• Mass Spectrometry Letters
• /
• v.7 no.4
• /
• pp.85-90
• /
• 2016

Post-translational modifications (PTMs) of proteins regulate self-renewal and differentiation in embryonic stem cells (ESCs). Nitration of tyrosine residues of proteins in ESCs modulates their downstream pathways, which can affect self-renewal and differentiation. However, protein tyrosine nitration (PTN) in ESCs has been rarely studied. We reviewed 23 nitrated sites in stem cell proteins. Functional enrichment analysis showed that these nitrated proteins are involved in signal transduction, cell adhesion and migration, and cell proliferation in ESCs. Comparison between the nitrated and known phosphorylated sites revealed that 7 nitrated sites had overlapping phosphorylated sites, indicating functional links of PTNs to their associated signaling pathways in ESCs. Therefore, nitrated proteome provides a basis for understanding potential roles of PTN in self-renewal and differentiation of ESCs.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.5
• /
• pp.711-714
• /
• 2004

Peroxynitrite enters erythrocytes through band 3 anion exchanger and oxidizes cytosolic proteins therein. As a protein associated with band 3, carbonic anhydrase II may suffer from peroxynitrite-induced oxidative damages. Esterase activity of carbonic anhydrase II decreased as the concentration of peroxynitrite increased. Neither hydrogen peroxide nor hypochlorite affected the enzyme activity. Inactivation of the enzyme was in parallel with the release of zinc ion, which is a component of the enzyme's active site. SDS-PAGE of peroxynitrite-treated samples showed no indication of fragmentation but non-denaturing PAGE exhibited new bands with lower positive charges. Western analysis demonstrated that nitration of tyrosine residues increased with the peroxynitrite concentration but the sites of nitration could not be determined. Instead MALDI-TOF analysis identified tryptophan-245 as a site of nitration. Such modification of tryptophan residues is responsible for the decrease in tryptophan fluorescence. These results demonstrate that peroxynitrite nitrates tyrosine and tryptophan residues of carbonic anhydrase II without causing fragmentation or dimerization. The peroxynitrite-induced inactivation of the enzyme is primarily due to the release of zinc ion in the enzyme's active site.

• BMB Reports
• /
• v.41 no.3
• /
• pp.194-203
• /
• 2008

Nitrosative modifications regulate cellular signal transduction and pathogenesis of inflammatory responses and neuro-degenerative diseases. Protein tyrosine nitration is a biomarker of oxidative stress and also influences protein structure and function. Recent advances in mass spectrometry have made it possible to identify modified proteins and specific modified amino acid residues. For analysis of nitrated peptides with low yields or only a subset of peptides, affinity 'tags' can be bait for 'fishing out' target analytes from complex mixtures. These tagged peptides are then extracted to a solid phase, followed by mass analysis. In this review, we focus on protein tyrosine modifications caused by nitrosative stresses and proteomic methods for selective enrichment and identification of nitrosative protein modifications.

• BMB Reports
• /
• v.39 no.2
• /
• pp.189-196
• /
• 2006

Alterations in the amino acid structure or sequence can generate neo-epitopes from self-proteins causing autoaggressive immune attack. Reactive nitrogen species are an important factor that induces post-translational modification of proteins by cellular reduction and oxidation mechanism; cysteinyl-nitrosylation or tyrosine nitration leading to potentially pathogenic pathways. It was thought of interest to investigate the immunogenicity of nitrated poly L-tyrosine vis-$\`{a}$-vis its possible role in the induction of antibodies in systemic lupus erythematosus (SLE). Commercially available poly L-tyrosine was exposed to nitrating species and the damage was monitored by UV spectroscopy and alkaline gel electrophoresis. The results indicated the formation of 3-nitrotyrosine. Nitrated poly L-tyrosine induced higher titre antibodies as compared to the native form. Nitrated poly L-tyrosine was recognized by the autoantibodies present in the sera of patients suffering from SLE by enzyme immunoassays and band shift assay. The possible role of nitrated self-proteins has been discussed in the production of circulating anti-DNA antibodies in SLE.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.3
• /
• pp.709-714
• /
• 2014

