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Photo-tuneable protein nitration by sensitiser tris(bipyridine)-Ruthenium(II) chloride complex
Abstract
Post-translational modifications (PTMs) of proteins are a diverse source of variability that impacts on their functions, localisation, regulation, and lifetime. However, one of the main pitfalls in their study is that they appear in rather low frequencies and/or are only transiently observed. To overcome this issue and ease the study in vitro of stress-related protein PTMs, several methods have been proposed to model stress conditions and chemically introduce them. These techniques employ the combination of peroxides with transition metal ions or haem-containing proteins, as well as other possibilities such as peroxy radicals or UV radiation. However, their control, reproducibility and undesired secondary reactions that reduce the process yield are often a matter of concern. Here we introduce a photo-tuneable method that selectively targets nitration of aromatic residues. We initially present the adaptation of an oxidation method based on the photosensitiser tris(2,2′-bipyridine)-Ruthenium(II) chloride complex and ammonium persulfate, in which we employ an alternative radical neutralisation/trapping pathway that uses nitrite ions for the nitration of free l-Tyrosine and L-Tryptophan amino acids. After analysing the effect of several factors, we report the application of the photo-tuneable protein nitration (PTPN) method to four different model proteins in which we evaluate the nitration and oxidation of residues in each case. A mass spectrometry label-free quantitation of Tyr and Trp nitration is also described in order to compare the degree of modification and the accessibility of these residues. The method described could be employed to scale up the production of proteins with a selected range of oxidative PTMs for their characterisation, the assessment of their pathophysiological roles, and the development of detection and quantification methods to validate these PTMs as novel biomarkers associated with oxidative stress-related pathologies, such as in cardiovascular or neurodegenerative diseases.
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Various internal and external factors negatively affect the homeostatic equilibrium of organisms at the molecular to the whole-body level, inducing the so-called state of stress. Stress affects an organism’s welfare status and induces energy-consuming mechanisms to combat the subsequent ill effects; thus, the individual may be immunocompromised, making them vulnerable to pathogens. The information presented here has been extensively reviewed, compiled, and analyzed from authenticated published resources available on Medline, PubMed, PubMed Central, Science Direct, and other scientific databases. Stress levels can be monitored by the quantitative and qualitative measurement of biomarkers. Potential markers of stress include thermal stress markers such as heat shock proteins (HSPs), innate immune markers such as Acute Phase Proteins (APPs), oxidative stress markers, and chemical secretions in the saliva and urine. In addition, stress biomarkers also play critical roles in the prognosis of stress-related diseases and disorders, and therapy guidance. Moreover, different components have been identified as potent mediators of cardiovascular, central nervous system, hepatic, and nephrological disorders, which can also be employed to evaluate these conditions precisely, but with stringent validation and specificity. Considerable scientific advances have been made in the detection, quantitation, and application of these biomarkers. The present review describes the current progress of identifying biomarkers, their prognostic, and therapeutic values.
The use of enzymes for synthetic applications is a powerful and environmentally-benign approach to increase molecular complexity. Oxidoreductases selectively introduce oxygen and hydrogen atoms in myriad substrates, catalyzing the synthesis of chemical and pharmaceutical building blocks for chemical production. However, broader application of this class of enzymes is limited by the requirement of expensive cofactors and low operational stability. Herein, we show that morpholine-based buffers, specially 3-(N-morpholino)propanesulfonic acid (MOPS), promote photoinduced flavoenzyme-catalyzed asymmetric redox transformations by regenerating the flavin cofactor via sacrificial electron donation and by increasing the operational stability of flavin-dependent oxidoreductases. The stabilization of the active forms of the flavin by MOPS via formation of the spin correlated ion ³[Flavin●–-MOPS●+] ensemble reduces the formation of hydrogen peroxide, circumventing the oxygen dilemma under aerobic conditions detrimental to fragile enzymes.
The management of patients with autoimmune rheumatic diseases such as rheumatoid arthritis (RA) remains a significant challenge. Often the rheumatologist is restricted to treating and relieving the symptoms and consequences and not the underlying cause of the disease. Oxidative stress occurs in many autoimmune diseases, with the excess production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). The sources of such reactive species include NADPH oxidases (NOXs), the mitochondrial electron transport chain, nitric oxide synthases, nitrite reductases, and the hydrogen sulfide producing enzymes cystathionine-β synthase and cystathionine-γ lyase. Superoxide undergoes a dismutation reaction to generate hydrogen peroxide which, in the presence of transition metal ions (e.g. ferrous ions), forms the hydroxyl radical. The enzyme myeloperoxidase, present in inflammatory cells, produces hypochlorous acid, and in healthy individuals ROS and RNS production by phagocytic cells is important in microbial killing. Both low molecular weight antioxidant molecules and antioxidant enzymes, such as superoxide dismutase, catalase, glutathione peroxidase, and peroxiredoxin remove ROS. However, when ROS production exceeds the antioxidant protection, oxidative stress occurs. Oxidative post-translational modifications of proteins then occur. Sometimes protein modifications may give rise to neoepitopes that are recognized by the immune system as 'non-self' and result in the formation of autoantibodies. The detection of autoantibodies against specific antigens, might improve both early diagnosis and monitoring of disease activity. Promising diagnostic autoantibodies include anti-carbamylated proteins and anti-oxidized type II collagen antibodies. Some of the most promising future strategies for redox-based therapeutic compounds are the activation of endogenous cellular antioxidant systems (e.g. Nrf2-dependent pathways), inhibition of disease-relevant sources of ROS/RNS (e.g. isoform-specific NOX inhibitors), or perhaps specifically scavenging disease-triggering ROS/RNS via site-specific antioxidants.
In 1841, the extraction of hematoporphyrin from dried blood by removing iron marked the birth of the photosensitizer. The last twenty years has witnessed extensive research in the application of photodynamic therapy (PDT) in tumor-bearing (or other diseases) animal models and patients. The period has seen development of photosensitizers from the first to the third generation, and their evolution from simple to more complex entities. This review focuses on porphyrin photosensitizers and their effect on tumors, mediated via several pathways involved in cell necrosis, apoptosis or autophagic cell death, and the preventive and therapeutic application of PDT against atherosclerosis.
