Cross-linking and modification of fibronectin by peroxynitrous acid: Mapping and quantification of damage provides a new model for domain interactions

Modification of extracellular matrix proteins by oxidants and electrophiles

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

Exposure to peroxynitrite impacts the ability of anastellin to modulate the structure of extracellular matrix

The extracellular matrix (ECM) of tissues consists of multiple proteins, proteoglycans and glycosaminoglycans that form a 3-dimensional meshwork structure. This ECM is exposed to oxidants including peroxynitrite (ONOO-/ONOOH) generated by activated leukocytes at sites of inflammation. Fibronectin, a major ECM protein targeted by peroxynitrite, self-assembles into fibrils in a cell-dependent process. Fibrillation of fibronectin can also be initiated in a cell-independent process in vitro by anastellin, a recombinant fragment of the first type-III module in fibronectin. Previous studies demonstrated that modification of anastellin by peroxynitrite impairs its fibronectin polymerization activity. We hypothesized that exposure of anastellin to peroxynitrite would also impact on the structure of ECM from cells co-incubated with anastellin, and influence interactions with cell surface receptors. Fibronectin fibrils in the ECM of primary human coronary artery smooth muscle cells exposed to native anastellin are diminished, an effect which is reversed to a significant extent by pre-incubation of anastellin with high (200-fold molar excess) concentrations of peroxynitrite. Treatment with low or moderate levels of peroxynitrite (2-20 fold molar excess) influences interactions between anastellin and heparin polysaccharides, as a model of cell-surface proteoglycan receptors, and modulates anastellin-mediated alterations in fibronectin cell adhesiveness. Based on these observations it is concluded that peroxynitrite has a dose-dependent influence on the ability of anastellin to modulate ECM structure via interactions with fibronectin and other cellular components. These observations may have pathological implications since alterations in fibronectin processing and deposition have been associated with several pathologies, including atherosclerosis.

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

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

Identification and quantification of protein nitration sites in human coronary artery smooth muscle cells in the absence and presence of peroxynitrous acid/peroxynitrite

Peroxynitrous acid/peroxynitrite (ONOOH/ONOO^-) is a powerful oxidizing/nitrating system formed at sites of inflammation, which can modify biological targets, and particularly proteins. Here, we show that multiple proteins from primary human coronary artery smooth muscle cells are nitrated, with LC-MS peptide mass mapping providing data on the sites and extents of changes on cellular and extracellular matrix (ECM) proteins. Evidence is presented for selective and specific nitrations at Tyr and Trp on 11 cellular proteins (out of 3668, including 205 ECM species) in the absence of added reagent ONOOH/ONOO^-, with this being consistent with low-level endogenous nitration. A number of these have key roles in cell signaling/sensing and protein turnover. With added ONOOH/ONOO^-, more proteins were modified (84 total; with 129 nitrated Tyr and 23 nitrated Trp, with multiple modifications on some proteins), with this occurring at the same and additional sites to endogenous modification. With low concentrations of ONOOH/ONOO^- (50 μM) nitration occurs on specific proteins at particular sites, and is not driven by protein or Tyr/Trp abundance, with modifications detected on some low abundance proteins. However, with higher ONOOH/ONOO^- concentrations (500 μM), modification is primarily driven by protein abundance. ECM species are major targets and over-represented in the pool of modified proteins, with fibronectin and thrombospondin-1 being particularly heavily modified (12 sites in each case). Both endogenous and exogenous nitration of cell- and ECM-derived species may have significant effects on cell and protein function, and potentially be involved in the development and exacerbation of diseases such as atherosclerosis.

Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation

Glutamine synthetase (GS), which catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia, is a ubiquitous and conserved enzyme that plays a pivotal role in nitrogen metabolism across all life domains. In vertebrates, GS is highly expressed in astrocytes, where its activity sustains the glutamate-glutamine cycle at glutamatergic synapses and is thus essential for maintaining brain homeostasis. In fact, decreased GS levels or activity have been associated with neurodegenerative diseases, with these alterations attributed to oxidative post-translational modifications of the protein, in particular tyrosine nitration. In this study, we expressed and purified human GS (HsGS) and performed an in-depth analysis of its oxidative inactivation by peroxynitrite (ONOO^-) in vitro. We found that ONOO^- exposure led to a dose-dependent loss of HsGS activity, the oxidation of cysteine, methionine, and tyrosine residues and also the nitration of tryptophan and tyrosine residues. Peptide mapping by LC-MS/MS through combined H₂¹⁶O/H₂¹⁸O trypsin digestion identified up to 10 tyrosine nitration sites and five types of dityrosine cross-links; these modifications were further scrutinized by structural analysis. Tyrosine residues 171, 185, 269, 283, and 336 were the main nitration targets; however, tyrosine-to-phenylalanine HsGS mutants revealed that their sole nitration was not responsible for enzyme inactivation. In addition, we observed that ONOO^- induced HsGS aggregation and activity loss. Thiol oxidation was a key modification to elicit aggregation, as it was also induced by hydrogen peroxide treatment. Taken together, our results indicate that multiple oxidative events at various sites are responsible for the inactivation and aggregation of human GS.