Protein tyrosine nitration is considered as an important indicator of nitrosative stresses and as one of the main factors for pathogenesis of inflammation and neuronal degeneration. In this study, we investigated various nitrosative modifications of bovine carbonic anhydrase II (CAII) through qualitative and semi-quantitative analysis using the combined strategy of Fourier transformation ion cyclotron resonance mass spectrometry (FT-ICR MS) and ion-trap tandem mass spectrometry (IT-MS/MS). FT-ICR MS and its spectra were used for the search of the pattern of nitrosative modifications. Identification of nitrosatively modified tyrosine sites were executed through IT-MS/MS. In addition, we also tried to infer the reason for the site-specific nitrosative modifications in CAII. In view of the above purpose, we have explored- i) the side chain accessibility, ii) the electrostatic environment originated from the acidic/basic amino acid residues neighboring to the nitrosatively modified site and iii) the existence of competing amino acid residues for nitration.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.9
• /
• pp.2581-2587
• /
• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• The Journal of Korean Medicine
• /
• v.23 no.4
• /
• pp.55-63
• /
• 2002

Objectives: Peroxynitrite ($ONOO^{-}$), formed from the reaction of superoxide <${\cdot}O_2^{-}$) and nitric oxide (NO), is a cytotoxic species that can oxidize several cellular components such as proteins, lipids and DNA. It has been implicated in diseases such as aging process, Alzheimer's disease, rheumatoid arthritis, cancer and arteriosclerosis. Due to the lack of endogenous enzymes responsible for $ONOO^{-}$ inactivation, developing a specific $ONOO^{-}$ scavenger is of considerable importance. The aim of this study was to evaluate $ONOO^{-}$ scavenging activity and its mechanism in Cheonga-hwan (CAH). Methods: The $ONOO^{-}$ scavenging activity in CAH was assayed by measuring oxidized dihydrorhodamine 123 (DHR 123) by fluorescence. The scavenging efficacy was expressed as $IC_{50}$, showing the concentration of each sample required to cause 50% inhibition of DHR 123 oxidation. In a separate study, the protective effect of CAR on $ONOO^{-}$-induced nitration of bovine serum albumin (BSA) was investigated using immunoassay with a monoclonal anti-nitrotyrosine antibody, and a horseradish peroxidase-conjugated anti-mouse secondary antibody from sheep. Results: CAH showed potent scavenging activities of $ONOO^{-}$, NO and ${\cdot}O_2^{-}$. The data demonstrated that CAH led to decreased $ONOO^{-}$-mediated nitration of tyrosine through electron donation. CAH showed significant inhibition on nitration of bovine serum albumin by $ONOO^{-}$ in a dose-dependent manner. Conclusions: CAH can be developed as an effective peroxynitrite scavenger for the prevention of the $ONOO^{-}$ involved diseases.

• The Journal of Internal Korean Medicine
• /
• v.24 no.1
• /
• pp.75-83
• /
• 2003

Objectives : Peroxynitrite($ONOO^-$), formed from the reaction of $O2^-$ and NO, is a cytotoxic species that can oxidize several cellular components such as proteins, lipids and DNA. It has been involved in the aging process and age-related diseases such as Alzheimer's disease, rheumatoid arthritis, cancer and atherosclerosis. The aim of this study was to investigate scavenging activities of $ONOO^-$ and its precursors, NO and $O_{2^-}$ and its scavenging mechanism of Zingiberis Rhizoma (ZR). Methods : To investigate scavenging activities of $ONOO^-,\;NO,\;O_{2^-}$ and its scavenging mechanism, we used fluorescent probes like DCFDA, DAF-2 and DHR 123. The $ONOO^-$ scavenging activity on ZR was assayed by measuring oxidized dihydrorhodamine 123 (DHR 123) by fluorometry. The scavenging efficacy was expressed as IC50, showing the concentration of each sample that is required to cause 50% inhibition of DHR 123 oxidation. In a separate study, the protective effect of ZR on $ONOO^-$-induced nitration of bovine serum albumin was investigated through immuno-assay with a monoclonal anti-nitryrosine antibody, and a horseradish peroxidase-conjugated anti-mouse secondary antibody from sheep. Results : ZR markedly scavenged authentic $ONOO^-,\;O_{2^-}$ and NO. It also inhibited $ONOO^-$ induced by $O_{2^-}$ and NO which are derived from SIN-1. The data demonstrated that ZR led to decreased $ONOO^-$ mediated nitration of tyrosine through electron donation. It also inhibited the nitration of bovine serum albumin induced by $ONOO^-$ in a dose-dependent manner. Furtheremore, it blocked LPS-induced ROS and RNS generation. Conclusions : These results suggest that ZR can be developed as an effective $ONOO^-$ scavenger for the prevention of aging process and age-related diseases.