Tris and phosphate buffer are regularly used in experimental investigations. These buffers might have radical scavenger properties toward different kinds of Reactive Oxygen Species (ROS) produced in solutions during chemical reactions like Fenton reaction and gamma radiolysis. Hydroxyl radicals (ºOH) are the most reactive and oxidizing agents having a great potential in oxidization of macromolecules like DNA and proteins. This in vitro study was aimed to evaluate radio-protective effects of Tris and phosphate buffer toward hydroxyl radicals generated by Fenton reaction. Hence, ºOH radicals were produced using a mixture of Hydrogen Peroxideand Ferrous Sulfate, called Fenton system. Human serum albumin (500µM) was prepared in Tris (10mM) and phosphate buffer (10mM), separately. These two samples were incubated with Fenton reaction (Ferrous Sulfate + Hydrogen peroxide) (10 mM) for 30 minutes and carbonyl groups were quantified by spectrophotometric carbonylation assay. The results of this study revealed the values of 1.04 ± 0.02 and 1.73 ± 0.03 for Tris and phosphate buffer treated samples, respectively. In conclusion, these findings confirmed that Tris buffer is a stronger radical scavenger toward ºOH radicals than phosphate buffer. </strong
Significance:
Oxidative stress is considered to be an important component of various diseases. A vast number of methods have been developed and used in virtually all diseases to measure the extent and nature of oxidative stress, ranging from oxidation of DNA, to protein, lipids and free amino acids. Recent advances: An increased understanding of the biology behind diseases and redox biology has led to more specific and sensitive tools to measure oxidative stress markers, which are very diverse and sometimes very low in abundance.
Critical issues:
The literature is very heterogeneous. It is often difficult to draw general conclusions on the significance of oxidative stress biomarkers, as only in a limited proportion of diseases have a range of different biomarkers been used, and different biomarkers have been used to study different diseases. In addition biomarkers are often measured using non-specific methods, while specific methodologies are often too sophisticated or laborious for routine clinical use.
Future directions:
Several markers of oxidative stress still represent a viable biomarker opportunity for clinical use. However, positive findings with currently used biomarkers still need to be validated in larger sample sizes and compared to current clinical standards to establish them as clinical diagnostics. It is important to realize that oxidative stress is a nuanced phenomenon that is difficult to characterize, and one biomarker is not necessarily better than others. The vast diversity in oxidative stress between diseases and conditions has to be taken into account when selecting the most proper biomarker.
The use of buffers to maintain the pH within the desired range is a very common practice in chemical, biochemical and biological studies. Among them, zwitterionic N-substituted aminosulfonic acids, usually known as Good’s buffers, although widely used can complex metals and interact with biological systems. The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. In addition, their impact on the biological systems is also presented. The influence of these buffers on the results obtained in biological, biochemical and environmental studies, with special focus on their interaction with metal ions, are highlighted and critically reviewed. Using chemical speciation simulations, based on the current knowledge of the metal-buffer stability constants, a proposal of the most adequate buffer to employ for a given metal ion is presented.
The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To calculate RSA, a residue's solvent accessibility (ASA) needs to be normalized by a suitable reference value for the given amino acid; several normalization scales have previously been proposed. However, these scales do not provide tight upper bounds on ASA values frequently observed in empirical crystal structures. Instead, they underestimate the largest allowed ASA values, by up to 20%. As a result, many empirical crystal structures contain residues that seem to have RSA values in excess of one. Here, we derive a new normalization scale that does provide a tight upper bound on observed ASA values. We pursue two complementary strategies, one based on extensive analysis of empirical structures and one based on systematic enumeration of biophysically allowed tripeptides. Both approaches yield congruent results that consistently exceed published values. We conclude that previously published ASA normalization values were too small, primarily because the conformations that maximize ASA had not been correctly identified. As an application of our results, we show that empirically derived hydrophobicity scales are sensitive to accurate RSA calculation, and we derive new hydrophobicity scales that show increased correlation with experimentally measured scales.
Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need for improved label-free approaches. This need is particularly pressing for workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as isobaric tags for relative and absolute quantitation and tandem mass tags may prove problematic or where stable isotope labeling with amino acids in cell culture labeling cannot be readily applied. Skyline is a freely available, open source software tool for quantitative data processing and proteomic analysis. We expanded the capabilities of Skyline to process ion intensity chromatograms of peptide analytes from full scan mass spectral data (MS1) acquired during HPLC MS/MS proteomic experiments. Moreover, unlike existing programs, Skyline MS1 filtering can be used with mass spectrometers from four major vendors, which allows results to be compared directly across laboratories. The new quantitative and graphical tools now available in Skyline specifically support interrogation of multiple acquisitions for MS1 filtering, including visual inspection of peak picking and both automated and manual integration, key features often lacking in existing software. In addition, Skyline MS1 filtering displays retention time indicators from underlying MS/MS data contained within the spectral library to ensure proper peak selection. The modular structure of Skyline also provides well defined, customizable data reports and thus allows users to directly connect to existing statistical programs for post hoc data analysis. To demonstrate the utility of the MS1 filtering approach, we have carried out experiments on several MS platforms and have specifically examined the performance of this method to quantify two important post-translational modifications: acetylation and phosphorylation, in peptide-centric affinity workflows of increasing complexity using mouse and human models.
Solvent polarity and the local environment have profound effects on the emission spectral properties of fluorophores. The effects of solvent polarity are one origin of the Stokes shift, which is one of the earliest observations in fluorescence. Emission spectra are easily measured, resulting in numerous publications on emission spectra of fluorophores in different solvents, and when bound to proteins, membranes, and nucleic acids. One common use of solvent effects is to determine the polarity of the probe binding site on the macromolecule. This is accomplished by comparison of the emission spectra and/or quantum yields when the flu-orophore is bound to the macromolecule or dissolved in solvents of different polarity. However, there are many additional instances where solvent effects are used. Suppose a fluorescent ligand binds to a protein or membrane. Binding is usually accompanied by spectral shift or change in quantum yield due to the different environment for the bound ligand. Alternatively, the ligand may induce a spectral shift in the intrinsic or extrinsic protein fluorescence. In either case the spectral changes can be used to measure the extent of binding. The effects of solvent and environment on fluorescence spectra are complex, and are due to several factors in addition to solvent polarity. The factors that affect fluorescence emission spectra and quantum yields include:
Chemical cross-linking is a potentially useful technique for probing the architecture of multiprotein complexes. However, analyses using typical bifunctional cross-linkers often suffer from poor yields, and large-scale modification of nucleophilic side chains can result in artifactual results attributable to structural destabilization. We report here the de novo design and development of a type of protein cross-linking reaction that uses a photogenerated oxidant to mediate rapid and efficient cross-linking of associated proteins. The process involves brief photolysis of tris-bipyridylruthenium(II) dication with visible light in the presence of the electron acceptor ammonium persulfate and the proteins of interest. Very high yields of cross-linked products can be obtained with irradiation times of <1 second. This chemistry obviates many of the problems associated with standard cross-linking reagents.