Role of amino acid oxidation and protein unfolding in peroxyl radical and peroxynitrite-induced inactivation of glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides

The mechanisms underlying the inactivation of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase (G6PDH) induced by peroxyl radicals (ROO^●) and peroxynitrite (ONOO^-), were explored. G6PDH was incubated with AAPH (2,2' -azobis(2-methylpropionamidine)dihydrochloride), used as ROO^● source, and ONOO^-. Enzymatic activity was assessed by NADPH generation, while oxidative modifications were analyzed by gel electrophoresis and liquid chromatography (LC) with fluorescence and mass detection. Changes in protein conformation were studied by circular dichroism (CD) and binding of the fluorescent dye ANS (1-anilinonaphthalene-8-sulfonic acid). Incubation of G6PDH (54.4 μM) with 60 mM AAPH showed an initial phase without significant changes in enzymatic activity, followed by a secondary time-dependent continuous decrease in activity to ∼59% of the initial level after 90 min. ONOO^- induced a significant and concentration-dependent loss of G6PDH activity with ∼46% of the initial activity lost on treatment with 1.5 mM ONOO^-. CD and ANS fluorescence indicated changes in G6PDH secondary structure with exposure of hydrophobic sites on exposure to ROO^●, but not ONOO^-. LC-MS analysis provided evidence for ONOO^--mediated oxidation of Tyr, Met and Trp residues, with damage to critical Met and Tyr residues underlying enzyme inactivation, but without effects on the native (dimeric) state of the protein. In contrast, studies using chloramine T, a specific oxidant of Met, provided evidence that oxidation of specific Met and Trp residues and concomitant protein unfolding, loss of dimer structure and protein aggregation are involved in G6PDH inactivation by ROO^●. These two oxidant systems therefore have markedly different effects on G6PDH structure and activity.

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

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

Mimicking the Natural Basement Membrane for Advanced Tissue Engineering

Advancements in the field of tissue engineering have led to the elucidation of physical and chemical characteristics of physiological basement membranes (BM) as specialized forms of the extracellular matrix. Efforts to recapitulate the intricate structure and biological composition of the BM have encountered various advancements due to its impact on cell fate, function, and regulation. More attention has been paid to synthesizing biocompatible and biofunctional fibrillar scaffolds that closely mimic the natural BM. Specific modifications in biomimetic BM have paved the way for the development of in vitro models like alveolar-capillary barrier, airway models, skin, blood-brain barrier, kidney barrier, and metastatic models, which can be used for personalized drug screening, understanding physiological and pathological pathways, and tissue implants. In this Review, we focus on the structure, composition, and functions of in vivo BM and the ongoing efforts to mimic it synthetically. Light has been shed on the advantages and limitations of various forms of biomimetic BM scaffolds including porous polymeric membranes, hydrogels, and electrospun membranes This Review further elaborates and justifies the significance of BM mimics in tissue engineering, in particular in the development of in vitro organ model systems.

Oxidant-mediated modification and cross-linking of beta-2-microglobulin

Beta-2-microglobulin (B2M) is synthesized by all nucleated cells and forms part of the major histocompatibility complex (MHC) class-1 present on cell surfaces, which presents peptide fragments to cytotoxic CD8⁺ T-lymphocytes, or by association with CD1, antigenic lipids to natural killer T-cells. Knockout of B2M results in loss of these functions and severe combined immunodeficiency. Plasma levels of this protein are low in healthy serum, but are elevated up to 50-fold in some pathologies including chronic kidney disease and multiple myeloma, where it has both diagnostic and prognostic value. High levels of the protein are associated with amyloid formation, with such deposits containing significant levels of modified or truncated protein. In the current study we examine the chemical and structural changes induced of B2M generated by both inflammatory oxidants (HOCl and ONOOH), and photo-oxidation (¹O₂) which is linked with immunosuppression. Oxidation results in oligomer formation, with this occurring most readily with HOCl and ¹O₂, and a loss of native protein conformation. LC-MS analysis provided evidence for nitrated (from ONOOH), chlorinated (from HOCl) and oxidized residues (all oxidants) with damage detected at Tyr, Trp, and Met residues, together with cleavage of the disulfide (cystine) bond. An intermolecular di-tyrosine crosslink is also formed between Tyr10 and Tyr63. The pattern of these modifications is oxidant specific, with ONOOH inducing a greater range of modifications than HOCl. Comparison of the sites of modification with regions identified as amyloidogenic indicate significant co-localization, consistent with the hypothesis that oxidation may contribute, and predispose B2M, to amyloid formation.

