Generation and propagation of radical reactions on proteins

Novel Modification of Collagen: Realizing Desired Water Solubility and Thermostability in a Conflict-Free Way

Because of poor water solubility and low thermostability, the application of collagen is limited seriously in fields such as injectable biomaterials and cosmetics. In order to overcome the two drawbacks simultaneously, a novel bifunctional modifier based on the esterification of polyacrylic acid (PAA) with N-hydroxysuccinimide (NHS) was prepared. The esterification degree of PAA-NHS esters was increased upon increasing the NHS dose, which was confirmed by Fourier-transform infrared (FTIR) and nuclear magnetic resonance spectrascopy. FTIR results indicated that the triple helix of the modified collagens remained integrated, whereas the molecular weight became larger, as reflected by the sodium dodecyl sulfate-polyacrylamide gel electrophoresis pattern. The modified collagens displayed excellent water solubility under neutral condition, owing to lower isoelectric point (3.1-4.3) than that of native collagen (7.1). Meanwhile, denaturation temperatures of the modified collagens were increased by 4.8-5.9 °C after modification. The modified collagen displayed hierarchical microstructures, as reflected by field-emission scanning electron microscopy, while atomic force microscopy further revealed a "fishing net-like" network in the nanoscale, reflecting a unique aggregation behavior of collagen macromolecules after modification. As a whole, the PAA-NHS ester as a bifunctional modifier endowed collagen with desired water solubility and thermostability in a conflict-free manner, which was beneficial to the process and application of the water-soluble collagen.

Refolding with Simultaneous Purification of Recombinant Serratia marcescens Lipase by One-Step Ultrasonication Process

A new lipase from Serratia marcescens SRICI-01 (Trx-SmL) was successfully overexpressed in Escherichia coli with thioredoxin (Trx) fusion tag. Intriguingly, the concentration of potassium phosphate buffer (KPB) showed significant impact on the aggregation state of Trx-SmL during ultrasonic disruption. The proportion of inclusion bodies increased dramatically with the increase of KPB concentration from almost completely soluble in 10 mM KPB to insoluble in 200 mM KPB. Based on this new finding, a novel method for refolding and purification of recombinant Trx-SmL was developed by one-step ultrasonication. The Trx-SmL was firstly precipitated in 200 mM KPB, washed for three times, and subsequently subjected to ultrasonic process in 10 mM KPB where refolding and purification occurred simultaneously. This established method was proved to be a straightforward, economical, and efficient purification approach to facilely obtain recombinant Trx-SmL protein with high purity (> 90%) and activity recovery yield (> 80%) from cell lysates. The application potential of the purified fusion Trx-SmL was further demonstrated by kinetic bioresolution of (±)-trans-3-(4-methoxyphenyl)glycidic acid methyl ester [(±)-MPGM] producing optically pure (-)-MPGM, a key intermediate for diltiazem, with an overall yield of 41.5% and ee of 99%.

Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry

The functional properties of a protein are strongly influenced by its topography, or the solvent-facing contour map of its surface. Together with crosslinking, covalent labeling mass spectrometry (CL-MS) has the potential to contribute topographical data through the measurement of surface accessibility. However, recent efforts to correlate measures of surface accessibility with labeling yield have been met with mixed success. Most applications of CL-MS involve differential analysis of protein interactions (i.e., footprinting experiments) where such inconsistencies have limited effect. Extending CL-MS into structural analysis requires an improved evaluation of the relationship between labeling and surface exposure. In this study, we applied recently developed diazirine reagents to obtain deep coverage of the large motor domain of Eg5 (a mitotic kinesin), and together with computational methods we correlated labeling yields with accessibility data in a number of ways. We observe that correlations can indeed be seen at a local structural level, but these correlations do not extend across the structure. The lack of correlation arises from the influence of protein dynamics and chemical composition on reagent partitioning and, thus, also on labeling yield. We conclude that our use of CL-MS data should be considered in light of "chemical accessibility" rather than "solvent accessibility" and suggest that CL-MS data would be a useful tool in the fundamental study of protein-solute interactions.

UV damage to hair and the effect of antioxidants and metal chelators

OBJECTIVE

To study the effects of addition of a redox metal, copper, antioxidants and metal chelators on the formation of free radicals in natural white Caucasian hair subsequently exposed to UV light. Three different methods, electron paramagnetic resonance (EPR), a fluorescent probe for hydroxyl radical formation (terephthalate) and free radical photoyellowing, were used. These methods utilized different UV sources and reaction conditions, and so can give insights into the different mechanisms of action occurring during UV oxidation of hair. In addition, this study demonstrates how antioxidants and chelators can be screened to determine whether they can protect hair from UV damage.

RESULTS

The three methods gave somewhat different results, illustrating the importance of reaction conditions and wavelength on the photochemical mechanisms, and the efficacy of additives to influence these reactions. EPR results showed that N-acetylcysteine (NAC) pre-treatment eliminated the intensity of the signal because of sulphur and carbon free radicals in white hair both before and after exposure to UVB radiation. Doping the hair with copper ions had no effect on the intensity of the EPR signal under dry conditions. Terephthalate fluorescent probe data showed that under wet conditions, irradiation of white hair with UVA produced significant amounts of hydroxyl radicals. Pre-treatment of hair with NAC reduced the number of •OH radicals produced by natural white hair compared to an untreated control. In contrast to the EPR result, white hair doped with copper ions produced significantly higher levels of •OH radicals under wet conditions. It appears that the ability of copper ions to catalyse the photogeneration free radicals in hair is highly dependent on water content. Photoyellowing data showed a benefit for oxalic acid but no difference for NAC and an increase in yellowing for EDTA.

