Proteomics in Aging Research

Handbook of Models for Human Aging

Volumn , Issue , 2006, Pages 99-108

  Schöneich, Christian ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955050721     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012369391-4/50010-2     Document Type: Chapter

References (90)

1. R. Aebersold and D.R. Goodlett (2001) Mass spectrometry in proteomics. Chem. Rev. 101 269-295.
2. H. Aguilaniu, L. Gustafsson, M. Rigoulet and T. Nyström (2001) Protein oxidation in G0 cells of Saccharomyces cervisiae depends on the state rather than rate of respiration and is enhanced in pos9 but not yap1 mutants. J. Biol. Chem. 276 35396-35404.
3. H. Aguilaniu, L. Gustafsson, M. Rigoulet and T. Nyström (2003) Asymmetric inheritance of oxidatively damaged proteins during cytokinesis. Science 299 1751-1753.
4. K.S. Aulak, T. Koeck, J.W. Crabb and D.J. Stuehr (2004) Dynamics of protein nitration in cells and mitochondria. Am. J. Physiol. Heart Circ. Physiol. 286 H30-H38.
5. K.S. Aulak, M. Miyagi, L. Yan, K.A. West, D. Massillon, J.W. Crabb and D.J. Stuehr (2001) Proteomic method identifies proteins nitration in vivo during inflammatory challenge. Proc. Natl. Acad. Sci. USA 98 12056-12061.
6. M. Ballesteros, A. Fredrikson, J. Henriksson and T. Nyström (2001) Bacterial senescence: Protein oxidation in nonproliferating cells is dictated by the accuracy of the ribosomes. EMBO J. 20 5280-5289.
7. S. Benvenuti, R. Cramer, J. Bruce, M.D. Waterfield and P.S. Jat (2002) Identification of novel candidates for replicative senescence by functional proteomics. Oncogene 21 4403-4413.
8. S. Benvenuti, R. Cramer, C.C. Quinn, J. Bruce, M. Zvelebil, S. Corless, et al. (2002) Differential proteome analysis of replicative senescence in rat embryo fibroblasts. Mol. Cell. Proteomics 1 280-292.
9. B. Berlett and E.R. Stadtman (1997) Protein oxidation in aging, disease, and oxidative stress. J. Biol. Chem. 272 20313-20316.
10. D. Boyd-Kimball, R. Sultana, H.F. Poon, B.C. Lynn, F. Casamenti, G. Pepeu, et al. (2005) Proteomic identification of proteins specifically oxidized by intracerebral injection of amyloid β-peptide (1–42) into rat brain: implications for Alzheimer's disease. Neuroscience 132 313-324.
11. F. Casoni, M. Basso, T. Massignan, E. Gianazza, C. Cheroni, M. Salmona, et al. (2005) Protein nitration in a mouse model of familial amyotrophic lateral sclerosis. J. Biol. Chem. 280 16295-16304.
12. A. Castegna, M. Aksenov, M. Aksenova, V. Thongboonkerd, J.B. Klein, W.M. Pierce, et al. (2002) Proteomic identification of oxidatively modified proteins in Alzheimer's disease brain. Part 1. Creatine kinase BB, glutatmine synthetase, and ubiquitin carboxy-terminal hydrolase L-1. Free Radi. Biol. Med. 33 562-571.
13. A. Castegna, M. Aksenov, V. Thongboonkerd, J.B. Klein, W.M. Pierce, R. Booze, et al. (2002) Proteomic identification of oxidatively modified proteins in Alzheimer's disease brain. Part 2. Dihydropyrimidinase-related protein 2, alpha-enolase and heat shock cognate 71. J. Neurochem. 82 1524-1532.
14. J. Chang, H. van Remmen, J. Cornell, A. Richardson and W.F. Ward (2003) Comparative proteomics: Characterization of a two-dimensional gel electrophoresis system to study the effect of aging on mitochondrial proteins. Mech. Ageing Dev. 124 33-41.
15. S.L. Chen, M.J. Huddleston, W. Shou, R.J. Deshaies, R.S. Annan and S.A. Carr (2002) Mass spectrometry-based methods for phosphorylation site mapping of hyperphosphorylated proteins applied to Net1, a regulator of exit from mitosis in yeast. Mol. Cell. Proteomics 1 186-196.
16. Y.-M. Cho, S.-H. Bae, B.-K. Choi, S.Y. Cho, C.-W. Song, J.-K. Yoo and Y.-K. Paik (2003) Differential expression of the liver proteome in senescence-accelerated mice. Proteomics 3 1883-1894.
17. T.P. Conrads, H.J. Issaq and T.D. Veenstra (2002) New tools for quantitative phosphoproteome analysis. Biochem. Biophys. Res. Commun. 290 885-890.