α-Synuclein (α-syn), a small highly conserved presynaptic protein containing 140 amino acids, is thought to be the main pathological hallmark in related neurodegenerative disorders. Although the normal function of α-syn is closely involved in the regulation of vesicular neurotransmission in these diseases, the underlying mechanisms of post-translational modifications (PTMs) of α-syn in the pathogenesis of Parkinson's disease (PD) have not been fully characterized. The pathological accumulation of misfolded α-syn has a critical role in PD pathogenesis. Recent studies of factors contributing to α-syn-associated aggregation and misfolding have expanded our understanding of the PD disease process. In this Review, we summarize the structure and physiological function of α-syn, and we further highlight the major PTMs (namely phosphorylation, ubiquitination, nitration, acetylation, truncation, SUMOylation, and O-GlcNAcylation) of α-syn and the effects of these modifications on α-syn aggregation, which may elucidate mechanisms for PD pathogenesis and lay a theoretical foundation for clinical treatment of PD.
In the year of 2019, we celebrate the centenary of the publication of the remarkable paper by Otto Stern and Max Volmer concerning the kinetics analysis of fluorescence quenching. Their achievement changed enormously many fields of science with great impact in the studies of electronic spectroscopy and kinetics of organic, inorganic and biological compounds in condensed phase. The development of molecular photochemistry was in great part based on the use of the Stern-Volmer (SV) approach to investigate bimolecular interaction in the electronic excited-state. This paper reviews and summarizes the assumptions behind the Stern-Volmer equation and the extensions of the theory to other important situations. Discussions about the use of the SV approach to investigate probe and quencher distribution, association, diffusion and reaction at the molecular level obtained from advanced fluorescence microscopy methods are also included.
This work examined the hypothesis that interactions of Rose Bengal (RB2-) with lysozyme (Lyso) might mediate type 1 photoreactions resulting in protein cross-linking even under conditions favoring 1O2 formation. UV-visible spectrophotometry, isothermal titration calorimetry (ITC), and docking analysis were employed to characterize RB2--Lyso interactions, while oxidation of Lyso was studied by SDS-PAGE gels, extent of amino acid consumption, and liquid chromatography (LC) with mass detection (employing tryptic peptides digested in H218O and H2O). Docking studies showed five interaction sites including the active site. Hydrophobic interactions induced a red shift of the visible spectrum of RB2- giving a Kd of 4.8 μM, while data from ITC studies, yielded a Kd of 0.68 μM as an average of the interactions with stoichiometry of 3.3 RB2- per Lyso. LC analysis showed a high consumption of readily-oxidized amino acids (His, Trp, Met and Tyr) located at different and diverse locations within the protein. This appears to reflect extensive damage on the protein probably mediated by a type 2 (1O2) mechanism. In contrast, docking and mass spectrometry analysis provided evidence for the generation of specific intra- (Tyr23-Tyr20) and inter-molecular (Tyr23-Trp62) Lyso cross-links, and Lyso dimer formation via radical-radical, type 1 mechanisms.
The tyrosine dimer (Tyr2), a covalent bond between two tyrosines (Tyr), is one of the most important modifications of the oxidative damage of proteins. This compound is increasingly used as a marker of aging, stress and pathogenesis. At physiological pH, Tyr2 is able to absorb radiation at wavelengths significantly present in the solar radiation and artificial sources of light. As a result, when Tyr2 is formed in vivo, a new chromophore appears in the proteins. Despite the biomedical importance of Tyr2, the information of its photochemical properties is limited due to the drawbacks of its synthesis. Therefore, in this work we demonstrate that at physiological pH, Tyr2 undergoes oxidation upon UV excitation yielding different products which conserve the dimeric structure. During its photodegradation different reactive oxygen species, like hydrogen peroxide, superoxide anion and singlet oxygen, are produced. Otherwise, we demonstrated that Tyr2 is able to sensitize the photodegradation of tyrosine. The results presented in this work confirm that Tyr2 can act as a potential photosensitizer, contributing to the harmful effects of UV-A radiation on biological systems.
Ruthenium complexes exhibit a broad variety of biological and biomedical activities including anticancer efficiency. The reason is that the octahedral bonding of both Ru(II) and Ru(III) complexes affords an extensive repertoire of three-dimensional architectures, giving the potential for a high degree of site selectivity for binding to their biological targets. The mechanism of biological and biomedical action of ruthenium compounds is connected with their interactions with biomacromolecules. A lot of mechanistic studies revealed disposition of many ruthenium complexes to operate via mechanisms of action involving interactions with DNA, but distinctly different from those of the approved platinum anticancer drugs. In this Review, we discuss major DNA binding modes hitherto identified for ruthenium complexes of biological or biomedical significance and provide some typical examples. The introduction provides the reader with a brief overview of the approaches in the search for the new, transition metal-based agents of biological or biomedical significance to provide the context in which more recent research of DNA binding of ruthenium complexes has been evolved. We then describe main categories of binding modes between DNA and ruthenium compounds, such as coordinative, intercalative, minor groove binding, sequence specificity of DNA binding, the ability of ruthenium compounds to condense and cleave DNA, binding to A- and Z-DNA, DNA quadruplexes and other unusual DNA structures. A number of complexes based on ruthenium(II) centers have been reported to have excellent photophysical and radiosensitizing properties so that DNA photocleavage and synergistic enhancement of DNA damage due to a combined action of ruthenium complexes and ionizing radiation is also discussed. Finally, inhibition of DNA processing enzymes is reviewed as well. We believe that such a synthesis of disparate DNA binding modes of ruthenium complexes will help to generate new ruthenium complexes of improved biological and biomedical significance.
Oxidation can be induced by multiple processes in biological samples, with proteins being important targets due to their high abundance and reactivity. Oxidant reactions with proteins are not comprehensively understood, but it is known that structural and functional changes may be a cause, or a consequence, of disease. The mechanisms of oxidation of the model protein RNAse A by singlet oxygen (1O2) were examined and compared to peroxyl radical (ROO●) oxidation, both common biological oxidants. This protein is a prototypic member of the RNAse family that exhibits antiviral activity by cleaving single-stranded RNA. RNAse A lacks tryptophan and cysteine residues which are major oxidant targets, but contains multiple histidine, tyrosine and methionine residues; these were therefore hypothesized to be the major sites of damage. 1O2 and ROO● induce different patterns and extents of damage; both induce cross-links and side-chain oxidation, and 1O2 exposure modulates enzymatic activity. Multiple products have been characterized including methionine sulfoxide and sulfone, alcohols, DOPA, 2-oxohistidine, histidine-derived ring-opened species and inter- and intra-molecular cross-links (di-tyrosine, histidine-lysine, histidine-arginine, tyrosine-lysine). In addition to methionine modification, which appears not to be causative to activity loss, singlet oxygen also induces alteration to specific histidine, tyrosine and proline residues, including modification and cross-linking of the active site histidine, His12. The high homology among the RNAse family suggests that similar modifications may occur in humans, and be associated with the increased risk of viral infections in people with diabetes, as markers for 1O2 have been found in early stages of this pathology.
