A Novel Nitration Product Formed during the Reaction of Peroxynitrite with 2‘,3‘,5‘-Tri-<i>O</i>-acetyl-7,8-dihydro-8-oxoguanosine: <i>N</i>-Nitro-<i>N</i>‘-[1-(2,3,5-Tri-<i>O</i>-acetyl-β-d-<i>erythro</i>-pentofuranosyl)- 2,4-dioxoimidazolidin-5-ylidene]guanidine

A novel nitration product, formed during the reaction of peroxynitrite with 2‘,3‘,5‘-tri-O-acetyl-7,8-dihydro-8-oxoguanosine, has been characterized using a combination of UV/vis, CD, and NMR spectroscopy and mass spectrometry. This compound has been identified as N-nitro-N‘-[1-(2,3,5-tri-O-acetyl-β-d-erythro-pentofuranosyl)-2,4-dioxoimidazolidin-5-ylidene]guanidine (IV). Upon base hydrolysis, IV releases nitroguanidine (IVa) and an intermediate, 1-(2,3,5-tri-O-acetyl-β-d-erythro-pentofuranosyl)-5-iminoimidazolidine-2,4-dione (IVb). This intermediate is ultimately hydrolyzed to the stable 3-(2,3,5-tri-O-acetyl-β-d-erythro-pentofuranosyl)oxaluric acid (IVc). IV can be reduced by sodium borohydride to a pair of stable diastereomers (IVred). The formation of this product is rationalized in terms of initial oxidation of 2‘,3‘,5‘-tri-O-acetyl-7,8-dihydro-8-oxoguanosine to a quinonoid diimine intermediate, 3. Nucleophilic attack at C5 of 3 by peroxynitrite leads to formation of a C5-oxyl radical species, 5, which then undergoes a series of rearrangements to yield an ylidene radical, 7. Combination of this radical species with nitrogen dioxide results in the formation of product IV

Global Phosphoproteome of HT-29 Human Colon Adenocarcinoma Cells

Phosphorylation events in cellular signaling cascades triggered by a variety of cellular stimuli modulate protein function, leading to diverse cellular outcomes including cell division, growth, death, and differentiation. Abnormal regulation of protein phosphorylation due to mutation or overexpression of signaling proteins often results in various disease states. We provide here a list of protein phosphorylation sites identified from HT-29 human colon adenocarcinoma cell line by immobilized metal affinity chromatography (IMAC) combined with liquid chromatography (LC)-tandem mass spectrometry (MS/MS) analysis. In this study, proteins extracted from HT-29 whole cell lysates were digested with trypsin and carboxylate groups on the resulting peptides were converted to methyl esters. Derivatized phosphorylated peptides were enriched using Fe3+-chelated metal affinity resin. Phosphopeptides retained by IMAC were separated by high performance liquid chromatography (HPLC) and analyzed by electrospray ionization-quadrupole-time-of-flight (ESI-Q-TOF) mass spectrometry. We identified 238 phosphorylation sites, 213 of which could be conclusively localized to a single residue, from 116 proteins by searching MS/MS spectra against the human protein database using MASCOT. Peptide identification and phosphorylation site assignment were confirmed by manual inspection of the MS/MS spectra. Many of the phosphorylation sites identified in our results have not been described previously in the scientific literature. We attempted to ascribe functionality to the sites identified in this work by searching for potential kinase motifs with Scansite (http://scansite.mit.edu) and obtaining information on kinase substrate selectivity from Pattern Explorer (http://scansite.mit.edu/pe). The list of protein phosphorylation sites identified in the present experiment provides broad information on phosphorylated proteins under normal (asynchronous) cell culture conditions. Sites identified in this study may be utilized as surrogate bio-markers to assess the activity of selected kinases and signaling pathways from different cell states and exogenous stimuli. Keywords: phosphoproteome • IMAC • HT-29 • scansite • pattern explore

Spiroiminodihydantoin Is the Major Product of the 8-Oxo-7,8-dihydroguanosine Reaction with Peroxynitrite in the Presence of Thiols and Guanosine Photooxidation by Methylene Blue

The potent oxidant, peroxynitrite, will oxidize 8-oxo-7,8-dihydroguanosine to give several products. In the presence of a thiol agent, the major final product has been determined to be a spiroiminodihydantoin compound. Additionally, we have found that the spiroiminodihydantoin, and not the previously reported 4-hydroxy-8-oxo-4,8-dihydroguanosine, is the major final product formed during the methylene blue-mediated photooxidation of guanosine

Covalent Adducts Arising from the Decomposition Products of Lipid Hydroperoxides in the Presence of Cytochrome <i>c</i>