Peroxynitrous acid-modified extracellular matrix alters gene and protein expression in human coronary artery smooth muscle cells and induces a pro-inflammatory phenotype

Leukocytes produce oxidants at inflammatory sites, including within the artery wall during the development of atherosclerosis. Developing lesions contain high numbers of activated leukocytes that generate reactive nitrogen species, including peroxynitrite/peroxynitrous acid (ONOO^-/ONOOH), as evidenced by the presence of oxidized/nitrated molecules including extracellular matrix (ECM) proteins. ECM materials are critical for arterial wall integrity, function, and determine cell phenotype, with smooth muscle cells undergoing a phenotypic switch from quiescent/contractile to proliferative/synthetic during disease development. We hypothesized that ECM modification by ONOO^-/ONOOH might drive this switch, and thereby potentially contribute to atherogenesis. ECM generated by primary human coronary artery smooth muscle cells (HCASMCs) was treated with increasing ONOO^-/ONOOH concentrations (1-1000 μM). This generated significant damage on laminin, fibronectin and versican, and lower levels on collagens and glycosaminoglycans, together with the increasing concentrations of the damage biomarker 3-nitrotyrosine. Adhesion of naïve HCASMC to ECM modified by 1 μM ONOO^-/ONOOH was enhanced, but significantly diminished by higher ONOO^-/ONOOH treatment. Cell proliferation and metabolic activity were significantly enhanced by 100 μM ONOO^-/ONOOH pre-treatment. These changes were accompanied by increased expression of genes involved in mitosis (PCNA, CCNA1, CCNB1), ECM (LAMA4, LAMB1, VCAN, FN1) and inflammation (IL-1B, IL-6, VCAM-1), and corresponding protein secretion (except VCAM-1) into the medium. These changes induced by modified ECM are consistent with HCASMC switching to a synthetic/proliferative/pro-inflammatory phenotype, together with ECM remodelling. These changes model those in atherosclerosis, suggesting a link between oxidant-modified ECM and disease progression, and highlight the potential of targeting oxidant generation as a therapeutic strategy.

Oxidative Crosslinking of Peptides and Proteins: Mechanisms of Formation, Detection, Characterization and Quantification

Covalent crosslinks within or between proteins play a key role in determining the structure and function of proteins. Some of these are formed intentionally by either enzymatic or molecular reactions and are critical to normal physiological function. Others are generated as a consequence of exposure to oxidants (radicals, excited states or two-electron species) and other endogenous or external stimuli, or as a result of the actions of a number of enzymes (e.g., oxidases and peroxidases). Increasing evidence indicates that the accumulation of unwanted crosslinks, as is seen in ageing and multiple pathologies, has adverse effects on biological function. In this article, we review the spectrum of crosslinks, both reducible and non-reducible, currently known to be formed on proteins; the mechanisms of their formation; and experimental approaches to the detection, identification and characterization of these species.

Secondary Formation of Aromatic Nitroderivatives of Environmental Concern: Photonitration Processes Triggered by the Photolysis of Nitrate and Nitrite Ions in Aqueous Solution

Aromatic nitroderivatives are compounds of considerable environmental concern, because some of them are phytotoxic (especially the nitrophenols, and particularly 2,4-dinitrophenol), others are mutagenic and potentially carcinogenic (e.g., the nitroderivatives of polycyclic aromatic hydrocarbons, such as 1-nitropyrene), and all of them absorb sunlight as components of the brown carbon. The latter has the potential to affect the climatic feedback of atmospheric aerosols. Most nitroderivatives are secondarily formed in the environment and, among their possible formation processes, photonitration upon irradiation of nitrate or nitrite is an important pathway that has periodically gained considerable attention. However, photonitration triggered by nitrate and nitrite is a very complex process, because the two ionic species under irradiation produce a wide range of nitrating agents (such as •NO2, HNO2, HOONO, and H2OONO+), which are affected by pH and the presence of organic compounds and, in turn, deeply affect the nitration of aromatic precursors. Moreover, aromatic substrates can highly differ in their reactivity towards the various photogenerated species, thereby providing different behaviours towards photonitration. Despite the high complexity, it is possible to rationalise the different photonitration pathways in a coherent framework. In this context, this review paper has the goal of providing the reader with a guide on what to expect from the photonitration process under different conditions, how to study it, and how to determine which pathway(s) are prevailing in the formation of the observed nitroderivatives.