenal (4-HNE) and HNE protein adducts. We also analysed the role of lactate in the process of energy metabolism and cognitive functions in schizophrenia.

Multifarious analytical capabilities of the UV/Vis protein fluorescence in blood plasma

Autofluorescence of blood plasma has been broadly considered as a prospective disease screening method. However, the assessment of such intrinsic fluorescence is mostly phenomenological, and its origin is still not fully understood, complicating its use in the clinical practice. Here we present the detailed evaluation of analytical capabilities, variability, and formation of blood plasma protein fluorescence based on the open dataset of excitation-emission matrices measured for ∼300 patients with suspected colorectal cancer, and our supporting model experiments. Using high-resolution size-exclusion chromatography coupled with comprehensive spectral analysis, we demonstrate, for the first time, the dominant role of HSA in the formation of blood plasma fluorescence in the visible spectral range (excitation wavelength >350 nm), presumably caused by its oxidative modifications. Furthermore, the diagnostic value of the tryptophan emission, as well as of the tyrosine fluorescence and visible fluorescence of proteins is shown by building a tree-based classification model that uses a small subset of physically interpretable fluorescence features for distinguishing between the control group and cancer patients with >80% accuracy. The obtained results extend current understanding and approaches used for the analysis of blood plasma fluorescence and pave the way for novel autofluorescence-based disease screening methods.

Superoxide Anion Chemistry-Its Role at the Core of the Innate Immunity

Classically, superoxide anion O2•- and reactive oxygen species ROS play a dual role. At the physiological balance level, they are a by-product of O2 reduction, necessary for cell signalling, and at the pathological level they are considered harmful, as they can induce disease and apoptosis, necrosis, ferroptosis, pyroptosis and autophagic cell death. This revision focuses on understanding the main characteristics of the superoxide O2•-, its generation pathways, the biomolecules it oxidizes and how it may contribute to their modification and toxicity. The role of superoxide dismutase, the enzyme responsible for the removal of most of the superoxide produced in living organisms, is studied. At the same time, the toxicity induced by superoxide and derived radicals is beneficial in the oxidative death of microbial pathogens, which are subsequently engulfed by specialized immune cells, such as neutrophils or macrophages, during the activation of innate immunity. Ultimately, this review describes in some depth the chemistry related to O2•- and how it is harnessed by the innate immune system to produce lysis of microbial agents.

Proteomic Profiling of Major Peanut Allergens and Their Post-Translational Modifications Affected by Roasting

Post-translational modifications (PTMs) are covalent changes occurring on amino acid side chains of proteins and yet are neglected structural and functional aspects of protein architecture. The objective was to detect differences in PTM profiles that take place after roasting using open PTM search. We conducted a bottom-up proteomic study to investigate the impact of peanut roasting on readily soluble allergens and their PTM profiles. Proteomic PTM profiling of certain modifications was confirmed by Western blotting with a series of PTM-specific antibodies. In addition to inducing protein aggregation and denaturation, roasting may facilitate change in their PTM pattern and relative profiling. We have shown that Ara h 1 is the most modified major allergen in both samples in terms of modification versatility and extent. The most frequent PTM was methionine oxidation, especially in roasted samples. PTMs uniquely found in roasted samples were hydroxylation (Trp), formylation (Arg/Lys), and oxidation or hydroxylation (Asn). Raw and roasted peanut extracts did not differ in the binding of IgE from the serum of peanut-sensitised individuals done by ELISA. This study provides a better understanding of how roasting impacts the PTM profile of major peanut allergens and provides a good foundation for further exploration of PTMs.

Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production

The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA.

Redox post-translational modifications and their interplay in plant abiotic stress tolerance

The impact of climate change entails a progressive and inexorable modification of the Earth's climate and events such as salinity, drought, extreme temperatures, high luminous intensity and ultraviolet radiation tend to be more numerous and prolonged in time. Plants face their exposure to these abiotic stresses or their combination through multiple physiological, metabolic and molecular mechanisms, to achieve the long-awaited acclimatization to these extreme conditions, and to thereby increase their survival rate. In recent decades, the increase in the intensity and duration of these climatological events have intensified research into the mechanisms behind plant tolerance to them, with great advances in this field. Among these mechanisms, the overproduction of molecular reactive species stands out, mainly reactive oxygen, nitrogen and sulfur species. These molecules have a dual activity, as they participate in signaling processes under physiological conditions, but, under stress conditions, their production increases, interacting with each other and modifying and-or damaging the main cellular components: lipids, carbohydrates, nucleic acids and proteins. The latter have amino acids in their sequence that are susceptible to post-translational modifications, both reversible and irreversible, through the different reactive species generated by abiotic stresses (redox-based PTMs). Some research suggests that this process does not occur randomly, but that the modification of critical residues in enzymes modulates their biological activity, being able to enhance or inhibit complete metabolic pathways in the process of acclimatization and tolerance to the exposure to the different abiotic stresses. Given the importance of these PTMs-based regulation mechanisms in the acclimatization processes of plants, the present review gathers the knowledge generated in recent years on this subject, delving into the PTMs of the redox-regulated enzymes of plant metabolism, and those that participate in the main stress-related pathways, such as oxidative metabolism, primary metabolism, cell signaling events, and photosynthetic metabolism. The aim is to unify the existing information thus far obtained to shed light on possible fields of future research in the search for the resilience of plants to climate change.