Non-enzymatic post-translational modifications of proteins can occur when a nucleophilic or redox-sensitive amino acid side chain encounters a reactive metabolite. In many cases, the biological function of these modifications is limited by their irreversibility, and consequently these non-enzymatic modifications are often considered as indicators of stress and disease. Certain non-enzymatic post-translational modifications, however, can be reversed, which provides an additional layer of regulation and renders these modifications suitable for controlling a diverse set of cellular processes ranging from signaling to metabolism. Here we summarize recent examples of irreversible and reversible non-enzymatic modifications, with an emphasis on the latter category. We use two examples, lysine glutarylation and pyrophosphorylation, to highlight principles of the regulation of reversible non-enzymatic post-translational modifications in more detail. Overall, a picture emerges that goes well beyond nonspecific chemical reactions and cellular damage, and instead portrays multifaceted functions of non-enzymatic post-translational modifications.
Peroxynitrite is a short-lived and reactive biological oxidant formed from the diffusion-controlled reaction of the free radicals superoxide (O2•–) and nitric oxide (•NO). In this review, we first analyze the biochemical evidence for the formation of peroxynitrite in vivo and the reactions that lead to it. Then, we describe the principal reactions that peroxynitrite undergoes with biological targets and provide kinetic and mechanistic details. In these reactions, peroxynitrite has roles as (1) peroxide, (2) Lewis base, and (3) free radical generator. Physiological levels of CO2 can change the outcome of peroxynitrite reactions. The second part of the review assesses the formation of protein 3-nitrotyrosine (NO2Tyr) by peroxynitrite-dependent and -independent mechanisms, as one of the hallmarks of the actions of •NO-derived oxidants in biological systems. Moreover, tyrosine nitration impacts protein structure and function, tyrosine kinase signal transduction cascades and protein turnover. Overall, the review is aimed to provide an integrated biochemical view on the formation and reactions of peroxynitrite under biologically relevant conditions and the impact of this stealthy oxidant and one of its major footprints, protein NO2Tyr, in the disruption of cellular homeostasis.
Lactoferrin (LF) is an important multifunctional protein that comprises a large fraction of the protein mass in certain human fluids and tissues, and its concentration is often used to assess health and disease. LF can be nitrated by multiple routes, leading to changes in protein structure, and nitrated proteins can negatively impact physiological health via nitrosative stress. Despite an awareness of the detrimental effects of nitrated proteins and the importance of LF within the body, cost-effective methods for detecting and quantifying nitrated lactoferrin (NLF) are lacking. We developed a procedure to selectively quantify NLF using sandwich enzyme-linked immunosorbent assay (ELISA), utilizing a polyclonal anti-LF capture antibody paired with a monoclonal anti-nitrotyrosine detector antibody. The assay was applied to quantify NLF in samples of pure LF nitrated via two separate reactions at molar ratios of excess nitrating agent to the total number of tyrosine residues between 10/1 and 100/1. Tetranitromethane (TNM) was used as a laboratory surrogate for an environmental pathway selective for production of 3-nitrotyrosine, and sodium peroxynitrite (ONOO⁻) was used as a surrogate for an endogenous nitration pathway. UV-vis spectroscopy (increased absorbance at 350 nm) and fluorescence spectroscopy (emission decreased by > 96%) for each reaction indicate the production of NLF. A lower limit of NLF detection using the ELISA method introduced here was calculated to be 0.065 μg mL⁻¹, which will enable the detection of human-physiologically relevant concentrations of NLF. Our approach provides a relatively inexpensive and practical way to assess NLF in a variety of systems.
Protein oxidation is a frequent event as a result of the high abundance of proteins in biological samples and the multiple processes that generate oxidants. The reactions that occur are complex and poorly understood, but can generate major structural and functional changes on proteins. Current data indicate that pathophysiological processes and multiple human diseases are associated with the accumulation of damaged proteins. In this study we investigated the mechanisms and consequences of exposure of the key metabolic enzyme glucose-6-phosphate dehydrogenase (G6PDH) to peroxyl radicals (ROO●) and singlet oxygen (¹O2), with particular emphasis on the role of Trp and Tyr residues in protein cross-linking and fragmentation. Cross-links and high molecular mass aggregates were detected by SDS-PAGE and Western blotting using specific antibodies. Amino acid analysis has provided evidence for Trp and Tyr consumption and formation of oxygenated products (diols, peroxides, N-formylkynurenine, kynurenine) from Trp, and di-tyrosine (from Tyr). Mass spectrometric data obtained after trypsin-digestion in the presence of H2¹⁶O and H2¹⁸O, has allowed the mapping of specific cross-linked residues and their locations. These data indicate that specific Tyr-Trp and di-Tyr cross-links are formed from residues that are proximal and surface-accessible, and that the extent of Trp oxidation varies markedly between sites. Limited modification at other residues is also detected. These data indicate that Trp and Tyr residues are readily modified by ROO● and ¹O2 with this giving products that impact significantly on protein structure and function. The formation of such cross-links may help rationalize the accumulation of damaged proteins in vivo.
Oxidative damage to proteins leads to a variety of modifications that are markers of pathogenesis. One of the most important modifications is the dityrosine (Tyr2) cross-link, resulting from an oxidative covalent bond between two tyrosines (Tyr). An optimized methodology for preparation of pure Tyr2 is important to investigate in detail its physicochemical properties and reactivity. Pterin (Ptr), the parent and unsubstituted compound of oxidized pterins, is able to photosensitize the cross-linking of free tyrosine (Tyr) and tyrosine residues of peptides and proteins through a photoinduced electron transfer mechanism. We have optimized a simple, one-step photocatalyzed formation of Tyr2, using Ptr as photocatalyst. Our procedure is carried out in aqueous solutions under UV-A radiation for few minutes. The purification of Tyr2 is performed by reverse-phase chromatography. The obtained highly pure solution is used to fully characterize the Tyr2 (exact mass and ¹H, ¹H-¹H COSY; DEPT; HSQC and HMBC NMR experiments) and to deeper study its fluorescence properties.
Fibronectin is a large dimeric glycoprotein present in both human plasma and in basement membranes. The latter are specialized extracellular matrices underlying endothelial cells in the artery wall. Peroxynitrous acid (ONOOH) a potent oxidizing and nitrating agent, is formed in vivo from superoxide and nitric oxide radicals by stimulated macrophages and other cells. Considerable evidence supports ONOOH involvement in human atherosclerotic lesion development and rupture, possibly via extracellular matrix damage. Here we demonstrate that Tyr and Trp residues on human plasma fibronectin are highly sensitive to ONOOH with this resulting in the formation of 3-nitrotyrosine, 6-nitrotryptophan and dityrosine as well as protein aggregation and fragmentation. This occurs with equimolar or greater levels of oxidant, and in a dose-dependent manner. Modification of Tyr was quantitatively more significant than Trp (9.1% versus 1.5% conversion with 500 μM ONOOH) after accounting for parent amino acid abundance, but only accounts for a small percentage of the total oxidant added. LC-MS studies identified 28 nitration sites (24 Tyr, 4 Trp) with many of these present within domains critical to protein function, including the cell-binding and anastellin domains. Human coronary artery endothelial cells showed decreased adherence and cell-spreading on ONOOH-modified fibronectin compared to control, consistent with cellular dysfunction induced by the modified matrix. Studies on human atherosclerotic lesions have provided evidence for co-localization of 3-nitrotyrosine and fibronectin. ONOOH-mediated fibronectin modification and compromised cell-matrix interactions, may contribute to endothelial cell dysfunction, a weakening of the fibrous cap of atherosclerotic lesions, and an increased propensity to rupture.