CONCLUSION

The micro-EPR and terephthalate fluorescent probe methods are both effective techniques to study production of free radicals by hair exposed to UV light under wet and dry conditions, respectively. Both assays are simple methods for determining the effectiveness of potential protective hair treatments against UV damage, but because they assess free radical damage under dry vs wet conditions, the chemistry created on UV exposure is different. This gives insights into mechanism of action, but results may not be consistent between the two methods for actives added for reduction of UV damage. NAC pre-treatment did reduce free radical generation in UV-exposed hair under both wet and dry conditions. Photoyellowing data are more complicated as it is a less direct measure of UV damage and is highly dependent on irradiation source. Using UVB irradiation is experimentally convenient but may not be appropriate, because UVB wavelengths comprise only 0.3% of terrestrial sunlight. The photochemistry of hair exposed to sunlight involves concurrent photobleaching and photoyellowing processes and is far more complex. Under UVB irradiation conditions, oxalic acid showed a yellowing benefit.

Proteolysis and Oxidation of Therapeutic Proteins After Intradermal or Subcutaneous Administration

The intradermal (ID) and subcutaneous (SC) routes are commonly used for therapeutic proteins (TPs) and vaccines; however, the bioavailability of TPs is typically less than small molecule drugs given via the same routes. Proteolytic enzymes in the dermal, SC, and lymphatic tissues may be responsible for the loss of TPs. In addition, the TPs may be exposed to reactive oxygen species generated in the SC tissue and the lymphatic system in response to injection-related trauma and impurities within the formulation. The reactive oxygen species can oxidize TPs to alter their efficacy and immunogenicity potential. Mechanistic understandings of the dominant proteolysis and oxidative routes are useful in the drug discovery process, formulation development, and to assess the potential for immunogenicity and altered pharmacokinetics (PK). Furthermore, in vitro tools representing the ID or SC and lymphatic system can be used to evaluate the extent of proteolysis of the TPs after the injection and before systemic entry. The in vitro clearance data may be included in physiologically based pharmacokinetic models for improved PK predictions. In this review, we have summarized various physiological factors responsible for proteolysis and oxidation of TPs after ID and SC administration.

Formation and characterization of crosslinks, including Tyr–Trp species, on one electron oxidation of free Tyr and Trp residues by carbonate radical anion

Dityrosine and ditryptophan bonds have been implied in protein crosslinking. This is associated with oxidative stress conditions including those involved in neurodegenerative pathologies and age-related processes. Formation of dityrosine and ditryptophan derives from radical–radical reactions involving Tyr˙ and Trp˙ radicals. However, cross reactions of Tyr˙ and Trp˙ leading to Tyr–Trp crosslinks and their biological consequences have been less explored. In the present work we hypothesized that exposure of free Tyr and Trp to a high concentration of carbonate anion radicals (CO₃˙⁻), under anaerobic conditions, would result in the formation of Tyr–Trp species, as well as dityrosine and ditryptophan crosslinks. Here we report a simple experimental procedure, employing CO₃˙⁻ generated photochemically by illumination of a Co(iii) complex at 254 nm, that produces micromolar concentrations of Tyr–Trp crosslinks. Analysis by mass spectrometry of solutions containing only the individual amino acids, and the Co(iii) complex, provided evidence for the formation of o,o′-dityrosine and isodityrosine from Tyr, and three ditryptophan dimers from Trp. When mixtures of Tyr and Trp were illuminated in an identical manner, Tyr–Trp crosslinks were detected together with dityrosine and ditryptophan dimers. These results indicate that there is a balance between the formation of these three classes of crosslinks, which is dependent on the Tyr and Trp concentrations. The methods reported here allow the generation of significant yields of isolated Tyr–Trp adducts and their characterization. This technology should facilitate the detection, and examination of the biological consequences of Tyr–Trp crosslink formation in complex systems in future investigations.

Exposure of free Tyr and Trp to a high concentration of carbonate anion radicals (CO₃˙⁻), under anaerobic conditions, result in the formation of Tyr–Trp species, as well as dityrosine and ditryptophan crosslinks.

Detection, identification, and quantification of oxidative protein modifications

Exposure of biological molecules to oxidants is inevitable and therefore commonplace. Oxidative stress in cells arises from both external agents and endogenous processes that generate reactive species, either purposely (e.g. during pathogen killing or enzymatic reactions) or accidentally (e.g. exposure to radiation, pollutants, drugs, or chemicals). As proteins are highly abundant and react rapidly with many oxidants, they are highly susceptible to, and major targets of, oxidative damage. This can result in changes to protein structure, function, and turnover and to loss or (occasional) gain of activity. Accumulation of oxidatively-modified proteins, due to either increased generation or decreased removal, has been associated with both aging and multiple diseases. Different oxidants generate a broad, and sometimes characteristic, spectrum of post-translational modifications. The kinetics (rates) of damage formation also vary dramatically. There is a pressing need for reliable and robust methods that can detect, identify, and quantify the products formed on amino acids, peptides, and proteins, especially in complex systems. This review summarizes several advances in our understanding of this complex chemistry and highlights methods that are available to detect oxidative modifications-at the amino acid, peptide, or protein level-and their nature, quantity, and position within a peptide sequence. Although considerable progress has been made in the development and application of new techniques, it is clear that further development is required to fully assess the relative importance of protein oxidation and to determine whether an oxidation is a cause, or merely a consequence, of injurious processes.

