Accumulation of oxidatively modified proteins is widely observed in aged animal tissues. Protein carbonyls are mostly derived from lysine, arginine, proline and threonine residues under oxidative conditions. Many groups have investigated carbonylated proteins since a convenient immunochemical procedure was established for detecting dinitrophenyl derivatives of carbonyls and applied to proteomic research. An alternative method of tagging with biotin or fluorescent dyes has been also introduced to proteomic analysis of protein carbonyls. Nitrotyrosine was primarily identified as a biomarker of cellular damage and inflammation under nitrosative stress. Nitrated proteins have been subsequently detected in aged animal tissues and Alzheimer's disease affected brains by Western blotting, and identified by mass spectrometry. Protein s‐thiolation, a mixed‐derivatization of cysteine (Cys) by conjugation of low‐molecular‐weight thiol compounds, is recognized as protecting functional proteins from more serious damage. A method of biotin labeling has been used in proteomics for tracing protein s‐thiolation. Among all kinds of amino acid residues, methionine (Met) is the most susceptible to reactive oxygen species, and Met oxidation seems to occur in ordinary cellular circumstances because most cells contain Met sulfoxide reductases, which might prevent serious cellular damage. In proteomic analysis, Met sulfoxide‐containing peptides are generally observed as 16‐Da‐high mass peaks in peptide mass fingerprinting. A modified procedure of two‐dimensional gel electrophoresis, in which proteins are kept under non‐oxidative conditions throughout the procedure, is appropriate for the estimation of the Met sulfoxide level of each protein in aged animal tissues and cells to evaluate the pathophysiological significance of Met oxidation in the mechanism of aging. Geriatr Gerontol Int 2010; 10 (Suppl. 1): S25–S31.

Background: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies.

(Z)-2,2-Dimethyl-8-(3-methyl-2-butenyl)-benzopyran-6-propenoic acid (1) was isolated from Brazilian propolis, together with the known benzopyran derivative, (E)-2, 2-dimethyl-8-(3-methyl-2-butenyl)-benzopyran-6-propenoic acid (2). The structure was determined by spectroscopic analyses, which included 1D and 2D (1)H and (13)C NMR experiments, as well as MS, IR, and UV spectroscopy. Compound 2 rapidly changed to 1 under UV irradiation conditions (365 nm), and the reverse reaction was also observed. The ratio of 1 to 2 reached 2.3 when the reaction began from either 1 or 2, indicating a photostationary state. Compound 1 displayed an approximate 7-fold stronger cytotoxicity against human lung carcinoma cells (HLC-2) compared with 2.

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The free-radical theory predicts that the oxidative stress accelerates the rate of aging and increases the onset of degenerative disorders in the elderly. Dopaminergic neurons are especially vulnerable to age-related neuronal disorders due to reactive oxygen species generated in the pathway of dopamine metabolism. Biochemical changes occurring in substantia nigra of Parkinson's disease patients suggest that the oxidative-stress-induced cell damages may be involved in the neurodegeneration. In our previous researches, we found that the dephosphorylation of elongation factor-2 and phosphorylation of nuclear lamin A/ C might be neuronal cell specific response to oxidative stress. (Nakamura et al. BBA, 1763(9), 977-989, 2006) The dephosphorylation and phosphorylation of those proteins are significant biomarkers for analyzing the molecular mechanisms of the stress response, however, such a phosphoproteome analysis is thought to be inappropriate for clinical investigation of neurodegeneration if it was not detectable in cerebrospinal fluid or serum of patients. Thus, we proceeded to the 2D-DIGE analysis of secretome, proteome of secreted proteins, using the culture system in which oxidative stress was applied to human SH-SY5Y neuroblastoma cells. As the result of our secretome analysis, we identified ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2 N, ubiquitin C-terminal hydrorase-L1, 14-3-3 protein isoforms, Rab GDP dissociation inhibitor β, Rho GDP-dissociation inhibitor 1, peroxiredoxin-2, glutathione S-transferase P, α enolase, LDH B chain as oxidative-stress-reporting biomarker candidates.