Alzheimer disease (AD) is a progressive neurodegenerative disease that affects the elderly population with complex etiology. Many hypotheses have been proposed to explain different causes of AD, but the exact mechanisms remain unclear. In this review, we focus attention on the oxidative-stress hypothesis of neurodegeneration and we discuss redox proteomics approaches to analyze post-mortem human brain from AD brain. Collectively, these studies have provided valuable insights into the molecular mechanisms involved both in the pathogenesis and progression of AD, demonstrating the impairment of numerous cellular processes such as energy production, cellular structure, signal transduction, synaptic function, mitochondrial function, cell cycle progression, and degradative systems. Each of these cellular functions normally contributes to maintain healthy neuronal homeostasis, so the deregulation of one or more of these functions could contribute to the pathology and clinical presentation of AD. In particular, we discuss the evidence demonstrating the oxidation/dysfunction of a number of enzymes specifically involved in energy metabolism that support the view that reduced glucose metabolism and loss of ATP are crucial events triggering neurodegeneration and progression of AD.
Singlet molecular oxygen ((1)O2) contributes to protein damage triggering biophysical and biochemical changes that can be related with aging and oxidative stress. Serum albumins, such as bovine serum albumin (BSA), are abundant proteins in blood plasma with different biological functions. This paper presents a kinetic and spectroscopic study of the (1)O2-mediated oxidation of BSA using the tris(2,2'-bipyridine)ruthenium(II) cation [Ru(bpy)3](2+) as sensitizer. BSA quenches efficiently (1)O2 with a total (chemical+physical interaction) rate constant kt(BSA)=7.3(±0.4)×10(8)M(-1)s(-1), where the chemical pathway represented 37% of the interaction. This efficient quenching by BSA indicates the participation of several reactive residues. MALDI-TOF MS analysis of intact BSA confirmed that after oxidation by (1)O2, the mass protein increased the equivalent of 13 oxygen atoms. Time-resolved emission spectra analysis of BSA established that Trp residues were oxidized to N'-formylkynurenine, being the solvent-accessible W134 preferentially oxidized by (1)O2 as compared with the buried W213. MS confirmed oxidation of only two Tyr residues to form dihydroxyphenylalanine, with a global reactivity towards (1)O2 six-times lower than for Trp residues. Despite of the lack of MS evidences, kinetic and chemical analysis also suggested that other residues than Trp and Tyr, e.g. Met, must react with (1)O2. Modeling of the 3D-structure of BSA indicated that the oxidation pattern involves a random distribution of (1)O2 into BSA; allowing also the interaction of (1)O2 with buried residues by its diffusion from the bulk solvent through interconnected internal hydrophilic and hydrophobic grooves.
The solvent accessible surface area (SASA) of the polypeptide chain plays a key role in protein folding, conformational change and interaction. This fundamental biophysical parameter is elusive in experimental measurement. Our approach to this problem relies on the reaction of the minimal photochemical reagent diazirine (DZN) with polypeptides. This reagent (i) exerts solvent mimicry because its size is comparable to water and (ii) shows scant chemical selectivity because it generates extremely reactive methylene carbene. Methylation gives rise to the EM (extent of modification) signal, which is useful for scrutinizing the conformational change triggered by Ca2+ binding to calmodulin (CaM). The increased EM observed for the full protein is dominated by the enhanced exposure of hydrophobic area in Ca2+-CaM. Fragmentation allowed us to quantify the methylene incorporation at specific sites. Peptide 91-106 reveals a major reorganization around the calcium 151 binding site, resulting in local ordering and a greater exposure of the hydrophobic surface. Additionally, this technique shows a high sensitivity to probe recognition between CaM and melittin (Mel). The large decrease in EM indicates the occlusion of a significant hydrophobic area upon complexation. Protection from labeling reveals a larger involvement of the N-terminal and central regions of CaM in this interaction. Despite its smaller size, Mel's differential exposure can also be quantified. Moreover, MS/MS fragmentation realizes the goal of extending the resolution of labeled sites at the amino acid level. Overall, DZN labeling emerges as a useful footprinting method capable of shedding light on physiological conformational changes and interactions.
In this method paper we describe the spectral phasor analysis applied to Laurdan emission for the assessment of the fluidity of different membranes in live cells. We first introduce the general context and then we show how to obtain the spectral phasor from data acquired using a commercial microscope.
Nitrotyrosine has been found in the urine of humans with no known exposure to exogenous nitrating agents. We have shown that peroxynitrite, a nitrating agent formed by the near diffusion-limited reaction of nitric oxide with superoxide, is formed by activated macrophages. Using an antibody which recognizes nitrated tyrosine residues in proteins, we have obtained immunohistological evidence for nitration in a number of pathological conditions amenable to peroxynitrite formation. We have developed an HPLC method as a means of confirming the presence of nitrotyrosine. Quantitation of small amounts of nitrotyrosine in complex protein mixtures presents special problems of sensitivity and specificity which are often exacerbated by traditional amine-derivatization of all amino acids. An HPLC method for proteins hydrolysates is described which relies on intinsic UV absorbance of nitrotyrosine at 280 nm (which is fivefold higher than tyrosine at pH 3.5) for quantitation and on its unique absorbance at 355-365 nm for partial identification. Since only aromatic acids are detected, sample sizes can be increased to permit detection of small amounts of nitrotyrosine without introducing interference. Treatment of BSA with 4mM peroxynitrite resulted in nitration of 12.8% of total tyrosine residues; a small fraction (0.9%) of the total was detected as aminotyrosine. A total of 9.6% of the tyrosine residues in fresh plasma were nitrated as a result of treatment with 4mM peroxytyrosinee during hydrolysis. The advantages of this method over traditional amine-dervatized amino acid analysis are discussed and modifications which would further increase sensitivity to aminotyrosine are presented.