Binding and Reactivity of Copper to R1 and R3 Fragments of tau Protein

Tau protein is present in significant amounts in neurons, where it contributes to the stabilization of microtubules. Insoluble neurofibrillary tangles of tau are associated with several neurological disorders known as tauopathies, among which is Alzheimer's disease. In neurons, tau binds tubulin through its microtubule binding domain which comprises four imperfect repeats (R₁-R₄). The histidine residues contained in these fragments are potential binding sites for metal ions and are located close to the regions that drive the formation of amyloid aggregates of tau. In this study, we present a detailed characterization through potentiometric and spectroscopic methods of the binding of copper in both oxidation states to R₁ and R₃ peptides, which contain one and two histidine residues, respectively. We also evaluate how the redox cycling of copper bound to tau peptides can mediate oxidation that can potentially target exogenous substrates such as neuronal catecholamines. The resulting quinone oxidation products undergo oligomerization and can competitively give post-translational peptide modifications yielding catechol adducts at amino acid residues. The presence of His-His tandem in the R₃ peptide strongly influences both the binding of copper and the reactivity of the resulting copper complex. In particular, the presence of the two adjacent histidines makes the copper(I) binding to R₃ much stronger than in R₁. The copper-R₃ complex is also much more active than the copper-R₁ complex in promoting oxidative reactions, indicating that the two neighboring histidines activate copper as a catalyst in molecular oxygen activation reactions.

Structural Lesions of Proteins Connected to Lipid Membrane Damages Caused by Radical Stress: Assessment by Biomimetic Systems and Raman Spectroscopy

Model systems constituted by proteins and unsaturated lipid vesicles were used to gain more insight into the effects of the propagation of an initial radical damage on protein to the lipid compartment. The latter is based on liposome technology and allows measuring the trans unsaturated fatty acid content as a result of free radical stress on proteins. Two kinds of sulfur-containing proteins were chosen to connect their chemical reactivity with membrane lipid transformation, serum albumins and metallothioneins. Biomimetic systems based on radiation chemistry were used to mimic the protein exposure to different kinds of free radical stress and Raman spectroscopy to shed light on protein structural changes caused by the free radical attack. Among the amino acid residues, Cys is one of the most sensitive residues towards the attack of free radicals, thus suggesting that metal-Cys clusters are good interceptors of reactive species in metallothioneins, together with disulfides moieties in serum albumins. Met is another important site of the attack, in particular under reductive conditions. Tyr and Phe are sensitive to radical stress too, leading to electron transfer reactions or radical-induced modifications of their structures. Finally, modifications in protein folding take place depending on reactive species attacking the protein.

Effects of cavitation on different microorganisms: The current understanding of the mechanisms taking place behind the phenomenon. A review and proposals for further research

A sudden decrease in pressure triggers the formation of vapour and gas bubbles inside a liquid medium (also called cavitation). This leads to many (key) engineering problems: material loss, noise, and vibration of hydraulic machinery. On the other hand, cavitation is a potentially useful phenomenon: the extreme conditions are increasingly used for a wide variety of applications such as surface cleaning, enhanced chemistry, and wastewater treatment (bacteria eradication and virus inactivation). Despite this significant progress, a large gap persists between the understanding of the mechanisms that contribute to the effects of cavitation and its application. Although engineers are already commercializing devices that employ cavitation, we are still not able to answer the fundamental question: What precisely are the mechanisms how bubbles can clean, disinfect, kill bacteria and enhance chemical activity? The present paper is a thorough review of the recent (from 2005 onward) work done in the fields of cavitation-assisted microorganism's destruction and aims to serve as a foundation to build on in the next years.

Peroxymonosulfate Oxidizes Amino Acids in Water without Activation

A variety of peptidic and proteinaceous contaminants (e.g., proteins, toxins, pathogens) present in the environment may pose risk to human health and wildlife. Peroxymonosulfate is a strong oxidant (E_H⁰ = 1.82 V for HSO₅^-, the predominant species at environmental pH values) that may hold promise for the deactivation of proteinaceous contaminants. Relatively little quantitative information exists on the rates of peroxymonosulfate reactions with free amino acids. Here, we studied the oxidation of 19 of the 20 standard proteinogenic amino acids (all except cysteine) by peroxymonosulfate without explicit activation. Reaction half-lives at pH 7 ranged from milliseconds to hours. Amino acids possessing sulfur-containing, heteroaromatic, or substituted aromatic side chains were the most susceptible to oxidation by peroxymonosulfate, with rates of transformation decreasing in the order methionine > tryptophan > tyrosine > histidine. The rate of tryptophan oxidation did not decrease in the presence of an aquatic natural organic matter. Singlet oxygen resulting from peroxymonosulfate self-decomposition, while detected by electron paramagnetic resonance spectroscopy, was unlikely to be the principal reactive species. Our results demonstrate that peroxymonosulfate is capable of oxidizing 19 amino acids without explicit activation and that solvent-exposed methionine and tryptophan residues are likely initial targets of oxidation in peptides and proteins.

Catalysis of Peroxide Reduction by Fast Reacting Protein Thiols

Life on Earth evolved in the presence of hydrogen peroxide, and other peroxides also emerged before and with the rise of aerobic metabolism. They were considered only as toxic byproducts for many years. Nowadays, peroxides are also regarded as metabolic products that play essential physiological cellular roles. Organisms have developed efficient mechanisms to metabolize peroxides, mostly based on two kinds of redox chemistry, catalases/peroxidases that depend on the heme prosthetic group to afford peroxide reduction and thiol-based peroxidases that support their redox activities on specialized fast reacting cysteine/selenocysteine (Cys/Sec) residues. Among the last group, glutathione peroxidases (GPxs) and peroxiredoxins (Prxs) are the most widespread and abundant families, and they are the leitmotif of this review. After presenting the properties and roles of different peroxides in biology, we discuss the chemical mechanisms of peroxide reduction by low molecular weight thiols, Prxs, GPxs, and other thiol-based peroxidases. Special attention is paid to the catalytic properties of Prxs and also to the importance and comparative outlook of the properties of Sec and its role in GPxs. To finish, we describe and discuss the current views on the activities of thiol-based peroxidases in peroxide-mediated redox signaling processes.