Recent advances on characterization of protein oxidation in aquatic products: A comprehensive review

In addition to microbial spoilage and lipid peroxidation, protein oxidation is increasingly recognized as a major cause for quality deterioration of muscle-based foods. Although protein oxidation in muscle-based foods has attracted tremendous interest in the past decade, specific oxidative pathways and underlying mechanisms of protein oxidation in aquatic products remain largely unexplored. The present review covers the aspects of the origin and site-specific nature of protein oxidation, progress on the characterization of protein oxidation, oxidized proteins in aquatic products, and impact of protein oxidation on protein functionalities. Compared to meat protein oxidation, aquatic proteins demonstrate a less extent of oxidation on aromatic amino acids and are more susceptible to be indirectly oxidized by lipid peroxidation products. Different from traditional measurement of protein carbonyls and thiols, proteomics-based strategy better characterizes the targeted oxidation sites within proteins. The future trends using more robust and accurate targeted proteomics, such as parallel reaction monitoring strategy, to characterize protein oxidation in aquatic products are also given.

The Role of Tryptophan Metabolites in Neuropsychiatric Disorders

In recent decades, neuropsychiatric disorders such as major depressive disorder, schizophrenia, bipolar, etc., have become a global health concern, causing various detrimental influences on patients. Tryptophan is an important amino acid that plays an indisputable role in several physiological processes, including neuronal function and immunity. Tryptophan’s metabolism process in the human body occurs using different pathways, including the kynurenine and serotonin pathways. Furthermore, other biologically active components, such as serotonin, melatonin, and niacin, are by-products of Tryptophan pathways. Current evidence suggests that a functional imbalance in the synthesis of Tryptophan metabolites causes the appearance of pathophysiologic mechanisms that leads to various neuropsychiatric diseases. This review summarizes the pharmacological influences of tryptophan and its metabolites on the development of neuropsychiatric disorders. In addition, tryptophan and its metabolites quantification following the neurotransmitters precursor are highlighted. Eventually, the efficiency of various biomarkers such as inflammatory, protein, electrophysiological, genetic, and proteomic biomarkers in the diagnosis/treatment of neuropsychiatric disorders was discussed to understand the biomarker application in the detection/treatment of various diseases.

X-ray perception: Animal studies of sensory and behavioral responses to X-rays

Since their discovery in 1895, many studies have been conducted to understand the effect of X-rays on neural function and behavior in animals. These studies examined a range of acute and chronic effects, and a subset of studies has attempted to determine if X-rays can produce any sensory responses. Here we review literature on animal behavioral responses to X-rays from 1895 until 2021 to assess the evidence for detection of X-rays by sensory receptors in animals. We focus on the changes in appetitive and consummatory behavior, radiotaxis, behavioral arousal, and olfactory responses to X-rays that have been reported in the literature. Taken together, the reviewed literature provides a large body of evidence that X-rays can induce sensory responses in a wide variety of animals and also suggests that these responses are mediated by known sensory receptors. Furthermore, we postulate the role of reactive oxygen species (ROS), the most biologically active byproduct of X-rays, as a key mediator of sensory receptor responses to X-rays.

Influence of plasma halide, pseudohalide and nitrite ions on myeloperoxidase-mediated protein and extracellular matrix damage