• The Journal of Internal Korean Medicine
• /
• v.25 no.2
• /
• pp.268-276
• /
• 2004

Objective : Peroxynitrite $(ONOO^-)$, formed from the reaction of $O_2^-$ and NO, is a cytotoxic species that can oxidize several cellular components such as proteins, lipids and DNA. It has been implicated in the aging process and age-related disease such as Alzheimer's disease, rheumatoid arthritis, cancer and atherosclerosis. The aim of this study was to investigate scavenging activities of $ONOO^-$ and its precursors. NO and $O_2^-$ and its scavenging mechanism using fluorescent probes, DCFDA, DAF-2 and DHR 123.. Methods : Psoralea corylifolia was crushed. The crushed Psoralea corylifolia was extracted 3 times, each time with 3 volumes of methyl alcohol at $60^{\circ}C$ for 24 h. The extract was filtered and evaporated under reduced pressured using a rotary evaporator to yield 16g. This was done to investigate scavenging activities of $ONOO^-$, NO, $O_2^-$ and its scavenging mechanism using fluorescent probes, DCFDA, DAF-2 and DHR 123. Results : After Psoralea corylifolia was added authentic $ONOO^-,\;{\cdot}\;O_2^-$ and NO was markedly scavenged. Also, $ONOO^-$ induced by $O_2^-$ and NO (these derived from SIN-1) was inhibited. The data showed a decrease in $ONOO^-$ mediated nitration of tyrosine through electron donation after Psoralea corylifolia was added. Data showed a dose-dependent correlation with inhibition of nitration of bovine serum albumin induced by $ONOO^-$, Furtheremore, LPS-induced ROS and RNS generation was blocked. Conclusions: These results suggest potential for use of Psoralea corylifolia as an effective $ONOO^-$ scavenger to counter the aging process and age-related diseases.

• Journal of Nutrition and Health
• /
• v.41 no.8
• /
• pp.691-700
• /
• 2008

One suggested mechanism underlying copper (Cu) deficiency teratogenicity is a low availability of nitric oxide (NO), signaling molecule which is essential in developmental processes. Increased superoxide anions secondary to decreased activities of Cu-zinc superoxide dismutase (Cu-Zn SOD) in Cu deficiency can interact with NO to form peroxynitrite, which can nitrate proteins at tyrosine residues. In addition, peroxynitrite formation can limit NO bioavailability. We previously reported low NO availability and increased protein nitration in Cu deficient (Cu-) embryos. In the current study, we tested whether Cu deficiency alters downstream signaling of NO by assessing cyclic GMP (cGMP) and phosphorylated vasodilator-stimulating phosphoprotein (VASP) levels, and whether NO supplementation can affect these targets as well as protein nitration. Gestation day 8.5 embryos from Cu adequate (Cu+) or Cu- dams were collected and cultured in either Cu+ or Cu- media for 48 hr. A subset of embryos was cultured in Cu- media supplemented with a NO donor (DETA/NONOate; 20 ${\mu}M$) and/or Cu-Zn SOD. Cu-/Cu- embryos showed a higher incidence of embryonic and yolk sac abnormalities, low NO availability, blunted dose-response in NO concentrations to increasing doses of acetylcholine, low mRNA expression of endothelial nitric oxide synthase (eNOS), increased levels of 3-nitrotyrosine (3-NT) compared to Cu+/Cu+ controls. cGMP concentrations tended to be low in Cu-/Cu- embryos, and they were significantly lower in Cu-/Cu- yolk sacs than in controls. Levels of phosphorylated VASP at serine 239 (P-VASP) were similar in all groups. NO donor supplementation to the Cu- media ameliorated embryonic and yolk sac abnormalities, and resulted in increased levels of cGMP without altering levels of P-VASP and 3-NT. Taken together, these data support the concept that Cu deficiency limits NO availability and alters NO/cGMP-dependent signaling in Cu- embryos and yolk sacs, which contributes to Cu deficiency-induced abnormal development.