Pterins are normal components of cells and they have been previously identified as good photosensitizers under UV-A irradiation, inducing DNA damage and oxidation of nucleotides. In this work, we have investigated the ability of pterin (Ptr), the parent compound of oxidized pterins, to photosensitize the oxidation of another class of biomolecules, aminoacids, using tryptophan (Trp) as a model compound. Irradiation of Ptr in the UV-A spectral range (350nm) in aerated aqueous solutions containing Trp led to the consumption of the latter, whereas the Ptr concentration remained unchanged. Concomitantly, hydrogen peroxide (H2O2) was produced. Although Ptr is a singlet oxygen ((1)O2) sensitizer, the degradation of Trp was inhibited in O2-saturated solutions, indicating that a (1)O2-mediated process (Type II oxidation) was not an important pathway leading to Trp oxidation. By combining different analytical techniques, we could establish that a Type I photooxidation was the prevailing mechanism, initiated by an electron transfer from the Trp molecule to the Ptr triplet excited state yielding the corresponding radical ions (Trp(•+)/Trp(-H)(•) and Ptr(•-)). The Trp reaction products that could be identified by UPLC-mass spectrometry are in agreement with this conclusion.
Photo-induced cross-linking (PIC) is a powerful strategy for generating information on biomolecular interactions. In PIC, the utility of traditional cross-linking methods is supplemented by the temporal control of photo-activation, enabling the study of non-covalent kinetic intermediates and heterogeneous mixtures. This tutorial review will introduce the photochemistry of activation, reactive intermediates, methods for the functionalisation of biomolecules and the installation of additional functionalities (e.g., affinity tags). In doing so, we shall illustrate the wealth of data that can be obtained using this approach, ranging from the identification of interacting partners and structural data to temporal information. Alongside a discussion of the strengths and weaknesses of the various approaches, their applicability to different types of biological system will be described.
In proteins, the nitration of tyrosine residues to 3-nitro-tyrosine represents an oxidative post-translational modification that disrupts nitric oxide (•NO) signaling and skews metabolism towards pro-oxidant processes. Indeed, excess levels of reactive oxygen species in the presence of •NO or •NO-derived metabolites lead to the formation of nitrating species such as peroxynitrite. Thus, protein 3-nitrotyrosine has been established as a biomarker of cell, tissue, and systemic “nitroxidative stress”. Moreover, tyrosine nitration modifies key properties of the amino acid: phenol group pKa, redox potential, hydrophobicity, and volume. Thus, the incorporation of a nitro group (-NO2) into protein tyrosines can lead to profound structural and functional changes, some of which contribute to altered cell and tissue homeostasis.
Alpha-synuclein (αS), a 140 amino acid presynaptic protein, is the major component of the fibrillar aggregates (Lewy bodies) observed in dopaminergic neurons of patients affected by Parkinson's disease. It is currently believed that noncovalent oligomeric forms of αS, arising as intermediates in its aggregation, may constitute the major neurotoxic species. However, attempts to isolate and characterize such oligomers in vitro, and even more so in living cells, have been hampered by their transient nature, low concentration, polymorphism, and inherent instability. In this work, we describe the preparation and characterization of low molecular weight covalently bound oligomeric species of αS obtained by crosslinking via tyrosyl radicals generated by blue-light photosensitization of the metal coordination complex ruthenium (II) tris-bipyridine in the presence of ammonium persulfate. Numerous analytical techniques were used to characterize the αS oligomers: biochemical (anion-exchange chromatography, SDS-PAGE, and Western blotting); spectroscopic (optical: UV/Vis absorption, steady state, dynamic fluorescence, and dynamic light scattering); mass spectrometry; and electrochemical. Light-controlled protein oligomerization was mediated by formation of Tyr-Tyr (dityrosine) dimers through -C-C- bonds acting as covalent bridges, with a predominant involvement of residue Y39. The diverse oligomeric species exhibited a direct effect on the in vitro aggregation behavior of wild-type monomeric αS, decreasing the total yield of amyloid fibrils in aggregation assays monitored by thioflavin T (ThioT) fluorescence and light scattering, and by atomic force microscopy (AFM). Compared to the unmodified monomer, the photoinduced covalent oligomeric species demonstrated increased toxic effects on differentiated neuronal-like SH-SY5Y cells. The results highlight the importance of protein modification induced by oxidative stress in the initial molecular events leading to Parkinson's disease.
Ruthenium(II) (Ru(II)) complexes are the focus of numerous research works with various applications mainly due to their attractive photophysical and photochemical properties. In biological research areas, in particular, they are developed as efficient photoprobes or photosensors of biological molecules. More interestingly specific Ru(II) complexes bearing π-deficient ligands such as TAP = 1,4,5,8-tetraazaphenanthrene, bpz = 2,2′-bipyrazyl or HAT = 1,4,5,8,9,12-hexaazatriphenylene exhibit interesting photoreactivity with biomolecules (DNA, polypeptides). The photoreactions are initiated by a photo-electron transfer from the biomolecule to the excited metal complex. A back electron transfer (BET) succeeds this primary process. However in competition with this BET, a DNA photocleavage and/or formation of adducts of the complex with guanine units of DNA or with tryptophan (Trp) residues of polypeptides can take place. In this review we highlight the studies of these photo-adducts carried out by our laboratories, and connected to some applications. Copyright © 2008 John Wiley & Sons, Ltd.
Methylene blue photosensitized oxidation of tyrosine in the presence of nitrite produces 3-nitrotyrosine, with maximum yield at pH 6. The formation of 3-nitrotyrosine requires oxygen and increases using deuterium oxide as solvent, suggesting the involvement of singlet oxygen in the reaction. The detection of dityrosine as an additional reaction product suggests that the first step in the interaction of tyrosine with singlet oxygen generates tyrosyl radicals which can dimerize to form dityrosine or react with a nitrite-derived species to produce 3-nitrotyrosine. Although the chemical identity of the nitrating species has not been established, the possible generation of nitrogen dioxide (•NO2) by indirect oxidation of nitrite by intermediately produced tyrosyl radical, via electron transfer, is proposed. One important implication of the results of this study is that the oxidation of tyrosine by singlet oxygen in the presence of nitrite may represent an alternative or additional pathway of 3-nitrotyrosine formation of potential importance in oxidative injures such as during inflammatory processes.
The oxidation of proteins by free radicals is thought to play a major role in many oxidative processes within cells and is implicated in a number of human diseases as well as ageing. This review summarises information on the formation of radicals on peptides and proteins and how radical damage may be propagated and transferred within protein structures. The emphasis of this article is primarily on the deleterious actions of radicals generated on proteins, and their mechanisms of action, rather than on enzymatic systems where radicals are deliberately formed as transient intermediates. The final section of this review examines the control of protein oxidation and how such damage might be limited by antioxidants.