Ethanol Exacerbates Manganese-Induced Neurobehavioral Deficits, Striatal Oxidative Stress, and Apoptosis Via Regulation of p53, Caspase-3, and Bax/Bcl-2 Ratio-Dependent Pathway

This study investigated the effects of ethanol (EtOH) on manganese (Mn)-induced striatal toxicity in rat by evaluating the neurobehavioral changes, biochemical and molecular events in rats exposed to Mn alone at 30 mg/kg, or their combination with EtOH at 1.25- and 5-g/kg body weight for 35 consecutive days. Locomotive and exploratory profiles were assessed using a video tracking software (ANY-Maze software) during a 5-min trial in a novel environment. Subsequently, acetylcholinesterase (AChE) activity, oxidative stress markers, histological morphology, and expression of apoptotic proteins (p53 and Bax and caspase-3) and anti-apoptotic protein (Bcl-2) were assessed in the striatum. Results showed that Mn, EtOH, and their combination induced locomotor and motor deficits. Track plot analysis indicated that EtOH exacerbated the Mn-induced reduction in exploratory profiles of exposed rats. Similarly, exposure of rats to Mn, EtOH, or combination of Mn and EtOH resulted in decreased activities of anti-oxidant enzymes, diminished level of reduced glutathione, downregulated Bcl-2 expression, increased AChE activity, enhanced hydrogen peroxide and lipid peroxidation levels, and upregulated expressions of p53, Bax, and caspase-3. Moreover, potentiation of Mn-induced striatal toxicity by EtOH co-exposure was dose dependent. Taken together, it seems that EtOH exacerbates Mn-induced neurobehavioral deficits, oxidative stress, and apoptosis induction via the regulation of p53, caspase-3, and Bax/Bcl-2 ratio-dependent pathway in rat striatum.

Trigonella foenum-graceum seed (Fenugreek) hydroalcoholic extract improved the oxidative stress status in a rat model of diabetes-induced memory impairment

Background

The antidiabetic and antioxidant effects of Trigonella foenum-graceum have been suggested. The effects of hydroalcoholic extract of the plant seeds and metformin against the diabetes-induced memory impairment were investigated.

Materials and methods

The rats were treated: (1) control, (2) diabetic (3–6) and diabetic rats treated by 50, 100 and 200 mg/kg of the plant extract or metformin. The rats were diabetic by streptozotocin (STZ, 55 mg/kg). After the passive avoidance test, malondialdehyde (MDA), nitric oxide (NO) metabolites, total thiol (SH), catalase (CAT) and superoxide dismutase (SOD) were determined in the brain.

Results

In the diabetic group, at 3, 24 and 48 h after receiving a shock, the latency to enter the dark room was lower than for the controls (p < 0.001). All doses of the extract and metformin increased the latencies to enter the dark at 3 and 24 h after the shock treatment (p < 0.05–p < 0.001). Additionally, the two higher doses of the extract and metformin increased the latency at 48 h after the shock (p < 0.05–p < 0.001). Diabetes also elevated MDA and NO metabolites, while it reduced thiol, SOD and CAT in the hippocampal and cortical tissues (p < 0.001). Treatment of the diabetic animals by the highest dose of the extract and also metformin reduced the MDA and NO metabolites, while it improved thiols, SOD and CAT (p < 0.01–p < 0.001).

Conclusions

Based on our findings, metformin and the hydro-alcoholic extract from the T. foenum-graceum seed prevented memory deficits resulting from diabetes. Preventing oxidative damage in the brain may at least, in part, be responsible for the positive effects of the extract and metformin.

Variation in the structure and emulsification of egg yolk high-density lipoprotein by lipid peroxide

To further clarify the effect of the oxidation of egg yolk high-density lipoprotein (EYHDL) on the protein structure and emulsification, 2,2'-azobis (2-methylpropionamidine) dihydrochloride (AAPH) was selected as a representative lipid peroxidation-derived peroxyl radical. The results of Raman spectroscopy indicated that, with the increase in the concentration of AAPH, the EYHDL carbonyl content increased significantly and the free sulfhydryl content declined sharply. Circular dichroism spectroscopy and intrinsic fluorescence indicated that exposure of EYHDL to AAPH led to destruction of the orderly structure and reduction of the structural stability. The particle size distribution and zeta potential indicated that the peroxyl radical caused molecular aggregation. Moderate oxidizing conditions can enhance the emulsification of EYHDL, and high-intensity oxidation decreased emulsification. The research results indicated that EYHDL made a significant change in the oxidation system and led to a change in its structure and emulsification, providing a theoretical basis to clarify the EYHDL oxidation mechanism. PRACTICAL APPLICATIONS: Egg yolk powder is prone to emulsification degradation during storage. The emulsification of egg yolk powder is mainly derived from high-density lipoprotein in egg yolk. Moreover, egg yolk powder contains a large amount of lipids, and, during the processing and storage of egg yolk powder, many lipid peroxyl radicals are inevitably generated. Therefore, it is desired to combine the lipid peroxyl radicals generated during the storage of egg yolk powder with the decrease in emulsifiability. In this paper, we first investigated the effects of peroxyl radicals on the structure and emulsifying properties of high-density lipoproteins and provided a theoretical basis to solve the problem that the emulsifiability of egg yolk powder is significantly reduced during storage.

The Chemistry of Protein Oxidation in Food

Oxidation is one of the deterioration reactions of proteins in food, the importance of which is comparable to others such as Maillard, lipation, or protein-phenol reactions. While research on protein oxidation has led to a precise understanding of the processes and consequences in physiological systems, knowledge about the specific effects of protein oxidation in food or the role of "oxidized" dietary protein for the human body is comparatively scarce. Food protein oxidation can occur during the whole processing axis, from primary production to intestinal digestion. The present review summarizes the current knowledge and mechanisms of food protein oxidation from a chemical, technological, and nutritional-physiological viewpoint and gives a comprehensive classification of the individual reactions. Different analytical approaches are compared, and the relationship between oxidation of food proteins and oxidative stress in vivo is critically evaluated.

