Table of Contents
International Journal of Proteomics
Volume 2012 (2012), Article ID 514847, 9 pages
http://dx.doi.org/10.1155/2012/514847
Research Article

Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues

1Department of Biochemistry and Molecular Biology, University of Córdoba and IMIBIC, 14071 Córdoba, Spain
2Cardiovascular Proteomics Laboratory, National Center for Cardiovascular Research, 28026 Madrid, Spain
3Department of Biochemistry, University College Cork, Cork, Ireland

Received 12 April 2012; Accepted 30 April 2012

Academic Editor: Qiangwei Xia

Copyright © 2012 Brian McDonagh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. P. Gygi, B. Rist, S. A. Gerber, F. Turecek, M. H. Gelb, and R. Aebersold, “Quantitative analysis of complex protein mixtures using isotope-coded affinity tags,” Nature Biotechnology, vol. 17, no. 10, pp. 994–999, 1999. View at Publisher · View at Google Scholar · View at Scopus
  2. S. E. Ong, B. Blagoev, I. Kratchmarova et al., “Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics,” Molecular & Cellular Proteomics, vol. 1, no. 5, pp. 376–386, 2002. View at Google Scholar · View at Scopus
  3. P. L. Ross, Y. N. Huang, J. N. Marchese et al., “Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents,” Molecular and Cellular Proteomics, vol. 3, no. 12, pp. 1154–1169, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. F. Q. Schafer and G. R. Buettner, “Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple,” Free Radical Biology and Medicine, vol. 30, no. 11, pp. 1191–1212, 2001. View at Publisher · View at Google Scholar · View at Scopus
  5. S. M. Marino and V. N. Gladyshev, “Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces,” Journal of Molecular Biology, vol. 404, no. 5, pp. 902–916, 2010. View at Publisher · View at Google Scholar · View at Scopus
  6. S. Mohr, H. Hallak, A. de Boitte, E. G. Lapetina, and B. Brüne, “Nitric oxide-induced S-glutathionylation and inactivation of glyceraldehyde-3-phosphate dehydrogenase,” Journal of Biological Chemistry, vol. 274, no. 14, pp. 9427–9430, 1999. View at Publisher · View at Google Scholar · View at Scopus
  7. X. J. Chen, X. Wang, and R. A. Butow, “Yeast aconitase binds and provides metabolically coupled protection to mitochondrial DNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 34, pp. 13738–13743, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. D. Susan-Resiga and T. Nowak, “Proton donor in yeast pyruvate kinase: chemical and kinetic properties of the active site Thr 298 to cys mutant,” Biochemistry, vol. 43, no. 48, pp. 15230–15245, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. D. Sheehan, B. McDonagh, and J. A. Brcena, “Redox proteomics,” Expert Review of Proteomics, vol. 7, no. 1, pp. 1–4, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Sethuraman, M. E. McComb, H. Huang et al., “Isotope-coded affinity tag (ICAT) approach to redox proteomics: identification and quantitation of oxidant-sensitive cysteine thiols in complex protein mixtures,” Journal of Proteome Research, vol. 3, no. 6, pp. 1228–1233, 2004. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Sethuraman, N. Clavreul, H. Huang, M. E. McComb, C. E. Costello, and R. A. Cohen, “Quantification of oxidative posttranslational modifications of cysteine thiols of p21ras associated with redox modulation of activity using isotope-coded affinity tags and mass spectrometry,” Free Radical Biology and Medicine, vol. 42, no. 6, pp. 823–829, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. L. I. Leichert, F. Gehrke, H. V. Gudiseva et al., “Quantifying changes in the thiol redox proteome upon oxidative stress in vivo,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 24, pp. 8197–8202, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. B. McDonagh, S. Ogueta, G. Lasarte, C. A. Padilla, and J. A. Bárcena, “Shotgun redox proteomics identifies specifically modified cysteines in key metabolic enzymes under oxidative stress in Saccharomyces cerevisiae,” Journal of Proteomics, vol. 72, no. 4, pp. 677–689, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. B. McDonagh, C. A. Padilla, J. R. Pedrajas, and J. A. Barcena, “Biosynthetic and iron metabolism is regulated by thiol proteome changes dependent on glutaredoxin-2 and mitochondrial peroxiredoxin-1 in Saccharomyces cerevisiae,” Journal of Biological Chemistry, vol. 286, no. 17, pp. 15565–15576, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. L. Men and Y. Wang, “The oxidation of yeast alcohol dehydrogenase-1 by hydrogen peroxide in vitro,” Journal of Proteome Research, vol. 6, no. 1, pp. 216–225, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. M. M. Bradford, “A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding,” Analytical Biochemistry, vol. 72, no. 1-2, pp. 248–254, 1976. View at Google Scholar · View at Scopus