Photo-induced damage to proteins occurs via multiple pathways. Direct damage induced by UVB (λ 280-320 nm) and UVA radiation (λ 320-400 nm) is limited to a small number of amino acid residues, principally tryptophan (Trp), tyrosine (Tyr), histidine (His) and disulfide (cystine) residues, with this occurring via both excited state species and radicals. Indirect protein damage can occur via singlet oxygen ((1)O(2)(1)Δ(g)), with this resulting in damage to Trp, Tyr, His, cystine, cysteine (Cys) and methionine (Met) residues. Although initial damage is limited to these residues multiple secondary processes, that occur both during and after radiation exposure, can result in damage to other intra- and inter-molecular sites. Secondary damage can arise via radicals (e.g. Trp, Tyr and Cys radicals), from reactive intermediates generated by (1)O(2) (e.g. Trp, Tyr and His peroxides) and via molecular reactions of photo-products (e.g. reactive carbonyls). These processes can result in protein fragmentation, aggregation, altered physical and chemical properties (e.g. hydrophobicity and charge) and modulated biological turnover. Accumulating evidence implicates these events in cellular and tissue dysfunction (e.g. apoptosis, necrosis and altered cell signaling), and multiple human pathologies.
Reactive nitrogen species are formed during a variety of disease states and have been shown to modify several amino acids on proteins. To date, the majority of research in this area has focused on the nitration of tyrosine residues to form 3-nitrotyrosine. However, emerging evidence suggests that another modification, nitration of tryptophan residues, to form nitrotryptophan (NO(2)-Trp), may also play a significant role in the biology of nitrosative stress. This review takes an in-depth look at NO(2)-Trp, presenting the current research about its formation, prevalence and biological significance, as well as the methods used to identify NO(2)-Trp-modified proteins. Although more research is needed to understand the full biological role of NO(2)-Trp, the data presented herein suggest a contribution to nitrosative stress-induced cell dysregulation and perhaps even in physiological cell processes.
The results of the present investigation show the susceptibility of tyrosine to undergo visible light-induced photomodification to 3-nitrotyrosine in the presence of nitrite and riboflavin, as sensitizer. By changing H2O by D2O, it could be established that singlet oxygen has a minor role in the reaction. The finding that nitration of tyrosine still occurred to a large extent under anaerobic conditions indicates that the process proceeds mainly through a type I mechanism, which involves the direct interaction of the excited state of riboflavin with tyrosine and nitrite to give tyrosyl radical and nitrogen dioxide radical, respectively. The tyrosyl radicals can either dimerize to yield 3,3'-dityrosine or combine with nitrogen dioxide radical to form 3-nitrotyrosine. The formation of 3-nitrotyrosine was found to increase with the concentration of nitrite added and was accompanied by a decrease in the recovery of 3,3'-dityrosine, suggesting that tyrosine nitration competes with dimerization reaction. The riboflavin photosensitizing reaction in the presence of nitrite was also able to induce nitration of tyrosine residues in proteins as revealed by the spectral changes at 430 nm, a characteristic absorbance of 3-nitrotyrosine, and by immunoreactivity using 3-nitrotyrosine antibodies. Since riboflavin and nitrite are both present endogenously in living organism, it is suggested that this pathway of tyrosine nitration may potentially occur in tissues and organs exposed to sunlight such as skin and eye.
The focus is to expand the original design of fast photochemical oxidation of proteins (FPOP) and introduce SO(4)(-•), generated by 248 nm homolysis of low millimolar levels of persulfate, as a radical reactant in protein footprinting. FPOP is a chemical approach to footprinting proteins and protein complexes by "snapshot" reaction with free radicals. The radical used until now is the OH radical, and it provides a measure of residue-resolved solvent accessibility of the native protein. We show that FPOP can accommodate other reagents, increasing its versatility. The new persulfate FPOP system is a potent, nonspecific, and tunable footprinting method; 3-5 times less persulfate is needed to give the same global levels of modification as seen with OH radicals. Although solvent-exposed His and Tyr residues are more reactive with SO(4)(-•) than with (•)OH, oxidation of apomyoglobin and calmodulin shows that (•)OH probes smaller accessible areas than SO(4)(-•), with the possible exception of histidine. His64, an axial ligand in the heme-binding pocket of apomyoglobin, is substantially up-labeled by SO(4)(-•) relative to (•)OH. Nevertheless, the kinds of modification and residue selectivity for both reagent radicals are strikingly similar. Thus, the choice of these reagents relies on the physical properties, particularly the membrane permeability, of the radical precursors.
The exposure of solution-phase proteins to reactive oxygen species (ROS) causes oxidative modifications, giving rise to the formation of covalent +16 Da adducts. Electrospray ionization (ESI) mass spectrometry (MS) is the most widely used method for monitoring the extent of these modifications. Unfortunately, protein oxidation can also take place as an experimental artifact during ESI, such that it may be difficult to assess the actual level of oxidation in bulk solution. Previous work has demonstrated that ESI-induced oxidation is highly prevalent when operating at strongly elevated capillary voltage V(0) (e.g., +8 kV) and with oxygen nebulizer gas in the presence of a clearly visible corona discharge. Protein oxidation under these conditions is commonly attributed to OH radicals generated in the plasma of the discharge. On the other hand, charge balancing oxidation reactions are known to take place at the metal/liquid interface of the emitter. Previous studies have not systematically explored whether such electrochemical processes could be responsible for the formation of oxidative +16 Da adducts instead of (or in combination with) plasma-generated ROS. Using hemoglobin as a model system, this work illustrates the occurrence of extensive protein oxidation even under typical operating conditions (e.g., V(0) = 3.5 kV, N(2) nebulizer gas). Surprisingly, measurements of the current flowing in the ESI circuit demonstrate that a weak corona discharge persists for these relatively gentle settings. On the basis of comparative experiments with nebulizer gases of different dielectric strength, it is concluded that ROS generated under discharge conditions are solely responsible for ESI-induced protein oxidation. This result is corroborated through off-line electrolysis experiments designed to mimic the electrochemical processes taking place during ESI. Our findings highlight the necessity of using easily oxidizable internal standards in biophysical or biomedical ESI-MS studies where knowledge of protein oxidation in bulk solution is desired. Strategies for eliminating ESI-induced oxidation artifacts are discussed.
Characterization of peroxides by size exclusion chromatography (SEC) of milk following exposure to riboflavin and light showed that hydrogen peroxide was the most abundant peroxide formed since it could be removed by catalase. Formation of peroxides after separation by SEC showed that hydrogen peroxide formation was primarily increased in the presence of caseins and ascorbate, although whey proteins also were found to contribute. Caseins and beta-lactoglobulin also formed catalase-resistant peroxides, presumably protein hydroperoxides. A catalase-resistant and unstable peroxide was observed in fractions containing urate. Experiments performed with pure urate suggested that urate radicals reacted further with superoxide leading to a urate hydroperoxide. Electron paramagnetic resonance spectroscopy using spin-traps showed that the presence of oxygen was required for urate radical formation, which could be assigned as nitrogen-centered radicals. These results suggest a new route during light-induced oxidation sensitized by flavins, in effect making urate pro-oxidative.