Mechanism of the Formation of Electronically Excited Species by Oxidative Metabolic Processes: Role of Reactive Oxygen Species

It is well known that biological systems, such as microorganisms, plants, and animals, including human beings, form spontaneous electronically excited species through oxidative metabolic processes. Though the mechanism responsible for the formation of electronically excited species is still not clearly understood, several lines of evidence suggest that reactive oxygen species (ROS) are involved in the formation of electronically excited species. This review attempts to describe the role of ROS in the formation of electronically excited species during oxidative metabolic processes. Briefly, the oxidation of biomolecules, such as lipids, proteins, and nucleic acids by ROS initiates a cascade of reactions that leads to the formation of triplet excited carbonyls formed by the decomposition of cyclic (1,2-dioxetane) and linear (tetroxide) high-energy intermediates. When chromophores are in proximity to triplet excited carbonyls, the triplet-singlet and triplet-triplet energy transfers from triplet excited carbonyls to chromophores result in the formation of singlet and triplet excited chromophores, respectively. Alternatively, when molecular oxygen is present, the triplet-singlet energy transfer from triplet excited carbonyls to molecular oxygen initiates the formation of singlet oxygen. Understanding the mechanism of the formation of electronically excited species allows us to use electronically excited species as a marker for oxidative metabolic processes in cells.

Numerical Simulation of the Kinetics of Radical Decay in Single-Pulse High-Energy Electron-Irradiated Polymer Aqueous Solutions

A new method for the numerical simulation of the radiation chemistry of aqueous polymer solutions is introduced. The method makes use of a deterministic approach combining the conventional homogeneous radiation chemistry of water with the chemistry of polymer radicals and other macromolecular species. The method is applied on single-pulse irradiations of aqueous polymer solutions. The speciation of macromolecular species accounts for the variations in the number of alkyl radicals per chain, molecular weight, and number of internal loops (as a consequence of an intramolecular radical-radical combination). In the simulations, the initial polymer molecular weight, polymer concentration, and dose per pulse (function of pulse length and dose rate during the pulse) were systematically varied. In total, 54 different conditions were simulated. The results are well in line with the available experimental data for similar systems. At a low polymer concentration and a high dose per pulse, the kinetics of radical decay is quite complex for the competition between intra- and intermolecular radical-radical reactions, whereas at a low dose per pulse the kinetics is purely second-order. The simulations demonstrate the limitations of the polymer in scavenging all the radicals generated by water radiolysis when irradiated at a low polymer concentration and a high dose per pulse. They also show that the radical decay of lower-molecular-weight chains is faster and to a larger extent dominated by intermolecular radical-radical reactions, thus explaining the mechanism behind the experimentally observed narrowing of molecular weight distributions.

Chemical Basis of Reactive Oxygen Species Reactivity and Involvement in Neurodegenerative Diseases

Increasing numbers of individuals suffer from neurodegenerative diseases, which are characterized by progressive loss of neurons. Oxidative stress, in particular, the overproduction of Reactive Oxygen Species (ROS), play an important role in the development of these diseases, as evidenced by the detection of products of lipid, protein and DNA oxidation in vivo. Even if they participate in cell signaling and metabolism regulation, ROS are also formidable weapons against most of the biological materials because of their intrinsic nature. By nature too, neurons are particularly sensitive to oxidation because of their high polyunsaturated fatty acid content, weak antioxidant defense and high oxygen consumption. Thus, the overproduction of ROS in neurons appears as particularly deleterious and the mechanisms involved in oxidative degradation of biomolecules are numerous and complexes. This review highlights the production and regulation of ROS, their chemical properties, both from kinetic and thermodynamic points of view, the links between them, and their implication in neurodegenerative diseases.

Covalent Modification of Amino Acids and Peptides Induced by Ionizing Radiation from an Electron Beam Linear Accelerator Used in Radiotherapy

To identify modifications to amino acids that are directly induced by ionizing radiation, free amino acids and 3-residue peptides were irradiated using a linear accelerator (Linac) radiotherapy device. Mass spectrometry was performed to detail the relative sensitivity to radiation as well as identify covalent, radiation-dependent adducts. The order of reactivity of the 20 common amino acids was generally in agreement with published literature except for His (most reactive of the 20) and Cys (less reactive). Novel and previously identified modifications on the free amino acids were detected. Amino acids were far less reactive when flanked by glycine residues in a tripeptide. Order of reactivity, with GVG most and GEG least, was substantially altered, as were patterns of modification. Radiation reactivity of amino acids is clearly and strongly affected by conversion of the α-amino and α-carboxyl groups to peptide bonds, and the presence of neighboring amino acid residues.