18. J.W. Crabb, M. Miyagi, X. Gu, K. Shadrach, K.A. West, H. Sakaguchi, et al. (2002) Drusen proteome analysis: An approach to the etiology of age-related macular degeneration. Proc. Natl. Acad. Sci. USA 99 14682-14687.
19. N. Das, R.L. Levine, W.C. Orr and R.S. Sohal (2001) Selectivity of protein oxidative damage during aging in Drosophila melanogaster. Biochem. J. 360 209-216.
20. J.P. De Magalhães and O. Toussaint (2004) GenAge: A genomic and proteomic network map of human ageing. FEBS Lett. 571 243-247.
21. J.-F. Dierick, M. Dieu, J. Remacle, M. Raes, P. Rpepstorff and O. Toussaint (2002) Proteomics in experimental gerontology. Exp. Gerontol. 37 721-734.
22. J.-F. Dierick, F. Eliaers, J. Remacle, M. Raes, S.J. Fey, P.M. Larsen and O. Toussaint (2002) Stress-induced premature senescence and replicative sensescence are different phenotypes. Proteomic evidence. Biochem. Pharmacol. 64 1011-1017.
23. J.-F. Dierick, D.E. Kalume, F. Wenders, M. Salmon, M. Dieu, M. Raes, P. Roepstorff and O. Toussaint (2002) Identification of 30 protein species involved in replicative senescence and stress-induced premature senescence. FEBS Lett. 531 499-504.
24. S. Dukan, A. Farewell, M. Ballesteros, F. Taddei, M. Radman and T. Nyström (2000) Protein oxidation in response to increased transcriptional or translational errors. Proc. Natl. Acad. Sci. USA 97 5746-5749.
25. S. Dukan and T. Nyström (1999) Oxidative stress defense and deterioration of growth-arrested Escherichia coli cells. J. Biol. Chem. 274 26027-26032.
26. Z. Eshhar, M. Ofarim and T. Waks (1980) Generation of hybridomas secreting murine reaginic antibodies of anti-DNP specificity. J. Immunol. 124 775-780.
27. S.B. Ficarro, M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, et al. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cervisiae. Nat. Biotechnol. 20 301-305.
28. C.E. Finch and R.E. Tanzi (1997) Genetics of aging. Science 278 407-411.
29. M. Fratelli, H. Demol, M. Puype, S. Casagrande, I. Eberini, M. Salmona, et al. (2002) Identification by redox proteomics of glutathionylated proteins in oxidatively stressed human T lymphocytes. Proc. Natl. Acad. Sci. USA 99 3505-3510.
30. P.S. Gromov, M. Ostergaard, I. Gromova and J.E. Celis (2002) Human proteomic databases: A powerful reource for functional genomics in health and disease. Prog Biophys. Mol. Biol. 80 3-22.
31. M. Grønborg, T.K. Kristiansen, A. Stensballe, J.S. Andersen, O. Ohara, M. Mann, O.N. Jensen and A. Pandey (2002) A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies. Mol. Cell. Proteomics 1 517-527.
32. S.P. Gygi, G.L. Corthals, Y. Zhang, Y. Rochon and R. Aebersold (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97 9390-9395.
33. S.P. Gygi, B. Rist, T.J. Griffin, J. Eng and R. Aebersold (2002) Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope coded affinity tags. J. Proteome Res. 1 47-54.
34. Y. Irie, M. Saeki, Y. Kamisaki, E. Martin and F. Murad (2003) Histone H1.2 is a substrate for denitrase, an activity that reduces nitrotyrosine immunoreactivity. Proc. Natl. Acad. Sci. USA 100 5634-5639.
35. H. Ischiropoulos and J.S. Beckman (2003) Oxidative stress and nitration in neurodegeneration: Cause, effect, or association? J. Clin. Invest. 111 163-169.
36. S.M. Jazwinski (1996) Longevity, genes, and aging. Science 273 54-59.
37. E. Johannson, O. Olsson and T. Nyström (2004) Progression and specificity of protein oxidation in the life cycle of Arabidopsis thaliana. J. Biol. Chem. 279 22204-22208.
38. J. Kanski, M. Alterman and C. Schöneich Ch. (2003) Proteomic identification of age-dependent protein nitration in rat skeletal muscle. Free Radic. Biol. Med. 35 1229-1239.
39. J. Kanski, A. Behring, J. Pelling and C. Schöneich Ch. (2005) Proteomic identification of cardiac proteins in Fisher 344/BNF1 rats which undergo tyrosine nitration as a consequence of biological aging. Am. J. Physiol. Heart Circ. Physiol. 288 371-381.