By application of pulse radiolysis it was demonstrated that nitrogen dioxide (NO2.) oxidizes Gly-Tyr in aqueous solution with a strongly pH-dependent rate constant (k6 = 3.2 X 10(5) M-1 S-1 at pH 7.5 and k6 = 2.0 X 10(7) M-1 S-1 at pH 11.3), primarily generating phenoxyl radicals. The phenoxyl can react further with NO2. (k7 approximately 3 X 10(9) M-1 S-1) to form nitrotyrosine, which is the predominant final product in neutral solution and at low tyrosyl concentrations under gamma-radiolysis conditions. Tyrosine nitration is less efficient in acidic solution, due to the natural disproportionation of NO2., and in alkaline solutions and at high tyrosyl concentrations due to enhanced tyrosyl dimerization. Selective tyrosine nitration by interaction of NO2. with proteins (at pH 7 to 9) was demonstrated in the case of histone, lysozyme, ribonuclease A, and subtilisin Carlsberg. Nitrotyrosine developed slowly also under incubation of Gly-Tyr with nitrite at pH 4 to 5, where NO2. is formed by acid decomposition of HONO. It is recalled in this context that NO2.-induced oxidations, by regenerating NO2-, can propagate NO2./NO2- redox cycling under acidic conditions. Even faster than with tyrosine is the NO2.-induced oxidation of cysteine-thiolate (k9 = 2.4 X 10(8) M-1 S-1 at pH 9.2), involving the transient formation of cystinyl radical anions. The interaction of NO2. with Gly-Trp was comparably slow (k approximately 10(6) M-1 S-1), and no reaction was detectable by pulse radiolysis with Met-Gly and (Cys-Gly)2, or with DNA. Slow reactions of NO2. were observed with arachidonic acid (k approximately 10(6) M-1 S-1 at pH 9.0) and with linoleate (k approximately 2 X 10(5) M-1 S-1 at pH 9.4), indicating that NO2. is capable of initiating lipid peroxidation even in an aqueous environment. NO2.-Induced tyrosine nitration, using 50 microM Gly-Tyr at pH 8.2, was hardly inhibited, however, in the presence of 1 mM linoleate, and was not affected at all in the presence of 5 mM dimethylamine (a nitrosamine precursor). It is concluded that protein modifications, and particularly phenol and thiol oxidation, may be an important mechanism, as well as initiation of lipid peroxidation, of action of NO2. in biological systems.
With several proteins it has been shown that electrons can be transferred intramolecularly from tyrosine to electron-deficient tryptophan units. Rates vary from ∼ 102s−1 (in lysozyme) to ∼ 2×104 s−1 (in trypsin). For β-lactoglobulin the activation energy is 45kJ mol−1. This is incompatible with charge conduction along the polypeptide chain and rules out any mechanism involving temperature-labile hydrogen bonds as the main pathway. It seems likely that the electron transfer proceeds directly between the aromatic groups, while they are maintained at a distance from each other.
Quenching of singlet oxygen (1O2) in D2O-ethanol by the amino acids tryptophan, tyrosine, histidine, methionine, cysteine and their derivatives was measured by exciting the sensitizers rose bengal or meso-tetra (N-methyl-4-pyridyl)porphyrin tetratosylate in the presence of oxygen and the above quenchers in solution. In our polar solvent, containing 75% D2O on a molar basis it was found that (1) substitution of the aromatic ring in indole, phenol and imidazole by the electron-donating methyl group increases the total (i.e. nonreactive and reactive) quenching rate constant by a factor of five to eight. Free or blocked amino and carboxyl groups removed by two methylene groups from the ring counteract the above increase in the rate constant. The reactive quenching of singlet oxygen, which leads to oxidative destruction of the aromatic ring, correlates with the above substitution effects. It has been proposed that the quenching process takes place by formation of an exciplex between 1O2 and the quencher. Thus our results indicate that the better an electron donor the amino acid residue is the more pronounced is the charge transfer contribution in the exciplex formed with 1O2 and the more likely it is to lead to charge separation and hence to a chemical reaction. (2) Oligopeptides in solution or peptide bonds linked to the amino acid residue have only a minor effect on singlet oxygen. It can therefore be expected that the polypeptide chains per se in the protein network will not interact significantly with the single oxygen molecules present.(ABSTRACT TRUNCATED AT 250 WORDS)
Tyrosine nitration is a covalent posttranslational protein modification derived from the reaction of proteins with nitrating agents. Protein nitration appears to be a selective process since not all tyrosine residues in proteins or all proteins are nitrated in vivo. To investigate factors that may determine the biological selectivity of protein tyrosine nitration, we developed an in vitro model consisting of three proteins with similar size but different three-dimensional structure and tyrosine content. Exposure of ribonuclease A to putative in vivo nitrating agents revealed preferential nitration of tyrosine residue Y(115). Tyrosine residue Y(23) and to a lesser extent residue Y(20) were preferentially nitrated in lysozyme, whereas tyrosine Y(102) was the only residue modified by nitration in phospholipase A(2). Tyrosine Y(115) was the residue modified by nitration after exposure of ribonuclease A to different nitrating agents: chemically synthesized peroxynitrite, nitric oxide, and superoxide generated by SIN-1 or myeloperoxidase (MPO)/H(2)O(2) plus nitrite (NO(-2)) in the presence of bicarbonate/CO(2). The nature of the nitrating agent determined in part the protein that would be predominantly modified by nitration in a mixture of all three proteins. Ribonuclease A was preferentially nitrated upon exposure to MPO/H(2)O(2)/NO(-2), whereas phospholipase A(2) was the primary target for nitration upon exposure to peroxynitrite. The data also suggest that the exposure of the aromatic ring to the surface of the protein, the location of the tyrosine on a loop structure, and its association with a neighboring negative charge are some of the factors determining the selectivity of tyrosine nitration in proteins.
Thiols represent preferential targets of peroxynitrite in biological systems. In this work, we investigated the mechanisms and kinetics of the reaction of peroxynitrite with the dithiol dihydrolipoic acid (DHLA) and its oxidized form, lipoic acid (LA). Peroxynitrite reacted with DHLA being oxidation yields higher at alkaline pH. The stoichiometry for the reaction was two thiols oxidized per peroxynitrite. LA formation accounted for approximately 50% DHLA consumption at pH 7.4, probably reflecting secondary reactions between LA and peroxynitrite. Indeed, peroxynitrous acid reacted with LA with an apparent second-order rate constant (k(2app)) of 1400 M(-1) s(-1) at pH 7.4 and 37 degrees C. Nitrite and LA-thiosufinate were formed as reaction products. Surprisingly, the k(2app) for peroxynitrite-dependent DHLA oxidation was only 250 M(-1) s(-1) per thiol, at pH 7.4 and 37 degrees C. Testing various low-molecular-weight thiols, we found that an increase in the thiol pK (pK(SH)) value correlated with a decrease of k(2app) for the reaction with peroxynitrite at pH 7.4. The pK(SH) for DHLA is 10.7, in agreement with its modest reactivity with peroxynitrite.