Proteomic analysis of oxidized proteins in the brain and liver of the Nile tilapia (Oreochromis niloticus) exposed to a water-accommodated fraction of Maya crude oil

Crude oil (CO) is a super mixture of chemical compounds whose toxic effects are reported in fish species according to international guidelines. In the current study a proteomic analysis of oxidized proteins (ox) was performed on the brain and liver of Nile tilapia exposed to WAF obtained from relevant environmental loads (0.01, 0.1 and 1.0 g/L) of Maya CO. Results have shown that oxidation of specific proteins was a newly discovered organ-dependent process able to disrupt key functions in Nile tilapia. In control fish, enzymes involved on aerobic metabolism (liver aldehyde dehydrogenase and brain dihydrofolate reductase) and liver tryptophan--tRNA ligase were oxidized. In WAF-treated liver specimens, fructose-bisphosphate aldolase (FBA), β-galactosidase (β-GAL) and dipeptidyl peptidase 9 (DPP-9) were detected in oxidized form. oxDPP-9 could be favorable by reducing the risk associated with altered glucose metabolism, the opposite effects elicited by oxFBA and oxβ-GAL. oxTrypsin showed a clear adverse effect by reducing probably the hepatocyte capacity to achieve proteolysis of oxidized proteins as well as for performing the proper digestive function. Additionally, enzyme implicated in purine metabolism adenosine (deaminase) was oxidized. Cerebral enzymes of mitochondrial respiratory chain complex (COX IV, COX5B), of glycosphingolipid biosynthesis (β-N-acetylhexosaminidase), involved in catecholamines degradation (catechol O-methyltransferase), and microtubule cytoskeleton (stathmin) were oxidized in WAF-treated specimens. This response suggests, in the brain, an adverse scenario for the mitochondrial respiration process and for ATP provision as for ischemia/reoxygenation challenges. Proteomic analysis of oxidized proteins is a promising tool for monitoring environmental quality influenced by hydrocarbons dissolved in water.

Oxidative Damage in Aliphatic Amino Acids and Di- and Tripeptides by the Environmental Free Radical Oxidant NO3•: The Role of the Amide Bond Revealed by Kinetic and Computational Studies

Kinetic and computational data reveal a complex behavior of the important environmental free radical oxidant NO₃^• in its reactions with aliphatic amino acids and di- and tripeptides, suggesting that attack at the amide N-H bond in the peptide backbone is a highly viable pathway, which proceeds through a proton-coupled electron transfer (PCET) mechanism with a rate coefficient of about 1 × 10⁶ M^-1 s^-1 in acetonitrile. Similar rate coefficients were determined for hydrogen abstraction from the α-carbon and from tertiary C-H bonds in the side chain. The obtained rate coefficients for the reaction of NO₃^• with aliphatic di- and tripeptides suggest that attack occurs at all of these sites in each individual amino acid residue, which makes aliphatic peptide sequences highly vulnerable to NO₃^•-induced oxidative damage. No evidence for amide neighboring group effects, which have previously been found to facilitate radical-induced side-chain damage in phenylalanine, was found for the reaction of NO₃^• with side chains in aliphatic peptides.

Toxicant-mediated redox control of proteostasis in neurodegeneration

Disruption in redox signaling and control of cellular processes has emerged as a key player in many pathologies including neurodegeneration. As protein aggregations are a common hallmark of several neuronal pathologies, a firm understanding of the interplay between redox signaling, oxidative and free radical stress, and proteinopathies is required to sort out the complex mechanisms in these diseases. Fortunately, models of toxicant-induced neurodegeneration can be utilized to evaluate and report mechanistic alterations in the proteostasis network (PN). The epidemiological links between environmental toxicants and neurological disease gives further credence into characterizing the toxicant-mediated PN disruptions observed in these conditions. Reviewed here are examples of mechanistic interaction between oxidative or free radical stress and PN alterations. Additionally, investigations into toxicant-mediated PN disruptions, specifically focusing on environmental metals and pesticides, are discussed. Finally, we emphasize the need to distinguish whether the presence of protein aggregations are contributory to phenotypes related to neurodegeneration, or if they are a byproduct of PN deficiencies.

En route to metal-mediated and metal-catalysed reactions in water

This perspective report presents the key approaches for the development of various organometallic reactions in aqueous media. In view of future sustainability, the efficient use of natural resources, such as renewable biomass-based feedstocks, constitutes an important aspect for sustainable chemical industry. The exploration and discovery of efficient organometallic reactions or equivalents in water enrich the toolbox of organic chemists for the direct conversion of biomass-derived feedstocks into high-valued chemicals and the direct modification of biomolecules in their native aqueous environment, which contributes to future sustainability.

Organic radical imaging in plants: Focus on protein radicals

Biomolecule (lipid and protein) oxidation products formed in plant cells exposed to photooxidative stress play a crucial role in the retrograde signaling and oxidative damage. The oxidation of biomolecules initiated by reactive oxygen species is associated with formation of organic (alkyl, peroxyl and alkoxyl) radicals. Currently, there is no selective and sensitive technique available for the detection of organic radicals in plant cells. Here, based on the analogy with animal cells, immuno-spin trapping using spin trap, 5,5-dimethyl-1-pyrroline N-oxide (DMPO) was used to image organic radicals in Arabidopsis leaves exposed to high light. Using antibody raised against the DMPO nitrone adduct conjugated with the fluorescein isothiocyanate, organic radicals were imaged by confocal laser scanning microscopy. Organic radicals are formed predominantly in the chloroplasts located at the periphery of the cells and distributed uniformly throughout the grana stack. Characterization of protein radicals by standard immunological techniques using anti-DMPO antibody shows protein bands with apparent molecular weights of 32 and 34 kDa assigned to D1 and D2 proteins and two protein bands below the D1/D2 band with apparent molecular weights of 23 and 18 kDa and four protein bands above the D1/D2 band with apparent molecular weights of 41, 43, 55 and 68 kDa. In summary, imaging of organic radicals by immuno-spin trapping represents selective and sensitive technique for the detection of organic radicals that might help to clarify mechanistic aspects on the role of organic radicals in the retrograde signaling and oxidative damage in plant cell.