  17. J. Thaniyavarn, N. Roongsawang, T. Kameyama et al., “Production and characterization of biosurfactants from Bacillus licheniformis F2.2,” Bioscience, Biotechnology and Biochemistry, vol. 67, no. 6, pp. 1239–1244, 2003. View at Google Scholar · View at Scopus
  18. N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997. View at Publisher · View at Google Scholar · View at Scopus
  19. I. Jorge, E. M. Casas, M. Villar et al., “High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies,” Journal of Mass Spectrometry, vol. 42, no. 11, pp. 1391–1403, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. K. Kojima, K. Motohashi, T. Morota et al., “Regulation of translation by the Redox State of Elongation factor G in the cyanobacterium Synechocystis sp. PCC 6803,” Journal of Biological Chemistry, vol. 284, no. 28, pp. 18685–18691, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. D. R. Southworth, J. L. Brunelle, and R. Green, “EFG-independent translocation of the mRNA:tRNA complex is promoted by modification of the ribosome with thiol-specific reagents,” Journal of Molecular Biology, vol. 324, no. 4, pp. 611–623, 2002. View at Publisher · View at Google Scholar · View at Scopus
  22. T. D. Caldas, A. El Yaagoubi, M. Kohiyama, and G. Richarme, “Purification of elongation factors EF-Tu and EF-G from Escherichia coli by covalent chromatography on thiol-sepharose,” Protein Expression and Purification, vol. 14, no. 1, pp. 65–70, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. W. Hu, S. Tedesco, B. McDonagh, J. A. Bárcena, C. Keane, and D. Sheehan, “Selection of thiol- and disulfide-containing proteins of Escherichia coli on activated thiol-Sepharose,” Analytical Biochemistry, vol. 398, no. 2, pp. 245–253, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. P. H. Anborgh, A. Parmeggiani, and J. Jonak, “Site-directed mutagenesis of elongation factor Tu. The functional and structural role of residue Cys81,” European Journal of Biochemistry, vol. 208, no. 2, pp. 251–257, 1992. View at Google Scholar · View at Scopus
  25. I. Pe'er, C. E. Felder, O. Man, I. Silman, J. L. Sussman, and J. S. Beckmann, “Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla,” Proteins, vol. 54, no. 1, pp. 20–40, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. G. R. Grimsley, J. M. Scholtz, and C. N. Pace, “A summary of the measured pK values of the ionizable groups in folded proteins,” Protein Science, vol. 18, no. 1, pp. 247–251, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. C. N. Pace, G. R. Grimsley, and J. M. Scholtz, “Protein ionizable groups: pK values and their contribution to protein stability and solubility,” Journal of Biological Chemistry, vol. 284, no. 20, pp. 13285–13289, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. R. E. Hansen, D. Roth, and J. R. Winther, “Quantifying the global cellular thiol-disulfide status,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 2, pp. 422–427, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. J. Ying, N. Clavreul, M. Sethuraman, T. Adachi, and R. A. Cohen, “Thiol oxidation in signaling and response to stress: detection and quantification of physiological and pathophysiological thiol modifications,” Free Radical Biology and Medicine, vol. 43, no. 8, pp. 1099–1108, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. Y. O. Saw, M. Salim, J. Noirel, C. Evans, I. Rehman, and P. C. Wright, “ITRAQ underestimation in simple and complex mixtures: “the good, the bad and the ugly”,” Journal of Proteome Research, vol. 8, no. 11, pp. 5347–5355, 2009. View at Publisher · View at Google Scholar · View at Scopus
  31. N. A. Karp, W. Huber, P. G. Sadowski, P. D. Charles, S. V. Hester, and K. S. Lilley, “Addressing accuracy and precision issues in iTRAQ quantitation,” Molecular and Cellular Proteomics, vol. 9, no. 9, pp. 1885–1897, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. S. W. Fan, R. A. George, N. L. Haworth, L. L. Feng, J. Y. Liu, and M. A. Wouters, “Conformational changes in redox pairs of protein structures,” Protein Science, vol. 18, no. 8, pp. 1745–1765, 2009. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Barranco-Medina, J. J. Lázaro, and K. J. Dietz, “The oligomeric conformation of peroxiredoxins links redox state to function,” FEBS Letters, vol. 583, no. 12, pp. 1809–1816, 2009. View at Publisher · View at Google Scholar · View at Scopus