Polyunsaturated fatty acids can be converted to lipid hydroperoxides through nonenzymatic and enzymatic pathways. The prototypic ω-6 lipid hydroperoxide 13-hydroperoxy-octadecadienoic acid (13-HPODE) homolytically decomposes to form highly reactive α,β-unsaturated aldehydes, such as 9,12-dioxo-10(E)-dodecenoic acid (DODE), 4-oxo-2(E)-nonenal (ONE), 4,5-epoxy-2(E)-decenal (EDE), and 4-hydroxy-2(E)-nonenal (HNE), that can form covalent adducts with DNA. Both 4-oxo-2(E)-nonenal and 4-hydroxy-2(E)-nonenal can also modify proteins to form products that can potentially serve as biomarkers of lipid hydroperoxide-mediated macromolecule damage. In this study, cytochrome c was used to identify and individually characterize the modification sites for each of these aldehydes and also determine the most abundant adduct formed following the decomposition of 13-HPODE. The adducts were characterized by ESI-TOF/MS analysis of the intact proteins and by a combination of ESI-ion-trap/MSn and quadrupole-TOF/MS/MS analysis of the tryptic and chymotryptic peptides. The major adducts included an HNE-His Michael adduct on H33, EDE-Lys adducts on K7 and K8, ONE-Lys ketoamide adducts on K5, K7, and K8, an apparent ONE-Lys Michael adduct on K5, and DODE-Lys carboxyl ketoamide adducts on K86 and K87. DODE was the most reactive aldehyde toward cytochrome c. The major adduct from this reaction was analogous to the most abundant adduct resulting from the decomposition of 13-HPODE in the presence of cytochrome c

Nitric Oxide-Induced Interstrand Cross-Links in DNA

The DNA damaging effects of nitrous acid have been extensively studied, and the formation of interstrand cross-links have been observed. The potential for this cross-linking to occur through a common nitrosating intermediate derived from nitric oxide is investigated here. Using a HPLC laser-induced fluorescence (LIF) system, the amount of interstrand cross-link formed on nitric oxide treatment of the 5‘-fluorescein-labeled oligomer ATATCGATCGATAT was determined. This self-complimentary sequence contains two 5‘-CG sequences, which is the preferred site for nitrous acid-induced cross-linking. Nitric oxide was delivered to an 0.5 mM oligomer solution at 15 nmol/mL/min to give a final nitrite concentration of 652 μM. The resulting concentration of the deamination product, xanthine, in this sample was found to be 211 ± 39 nM, using GC/MS, and the amount of interstrand cross-link was determined to be 13 ± 2.5 nM. Therefore, upon nitric oxide treatment, the cross-link is found at approximately 6% of the amount of the deamination product. Using this system, detection of the cross-link is also possible for significantly lower doses of nitric oxide, as demonstrated by treatment of the same oligomer with NO at a rate of 18 nmol/mL/min resulting in a final nitrite concentration of 126 μM. The concentration of interstrand cross-link was determined to be 3.6 ± 0.1 nM in this sample. Therefore, using the same dose rate, when the total nitric oxide concentration delivered drops by a factor of approximately 5, the concentration of cross-link drops by a factor of about 4indicating a qausi-linear response. It may now be possible to predict the number of cross-links in a small genome based on the number of CpG sequences and the yield of xanthine derived from nitrosative deamination

Spirodihydantoin Is a Minor Product of 5-Hydroxyisourate in Urate Oxidation

Spirodihydantoin is a minor product from oxidation of uric acid (∼0.15% yield), while spiroiminodihydantoin is a major product from oxidation of 8-oxo-7,8-dihydroguanine (37% yield, pH 10.2). High pH and temperature favor the formation of both spiro compounds. 18O labeling experiments and in situ generation and decomposition of 5-hydroxy-N7-methylisouric acid indicate that spirodihydantoin and allantoin and spiroiminodihydantoin and guanidinohydantoin are products of 5-hydroxyisourate and 5-hydroxy-8-oxo-7,8-dihydroguanine intermediates, respectively

Quantitation of Four Guanine Oxidation Products from Reaction of DNA with Varying Doses of Peroxynitrite

The oxidation products obtained from the reaction of peroxynitrite (ONOO-) with dG includeamong others8-oxo-7,8-dihydro-2‘-deoxyguanosine (8-oxodG), 2,2-diamino-4[(2-deoxy-β-d-erythro-pentafuranosyl)amino]-5(2H)-oxazolone (oxazolone), spiroiminodihydantoin, and N1-(β-d-erythro-pentofuranosyl)-5-guanidinohydantoin (guanidinohydantoin). In the present work, the formation of these products from the treatment of calf thymus DNA with varying amounts of ONOO- was studied quantitatively in vitro. 13C-, 15N-labeled standards were synthesized for the nucleosides of interest, and calf thymus DNA was reacted with ONOO- and digested enzymatically down to the nucleoside level. Specific modifications in the DNA were measured by HPLC separation followed by electrospray ionization tandem mass spectrometric analysis in the selected reaction-monitoring mode. Artifacts of the above four oxidation products, arising from oxidation of dG and/or 8-oxodG during DNA digestion and subsequent workup, were evaluated with 7-15N-dG and/or stable-isotope-labeled 8-oxodG as internal standards. Levels of artifactual 8-oxodG were about 5/106 nucleosides. The artifacts of spiroiminodihydantoin and guanidinohydantoin, arising from 8-oxodG, were 3.7% and 0.6% of the measured 8-oxodG values, respectively. No artifacts of oxazolone were detected. 8-OxodG and oxazolone were formed dose-dependently in DNA treated with ONOO-, while the levels of spiroiminodihydantoin and guanidinohydantoin increased significantly at low ONOO- doses, and then dropped off at higher ONOO- doses. The complexity of these dose−response relationships is likely due to the dual role of peroxynitrite as both an oxidant and a nucleophile in competition with water