Protective Effect of Taurine on Apoptosis of Spinal Cord Cells in Diabetic Neuropathy Rats

Diabetes mellitus (DM) is a condition characterized by chronic hyperglycemia, which leads to diabetic neuropathy and apoptosis in the spinal cord. Taurine has been found to ameliorate the diabetic neuropathy and control apoptosis in various tissues. However, there are few reports that discuss the direct relationship between spinal cord and anti-apoptotic effect of taurine. In this study, DM was induced in male SD rats with STZ @ 25 mg/Kg of body weight in combination with high fat diet. After 2 weeks, they were divided into four groups as DM: diabetic rats, T1 (0.5%), T2 (1%) and T3 (2%) taurine solution, while control group was non-diabetic rats (no treatment). The results showed that DM increased apoptosis, decreased phosphorylated Akt and Bad. DM decreased expression of Bcl-2 and increased the Bax. Moreover, the release of cytochrome c into cytosol was increased in DM and activation of caspase-3 was also increased. However, taurine reversed all these abnormal changes in a dose dependent manner. Our results suggested the involvement of Akt/Bad signaling pathway and mitochondrial apoptosis pathway in protective effect of taurine against apoptosis in the spinal cord of diabetic rats. Therefore, taurine may be a potential medicine against diabetic neuropathy by controlling apoptosis.

Modelling the repair of carbon-centred protein radicals by the antioxidants glutathione and Trolox

GSH can repair carbon-centred protein radicals with rate constants in the diffusion limit, but Trolox repairs are much slower.

Taurine Ameliorates High Glucose Induced Apoptosis in HT-22 Cells

Diabetes causes memory loss. Hippocampus is responsible for memory and increased apoptosis was found in diabetes patients. Taurine improved memory in diabetes condition. However, mechanism is unclear. In current study, hippocampal cell line HT-22 cells were subjected to analysis as five groups i.e. Control, High glucose (HG) at concentration of 150 mM, HG + 10 mM (T1), 20 mM (T2) and 40 mM (T3) taurine solution. TUNEL assay showed that HG increased the number of apoptotic cell significantly while taurine reduced apoptosis. Taurine increased phosphorylation of Akt in HT-22 cell treated with HG, and increased phosphorylation of Bad (p-Bad) was seen suggesting involvement of Akt/Bad signaling pathway. Expression of Bcl-2 was reduced in HG group but taurine improved this. Bax expression showed opposite trend. This indicated that taurine may reduce apoptosis by controlling balance of Bcl-2 and Bax. When the activation of Akt was blocked by using of perifosine, the effect of taurine disappears either partially or altogether. Thus, it was clear that taurine reduces apoptosis via Akt/Bad pathway in HT-22 cells exposed to HG which further improves downstream balance of Bcl-2 and Bax. This mechanism may be involved in apoptosis of hippocampus cells in diabetic condition.

Analysis of the soybean metallothionein system under free radical stress: protein modification connected to lipid membrane damage

Metallothioneins are small Cys-rich peptides capable of coordinating metal ions, and proposed to be involved in radical stress. The four Zn(ii)-GmMT complexes of soybean (Glycine max) were recombinantly synthesised and exposed to oxidative (HO˙) and reductive (H˙ atoms and eaq-) stress conditions. Gamma-irradiation was used to simulate the endogenous formation of the reactive species in both aqueous solutions and unsaturated lipid vesicle suspensions, a biomimetic model that showed that tandem protein/lipid damage occurs, in particular under reductive radical stress. This is due to the formation of diffusible sulphur-centred radicals, which migrate from the aqueous phase to the lipid bilayer and are thus able to transform the cis double bond of the oleate moiety into the trans isomer. Among the amino acid residues present in GmMTs, Cys is one of the most sensitive residues towards the attack of free radicals, thus suggesting metal-clusters to be good interceptors of free radicals. Also Met, Tyr and Phe residues are sensitive amino acid sites of attack under both oxidative and reductive conditions. The modification of the Zn(ii)-GmMT complexes, in particular isoform 2, was monitored by Raman spectroscopy and mass spectrometry. Free radical stress on the Zn(ii)-GmMT complexes is able to induce significant structural changes such as partial deconstruction and/or rearrangement of the metal clusters, but not the complete demetallation of the proteins nor breaking of the backbone, thus confirming their capability to act as protectors under free radical stress conditions.

Oxidation of amino acids by peracetic acid: Reaction kinetics, pathways and theoretical calculations

Peracetic acid (PAA) is a sanitizer with increasing use in food, medical and water treatment industries. Amino acids are important components in targeted foods for PAA treatment and ubiquitous in natural waterbodies and wastewater effluents as the primary form of dissolved organic nitrogen. To better understand the possible reactions, this work investigated the reaction kinetics and transformation pathways of selected amino acids towards PAA. Experimental results demonstrated that most amino acids showed sluggish reactivity to PAA except cysteine (CYS), methionine (MET), and histidine (HIS). CYS showed the highest reactivity with a very rapid reaction rate. Reactions of MET and HIS with PAA followed second-order kinetics with rate constants of 4.6 ± 0.2, and 1.8 ± 0.1 M^-1⋅s^-1 at pH 7, respectively. The reactions were faster at pH 5 and 7 than at pH 9 due to PAA speciation. Low concentrations of H₂O₂ coexistent with PAA contributed little to the oxidation of amino acids. The primary oxidation products of amino acids with PAA were [O] addition compounds on the reactive sites at thiol, thioether and imidazole groups. Theoretical calculations were applied to predict the reactivity and regioselectivity of PAA electrophilic attacks on amino acids and improved mechanistic understanding. As an oxidative disinfectant, the reaction of PAA with organics to form byproducts is inevitable; however, this study shows that PAA exhibits lower and more selective reactivity towards biomolecules such as amino acids than other common disinfectants, causing less concern of toxic disinfection byproducts. This attribute may allow greater stability and more targeted actions of PAA in various applications.