40. J. Kanski, S.J. Hong and C. Schöneich Ch. (2005) Proteomic analysis of protein nitration in aging skeletal muscle and identification of nitrotyrosine-containing sequences in vivo by nanoelectrospray ionization tandem mass spectrometry. J. Biol. Chem. 280 24261-24266.
41. N. Khidekel and L.C. Hsieh-Wilson (2004) A “molecular switchboard”-covalent modification to proteins and impact on transcription. Org. Biomol. Chem. 2 1-7.
42. P. Klatt, E. Pineda Molina, D. Perez-Sala and S. Lamas (2000) Novel application of S-nitrosoglutathione-Sepharose to identify proteins that are potential targets for S-nitrosoglutathione-induced mixed-disulphide formation. Biochem. J. 349 567-578.
43. Z.A. Knight, B. Schilling, R.H. Row, D.M. Kenski, B.W. Gibson and K.M. Shokat (2003) Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol. 21 1047-1054.
44. T. Koeck, X. Fu, S.L. Hazen, J.W. Crabb, D.J. Stuehr and K.S. Aulak (2004) Rapid and selective oxygen-regulated protein tyrosine denitration and nitration in mitochondria. J. Biol. Chem. 279 27257-27262.
45. S.W.J. Lamberts, A.W. Van den Beld and A.-J. Van der Lely (1997) The endocrinology of aging. Science 278 419-424.
46. T.-K. Lin, G. Hughes, A. Muratovska, F.H. Blaikie, P.S. Brookes, V. Darley-Usmar, R.A.J. Smith and M.P. Murphy (2002) Specific modification of mitochondrial protein thiols in response to oxidative stress. J. Biol. Chem. 277 17048-17056.
47. M. Mann, S.E. Ong, M. Grønborg, H. Steen, O.N. Jensen and A. Pandey (2002) Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 20 261-268.
48. E.J. Masoro (1993) Concepts and hypothesis of basic aging processes. B.P. Yu, (Ed.) Free Radicals in Aging Boca Raton: CRC Press 1-9.
49. M. Merchant and S.R. Weinberger (2000) Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 21 1164-1167.
50. H. Mirzaei and F.E. Regnier (2005) Affinity chromatographic selection of carbonylated proteins followed by identification of oxidation sites using tandem mass spectrometry. Anal. Chem. 77 2386-2392.
51. M. Miyagi, H. Sakaguchi, R.M. Darrow, L. Yan, K.A. West, K.S. Aulak, et al. (2002) Evidence that light modulates protein nitration in rat retina. Mol. Cell. Proteomics 1 293-303.
52. J.H. Morrison and P.R. Hof (1997) Life and death of neurons in the aging brain. Science 278 412-419.
53. Y. Oda, T. Nagasu and B.T. Chait (2001) Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19 379-382.
54. A. Pandey and M. Mann (2000) Proteomics to study genes and genomes. Nature 405 837-846.
55. S. Poggioli, H. Bakala and B. Friguet (2002) Age-related increase of protein glycation in peripheral blood lymphocytes is restricted to preferential target proteins. Exp. Gerontol. 37 1207-1215.
56. H.F. Poon, A. Castegna, S.A. Farr, V. Thongboonkerd, B.C. Lynn, W.A. Banks, et al. (2004) Quantitative proteomics analysis of specific protein expression and oxidative modification in aged senescence-accelerated-prone 8 mice brain. Neuroscience 126 915-926.
57. T. Rabilloud, M. Heller, F. Gasnier, S. Luche, C. Rey, R. Aebersold, et al. (2002) Proteomic analysis of cellular response to oxidative stress. J. Biol. Chem. 277 19396-19401.
58. L. Riggs, E.H. Seeley and F.E. Regnier (2005) Quantification of phosphoproteins with global internal standard technology. J. Chromatogr. B 817 89-96.
59. L. Riggs, C. Sioma and F.E. Regnier (2001) Automated signature peptide approach for proteomics. J. Chromatogr. A 924 359-368.
60. P.H. Righetti, A. Castagna, P. Antonioli and E. Boschetti (2005) Prefractionation techniques in proteome analysis: The mining tools of the third millennium. Electrophoresis 26 297-319.
61. L.J. Robinson, N.G. Karlsson, A.S. Weiss and N.H. Packer (2003) Proteomic analysis of the genetic premature aging disease Hutchinson Gilford Progeria Syndrome reveals differential protein expression and glycosylation. J. Proteome Res. 2 556-557.
62. A. Schlosser, R. Pipkorn, D. Bossemeyer and W.D. Lehmann (2001) Analysis of protein phosphorylation by a combination of elastase digestion and neutral loss tandem mass spectrometry. Anal. Chem. 73 170-176.