Myeloperoxidase (MPO) mediates pathogen destruction by generating the bactericidal oxidant hypochlorous acid (HOCl). Formation of this oxidant is however associated with host tissue damage and disease. MPO also utilizes H₂O₂ to oxidize other substrates, and we hypothesized that mixtures of other plasma anions, including bromide (Br^-), iodide (I^-), thiocyanate (SCN^-) and nitrite (NO₂^-), at normal or supplemented concentrations, might modulate MPO-mediated HOCl damage. For the (pseudo)halide anions, only SCN^- significantly modulated HOCl formation (IC₅₀ ∼33 μM), which is within the normal physiological range, as judged by damage to human plasma fibronectin or extracellular matrix preparations detected by ELISA and LC-MS. NO₂^- modulated HOCl-mediated damage, in a dose-dependent manner, at physiologically-attainable anion concentrations. However, this was accompanied by increased tyrosine and tryptophan nitration (detected by ELISA and LC-MS), and the overall extent of damage remained approximately constant. Increasing NO₂^- concentrations (0.5-20 μM) diminished HOCl-mediated modification of tyrosine and methionine, whereas tryptophan loss was enhanced. At higher NO₂^- concentrations, enhanced tyrosine and methionine loss was detected. These analytical data were confirmed in studies of cell adhesion and metabolic activity. Together, these data indicate that endogenous plasma levels of SCN^- (but not Br^- or I^-) can modulate protein modification induced by MPO, including the extent of chlorination. In contrast, NO₂^- alters the type of modification, but does not markedly decrease its extent, with chlorination replaced by nitration. These data also indicate that MPO could be a major source of nitration in vivo, and particularly at inflammatory sites where NO₂^- levels are often elevated.

Utilizing cross-product prior knowledge to rapidly de-risk chemical liabilities in therapeutic antibody candidates

There is considerable pressure in the pharmaceutical industry to advance better molecules faster. One pervasive concern for protein-based therapeutics is the presence of potential chemical liabilities. We have developed a simple methodology for rapidly de-risking specific chemical concerns in antibody-based molecules using prior knowledge of each individual liability at a specific position in the molecule’s sequence. Our methodology hinges on the development of sequence-aligned chemical liability databases of molecules from different stages of commercialization and on sequence-aligned experimental data from prior molecules that have been developed at Amgen. This approach goes beyond the standard practice of simply flagging all instances of each motif that fall in a CDR. Instead, we de-risk motifs that are common at a specific site in commercial mAb-based molecules (and therefore did not previously pose an insurmountable barrier to commercialization) and motifs at specific sites for which we have prior experimental data indicating acceptably low levels of modification. We have used this approach successfully to identify candidates in a discovery phase program with exclusively very low risk potential chemical liabilities. Identifying these candidates in the discovery phase allowed us to bypass protein engineering and accelerate the program’s timeline by 6 months.

Open Search-Based Proteomics Reveals Widespread Tryptophan Modifications Associated with Hypoxia in Lung Cancer

The tryptophan residue has a large hydrophobic surface that plays a unique role in the folded protein conformation and functions. Tryptophan modifications are presumably to be readily detected in proteins due to the vulnerability of the indole structure to electrophilic attacks. In this study, we report a systematic identification of sequence variations at tryptophan, termed tryptophan variants, from the proteome of patients with nonsmall cell lung cancer (NSCLC). Using shotgun proteomics and a modified open search algorithm, 25 tryptophan variants on 2481 sites in over 858 proteins were identified. Among these, 6 tryptophan variants are previously identified, 15 are newly annotated, and 4 are still unknown, most of which are involved in the cascade of oxidation in the blood microparticle. Remarkably, Trp313 of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was up-oxidized whereas Trp16 and Trp38 of hemoglobin (HBB) were down-oxidized in NCSLC tissues. The results were further supported by an independent cohort of 103 lung adenocarcinoma samples, reflecting a negative feedback and potential detoxification mechanism against tumor glycolysis and hypoxia. Overall, the study reports a quick approach to explore tryptophan variants at the proteomic scale. Our findings highlight the predominant role of tryptophan oxidation in regulating the redox balance of cancer cells and its potential role as prognostic biomarker for patients with NSCLC.

Chloroplast ROS and stress signaling

Chloroplasts overproduce reactive oxygen species (ROS) under unfavorable environmental conditions, and these ROS are implicated in both signaling and oxidative damage. There is mounting evidence for their roles in translating environmental fluctuations into distinct physiological responses, but their targets, signaling cascades, and mutualism and antagonism with other stress signaling cascades and within ROS signaling remain poorly understood. Great efforts made in recent years have shed new light on chloroplast ROS-directed plant stress responses, from ROS perception to plant responses, in conditional mutants of Arabidopsis thaliana or under various stress conditions. Some articles have also reported the mechanisms underlying the complexity of ROS signaling pathways, with an emphasis on spatiotemporal regulation. ROS and oxidative modification of affected target proteins appear to induce retrograde signaling pathways to maintain chloroplast protein quality control and signaling at a whole-cell level using stress hormones. This review focuses on these seemingly interconnected chloroplast-to-nucleus retrograde signaling pathways initiated by ROS and ROS-modified target molecules. We also discuss future directions in chloroplast stress research to pave the way for discovering new signaling molecules and identifying intersectional signaling components that interact in multiple chloroplast signaling pathways.

Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques

UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.

Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond

Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.

Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment

The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.

Porphyrin-Schiff Base Conjugates Bearing Basic Amino Groups as Antimicrobial Phototherapeutic Agents

New porphyrin–Schiff base conjugates bearing one (6) and two (7) basic amino groups were synthesized by condensation between tetrapyrrolic macrocycle-containing amine functions and 4-(3-(N,N-dimethylamino)propoxy)benzaldehyde. This approach allowed us to easily obtain porphyrins substituted by positive charge precursor groups in aqueous media. These compounds showed the typical Soret and four Q absorption bands with red fluorescence emission (Φ_F ~ 0.12) in N,N-dimethylformamide. Porphyrins 6 and 7 photosensitized the generation of O₂(¹Δ_g) (Φ_Δ ~ 0.44) and the photo-oxidation of L-tryptophan. The decomposition of this amino acid was mainly mediated by a type II photoprocess. Moreover, the addition of KI strongly quenched the photodynamic action through a reaction with O₂(¹Δ_g) to produce iodine. The photodynamic inactivation capacity induced by porphyrins 6 and 7 was evaluated in Staphylococcus aureus, Escherichia coli, and Candida albicans. Furthermore, the photoinactivation of these microorganisms was improved using potentiation with iodide anions. These porphyrins containing basic aliphatic amino groups can be protonated in biological systems, which provides an amphiphilic character to the tetrapyrrolic macrocycle. This effect allows one to increase the interaction with the cell wall, thus improving photocytotoxic activity against microorganisms.

Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress

Thiol-based post-translational modifications (PTMs) play a key role in redox-dependent regulation and signaling. Functional cysteine (Cys) sites serve as redox switches, regulated through multiple types of PTMs. Herein, we aim to characterize the complexity of thiol PTMs at the proteome level through the establishment of a direct detection workflow. The LC-MS/MS based workflow allows for simultaneous quantification of protein abundances and multiple types of thiol PTMs. To demonstrate its utility, the workflow was applied to mouse pancreatic β-cells (β-TC-6) treated with thapsigargin to induce endoplasmic reticulum (ER) stress. This resulted in the quantification of >9000 proteins and multiple types of thiol PTMs, including intra-peptide disulfide (S–S), S-glutathionylation (SSG), S-sulfinylation (SO₂H), S-sulfonylation (SO₃H), S-persulfidation (SSH), and S-trisulfidation (SSSH). Proteins with significant changes in abundance were observed to be involved in canonical pathways such as autophagy, unfolded protein response, protein ubiquitination pathway, and EIF2 signaling. Moreover, ~500 Cys sites were observed with one or multiple types of PTMs with SSH and S–S as the predominant types of modifications. In many cases, significant changes in the levels of different PTMs were observed on various enzymes and their active sites, while their protein abundance exhibited little change. These results provide evidence of independent translational and post-translational regulation of enzyme activity. The observed complexity of thiol modifications on the same Cys residues illustrates the challenge in the characterization and interpretation of protein thiol modifications and their functional regulation.

•

Simultaneous quantification of protein abundances and multiple types of thiol PTMs.

•

Multiple types PTMs observed on the same Cys sites for redox-regulated proteins.

•

Data revealed complexity of thiol PTMs and their regulation.

•

Distinctive translational and post-translational regulation under ER stress in β-cells.

Amphiphilic tricationic Zn(II)phthalocyanine provides effective photodynamic action to eradicate broad-spectrum microorganisms