Soluble tau aggregates, not large fibrils, are the toxic species that display seeding and cross-seeding behavior

Several studies have proposed that fibrillary aggregates of tau and other amyloidogenic proteins are neurotoxic and result in numerous neurodegenerative diseases. However, these studies usually involve sonication or extrusion through needles before experimentation. As a consequence, these methods may fragment large aggregates producing a mixture of aggregated species rather than intact fibrils. Therefore, the results of these experiments may be reflective of other amyloidogenic species, such as oligomers and/or protofibrils/short fibrils. To investigate the effects of sonication on the aggregation of tau and other amyloidogenic proteins, fibrils were prepared and well characterized, then sonicated and evaluated by various biochemical and biophysical methods to identify the aggregated species present. We found that indeed a mixture of aggregated species was present along with short fibrils indicating that sonication leads to impure fibril samples and should be analyzed with caution. Our results corroborate the previous studies showing that sonication of prion and Aβ fibrils leads to the formation of toxic, soluble aggregates. We also show that the oligomeric forms are the most toxic species although it is unclear how sonication causes oligomer formation. Recent results suggest that these small toxic oligomers produced by sonication, rather than the stable fibrillar structures, are prion-like in nature displaying seeding and cross-seeding behavior.

Redox Signaling by Reactive Electrophiles and Oxidants

The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.

Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation

The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin's internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV + VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations. Graphical Abstract.

Achieving Controlled Biomolecule-Biomaterial Conjugation

The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.

Pyrethroid bifenthrin induces oxidative stress, neuroinflammation, and neuronal damage, associated with cognitive and memory impairment in murine hippocampus

Exposure to synthetic pyrethroid (SPs) pesticides such as bifenthrin (BF) has been associated with adverse neurodevelopmental outcomes and cognitive impairments, but the underlying neurobiological mechanism is poorly understood so far. The present study has been designed to evaluate changes in behavior and in biomarkers of oxidative stress and neuroinflammation in the hippocampus of rats subchronically treated with BF. Rats exposed daily to BF at doses of 0.6 and 2.1 mg/kg b. w. for 60 days exhibited spatial and cognitive impairments as well as memory dysfunction after 60 days. This repeated BF treatment also significantly increased mRNA expression of pro-inflammatory cytokines tumor necrosis factor (TNF-α), interleukin (IL-1β), (IL-6), nuclear factor erythroid-2 (Nrf2), cyclooxygenase-2 (COX-2), nuclear factor-kappaB pathway (NF-kappaB), and prostaglandin E₂ (PGE₂) in the hippocampus. It further resulted in a significant increase in protein levels of Nrf2, COX-2, microsomal prostaglandin synthase-1 (mPGES-1) and NF-kappaB. This was accompanied by oxidative/nitrosative stress in the hippocampus of treated rats, as shown by increased levels of malondialdehyde (MDA), protein carbonyls (PCO), and nitric oxide (NO), and reduced levels of enzymatic (catalase, superoxide dismutase, and glutathione peroxidase) and non-enzymatic (reduced glutathione) antioxidants. The data are in line with those obtained in organotypic hippocampal slice cultures (OHSCs) isolated from mouse brain and exposed to BF for 72 h, showing neuronal death only at the high dose of 20 μM when compared to controls. These findings suggest that exposure to BF induces neuronal damage, alters redox state, and causes neuroinflammation in the hippocampus, which might lead to cognitive and memory impairment.

Proteomics Approach To Trace Site-Specific Damage in Aquatic Extracellular Enzymes During Photoinactivation

Extracellular enzymes are major drivers of biogeochemical nutrient and carbon cycling in surface water. While photoinactivation is regarded as a major inactivation process of these enzymes, the underlying molecular changes have received little attention. This study demonstrates how light exposure leads to a rapid loss of phosphatase, aminopeptidase, and glucosidase activities of biofilm samples and model enzymes. Here, an optimized proteomics approach allowed simultaneous observation of inactivation and molecular changes. Site-specific fingerprints of degradation kinetics have been generated and visualized in the three-dimensional proteins. Oxidation of tryptophan, the chromophoric target, initiated secondary reactions. Evidence was obtained that tyrosine residues act as intramolecular antioxidants, reflected in decelerated decay of tryptophan-containing peptides and enhanced decay of tyrosine-containing peptides. In addition, subsequent methionine oxidation and disulfide reduction contribute to heterogeneous photodamage. The proximity to tryptophan residues explains >95% of the photodamage across the protein structures. The presence of redox active organic matter or a model antioxidant in solution quenched not only photoinactivation and tryptophan oxidation but also all subsequent damage. The developed analytical approach can be applied to other research questions in environmental sciences where site-specific damage in a protein is essential.

Oxidative functionalization of aliphatic and aromatic amino acid derivatives with H2O2 catalyzed by a nonheme imine based iron complex

The oxidation of a series of N-acetyl amino acid methyl esters with H₂O₂ catalyzed by a very simple iminopyridine iron(ii) complex 1 easily obtainable in situ by self-assembly of 2-picolylaldehyde, 2-picolylamine, and Fe(OTf)₂ was investigated. Oxidation of protected aliphatic amino acids occurs at the α-C–H bond exclusively (N-AcAlaOMe) or in competition with the side-chain functionalization (N-AcValOMe and N-AcLeuOMe). N-AcProOMe is smoothly and cleanly oxidized with high regioselectivity affording exclusively C-5 oxidation products. Remarkably, complex 1 is also able to catalyze the oxidation of the aromatic N-AcPheOMe. A marked preference for the aromatic ring hydroxylation over Cα–H and benzylic C–H oxidation was observed, leading to the clean formation of tyrosine and its phenolic isomers.

Amino acid derivatives are oxidized by the 1/H₂O₂ system. A marked preference for the aromatic over Cα–H and benzylic C–H oxidation is observed with phenylalanine.