Increase of Reaction Rate and Sensitivity of Low-Abundance Enzyme Assay Using Micro/Nanofluidic Preconcentration Chip

We report a novel method of increasing both the reaction rate and the sensitivity of low-abundance enzyme assay using a micro/nanofluidic preconcentration chip. The disposable preconcentration device made out of PDMS with a surface-patterned ion-selective membrane increases local enzyme/substrate concentrations for rapid monitoring of enzyme activity. As a model system, we used trypsin as the enzyme and BODIPY FL casein as the fluorogenic substrate. We demonstrated that the reaction rate of trypsin−BODIPY FL was significantly enhanced by increasing the local concentrations of both trypsin and BODIPY FL casein in the preconcentration chip. The reaction time required to turn over substrates at 1 ng/mL was only ∼10 min compared to ∼1 h without preconcentration, which demonstrates a significantly higher reaction rate through the increase of the concentrations of both the enzyme and substrate. Furthermore, trypsin activity can be measured down to a concentration level of 10 pg/mL, which is a ∼100 fold enhancement in sensitivity compared to the result without the preconcentration step. This micro/nanofluidic preconcentrator chip could be used as a generic micro reaction platform to study any enzyme−substrate systems, or other biochemical reaction systems in low concentration ranges

Comparative Plasma Proteome Analysis of Lymphoma-Bearing SJL Mice

In SJL mice, growth of RcsX lymphoma cells induces an inflammatory response by stimulatingVβ16+ T cells. During inflammation, various serum protein levels can increase (e.g., acute phase reactants) or decrease (e.g., albumin), and most of these altered proteins are thus potential biomarkers. Although blood plasma is a valuable and promising sample for biomarker discovery for diseases or for novel drug targets, its proteome is complex. To address this, we have focused on a comprehensive comparison of the plasma proteomes from normal and RcsX-tumor-bearing SJL mice using the 1D-Gel-LC−MS/MS method after removing albumin and immunoglobulins. This analysis resulted in the identification of a total of 1079 nonredundant mouse plasma proteins; more than 480 in normal and 790 in RcsX-tumor-bearing SJL mouse plasma. Of these, only 191 proteins were found in common. The molecular weights ranged from 2 to 876 kDa, covering the pI values between 4.22 and 12.09, and included proteins with predicted transmembrane domains. By comparing the plasma proteomic profile of normal and RcsX-tumor-bearing SJL mice, we found significant changes in the levels of many proteins in RcsX-tumor-bearing mouse plasma. Most of the up-regulated proteins were identified as acute-phase proteins (APPs). Also, several unique proteins i.e., haptoglobin, proteosome subunits, fetuin-B, 14-3-3 zeta, MAGE-B4 antigen, etc, were found only in the tumor-bearing mouse plasma; either secreted, shed by membrane vesicles, or externalized due to cell death. These results affirm the effectiveness of this approach for protein identification from small samples, and for comparative proteomics in potential animal models of human disorders. Keywords: lymphoma • tumor • inflammation • mouse • comparative • plasma biomarker • proteomics • mass spectrometry • spectrum mil

Characterization of the Secreted Proteome of Rat Hepatocytes Cultured in Collagen Sandwiches

Analysis of proteins in biological samples opens up the possibility of discovering new markers of toxicity. The liver is one of the primary targets of drug-induced toxicity, and it also secretes many plasma proteins, which can be measured clinically. Most of the plasma proteins produced by the liver are secreted by hepatocytes, but there is little information regarding the protein profile secreted by these cells. The purpose of this study was to analyze the secreted proteome of primary rat hepatocytes in a collagen gel sandwich configuration by a gel-LC-MS/MS procedure. We identified over 600 peptides corresponding to more than 200 proteins. The protein profile included over 50 plasma proteins, suggesting that the cultured hepatocytes secrete many of the proteins that they produce in vivo. Our data also suggests that the hepatocytes are actively remodeling their environment, since we identified several structural extracellular matrix proteins as well as some proteins known to be secreted specifically during liver regeneration. We also identified two proteins, α1-antitrypsin and α2-macroglobulin, whose secretions appear to be down-regulated in cells exposed to aflatoxin B1. It was noted that a 15 nM dose of aflatoxin B1 led to substantially diminished levels of these proteins and that day 6 of incubation was the ideal time point for medium collection. These data suggest that proteins in the conditioned medium of hepatocyte sandwich culture might lead to the discovery of biomarkers for drug-induced chemical toxicity