A novel tricationic Zn(II)phthalocyanine derivative, (NCH₃)₃ZnPc³⁺, was synthesized by ring expansion reaction of boron(III) [2,9(10),16(17)-trinitrosubphthalocyaninato]chloride. First, the reaction of this subphthalocyanine with 2,3-naphthalenedicarbonitrile and Zn(CH₃COO)₂ catalyzed by 8-diazabicyclo[5.4.0]undec-7-ene was used to obtain the A₃B-type nitrophthalocyanine. After reduction of nitro groups with Na₂S and exhaustive methylation of amino groups, (NCH₃)₃ZnPc³⁺ was formed in good yields. In addition, the tetracationic analog (NCH₃)₄ZnPc⁴⁺ was synthesized to compare their properties. The absorption and fluorescence spectra showed the Q-bands and the red emission, respectively, which are characteristic of the Zn(II)phthalocyanine derivatives in N,N-dimethylformamide. Furthermore, photodynamic activity sensitized by these compounds was studied in the presence of different molecular probes to sense the formation of reactive oxygen species. (NCH₃)₃ZnPc³⁺ efficiently produced singlet molecular oxygen and also it sensitized the formation of superoxide anion radical in the presence of NADH, while the photodynamic activity of (NCH₃)₄ZnPc⁴⁺ was very poor, possibly due to the partial formation of aggregates. Furthermore, the decomposition of L-tryptophan induced by (NCH₃)₃ZnPc³⁺ was mainly mediated by a type II mechanism. Antimicrobial photodynamic inactivation sensitized by these phthalocyanines was evaluated in Staphylococcus aureus, Escherichia coli, and Candida albicans, as representative microbial cells. In cell suspensions, (NCH₃)₃ZnPc³⁺ was rapidly bound to microbial cells, showing bioimages with red fluorescence emission. After 5 min of irradiation with visible light, (NCH₃)₃ZnPc³⁺ was able to completely eliminate S. aureus, E. coli and C. albicans, using 1.0, 2.5 and 5.0 μM phthalocyanine, respectively. In contrast, a low photoinactivation activity was found with (NCH₃)₄ZnPc⁴⁺ as a photosensitizer. Therefore, the amphiphilic tricationic phthalocyanine (NCH₃)₃ZnPc³⁺ is a promising photosensitizing structure for application as a broad-spectrum antimicrobial phototherapeutic agent.

Tracking structural modifications and oxidative status of myofibrillar proteins from silver carp (Hypophthalmichthys molitrix) fillets treated by different stunning methods and in vitro oxidizing conditions

In order to explain the increased susceptibility of stunning-stressed fillets to oxidative modifications, effect of stunning methods (percussion and gill cut) and in vitro metal-catalyzed oxidation on structural changes and oxidative status of myofibrillar proteins (MPs) from silver carp fillets was examined. In comparison to the percussion group, oxidized MPs (10 mM H₂O₂) from gill cut-stunned fillets exhibited higher extent of structural disintegration as well as elevated carbonyl levels. Using label-free proteomics, isoforms of myosin heavy chain and actin were major proteins underwent oxidative modifications including monooxidation of methionine, dioxidation of aromatic amino acids, adduction of lipid peroxidation products with aliphatic amino acids, and the carbonylation of lysine and arginine into semialdehydes. In addition, amino acids located at the tail portion of myosin were highly accessible to oxidation. Owing to the structural disorganization caused by stunning stress, MPs from gill cut-stunned fillets were more susceptible to oxidation in vitro.

Photoactive antimicrobial coating based on a PEDOT-fullerene C60 polymeric dyad

A photostable and photodynamic antimicrobial surface was successfully obtained and applied to photoinactivate microorganisms. This approach was based on the synthesis of a fullerene C60 derivative (EDOT-C60) where fullerene C60 is covalently linked to 3,4-ethylenedioxythiophene (EDOT) through a 1,3-dipolar cycloaddition reaction. This dual-functional monomer bears an EDOT center connected via an alkyl chain to a fullerene C60 moiety. In this structure, EDOT acts as an electropolymerizable unit that allows the film formation over conducting substrates, while fullerene C60 performs the photodynamic antimicrobial activity. Electrochemical polymerization of EDOT was used to obtain stable and photodynamic polymeric films (PEDOT-C60) in a controllable procedure. Cyclic voltammetry and UV-visible spectroscopy studies showed that the fullerene C60 units were not altered during the electropolymerization process, obtaining surfaces with high fullerene content. Photobleaching measurements demonstrated that the electropolymerized films were highly photostable. Moreover, photodynamic properties of PEDOT-C60 were compared with fullerene C60 and showed that electrodeposited films were able to generate reactive oxygen species (ROS) through the two photomechanisms, producing singlet molecular oxygen (type II) and superoxide radical anion (type I). All studies demonstrated that fullerene C60 moieties covalently attached to the polymeric matrix mainly conserve the photodynamic characteristics. Hence, photodynamic action sensitized by PEDOT-C60 was assessed in vitro against Staphylococcus aureus. The photosensitized inactivation by the electropolymerized films on bacteria suspensions produced >99.9% reduction in S. aureus survival. Fluorescence microscopy experiments with S. aureus adhered to the PEDOT-C60 surface showed a complete microbe annihilation. Also, the eradication of biofilms formed on PEDOT-C60 surfaces resulted in a photokilling >99.9% after visible light irradiation. Our results demonstrated that these antimicrobial photodynamic polymeric films are a promising and versatile platform to photoinactivate microorganisms and to obtain photostable self-sterilizing surfaces.