63. E.H. Seeley, L.D. Riggs and F.E. Regnier (2005) Reduction of non-specific binding in Ga(III) immobilized metal affinity chromatography for phosphopeptides by using endoproteinase glu-C as the digestive enzyme. J. Chromatogr. B 817 81-88.
64. E. Shacter, J.A. Williams, M. Lim and R.L. Levine (1994) Differential susceptibility of plasma proteins to oxidative modification: examination by Western blot immunoassay. Free Radic. Biol. Med. 17 429-437.
65. J. Shaw, R. Rowlinson, J. Nickson, T. Stone, A. Sweet, K. Williams and R. Tonge (2003) Evaluation of saturation labeling two-dimsnional difference gel electrophoresis fluorescent dyes. Proteomics 3 1181-1195.
66. Y. Shen and R.D. Smith (2002) Proteomics based on high-efficiency capillary separations. Electrophoresis 23 3106-3124.
67. J.R. Smith and O.M. Pereira-Smith (1996) Replicative senescence: Implications for in vivo aging and tumor suppression. Science 273 63-67.
68. M.G. Smith, G. Jone, J. Ptacek, G. Devgan, H. Zhu, X. Zhu and M. Snyder (2005) Global analysis of protein function using protein microarrays. Mech. Ageing Dev. 126 171-175.
69. M. Smolka, H. Zhou and R. Aebersold (2002) Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell. Proteomics 1 19-29.
70. R.S. Sohal and R. Weindruch (1996) Oxidative stress, calorie restriction, and aging. Science 273 59-63.
71. B.A. Soreghan, F. Yang, S.N. Thomas, J. Hsu and A.J. Yang (2003) High-throughput proteomic-based identification of oxidatively induced protein carbonylation in mouse brain. Pharm. Res. 20 1713-1720.
72. H. Steen, B. Kuster, M. Fernandez, A. Pandey and M. Mann (2002) Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J. Biol. Chem. 277 1031-1039.
73. H. Steen and M. Mann (2002) A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J. Am. Chem. Mass Spectrom. 13 996-1003.
74. H. Steen and M. Mann (2002) Analysis of bromotryptophan and hydroxyproline modifications by high-resolution, high-accuracy precursor ion scanning utilizing fragment ions with mass-deficient mass tags. Anal. Chem. 74 6230-6236.
75. D.M. Sullivan, N.B. Wehr, M.M. Fergusson, R.L. Levine and T. Finkel (2000) Identification of oxidant-sensitive proteins: TNF-α induces protein glutathiolation. Biochemistry 39 11121-11128.
76. I.V. Turku, L. Li, K.S. Aulak, D.J. Stuehr, J.-Y. Chang and F. Murad (2003) Protein tyrosine nitration in the mitochondria from diabetic mouse heart. J. Biol. Chem. 278 33972-33977.
77. Y. Ueda, M.K. Duncan and L.L. David (2002) Lens proteomics: the accumulation of crystalline modifications in the mouse lens with age. Invest. Ophtalmol. Vis. Sci. 43 205-215.
78. M. Uhlen and F. Ponten (2005) Antibody-based proteomics for human tissue profiling. Mol. Cell. Proteomics 4 384-393.
79. M.P. Washburn, D. Wolters and J.R. Yates III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotech. 19 242-247.
80. D.A. Wolters, M.P. Washburn and J.R. Yates III (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73 5683-5690.
81. A. Xu and N. Narayanan (1998) Effects of aging on sarcoplasmic reticulum Ca2+-cycling proteins and their phosphorylation in rat myocardium. Am. J. Physiol. 275 H2087-H2094.
82. L. Yan, H. Ge, H. Li, S.C. Lieber, F. Natividad, R.R.G. Resuello, S.-J. Kim, S. Akeju, A. Sun, K. Loo, A.P. Peppas, F. Rossi, E.D. Lewandowski, A.P. Thomas, S.F. Vatner and D.E. Vatner (2004) Gender-specific proteomic alterations in glycolytic and mitochondrial pathways in aging monkey hearts. J. Mol. Cell. Cardiol. 37 921-929.
83. B.-S. Yoo and F. regnier (2004) Proteomic analysis of carbonylated proteins in two-dimensional gel electrophoresis using avidin-fluorescein affinity staining. Electrophoresis 25 1334-1341.
84. A.L. Zarling, S.B. Ficarro, F.M. White, J. Shabanowitz, D.F. Hunt and V.H. Engelhardt (2000) Phosphorylated peptides are naturally processed by major histocompatibility complex I molecules in vivo. J. Exp. Med. 192 1755-1762.
85. X. Zhan and D.M. Desiderio (2004) The human pituitary nitroproetome: detection of nitrotyrosyl-proteins with two-dimensional Western blotting, and amino acid sequence determination with mass spectrometry. Biochem. Biophys. Res. Commun. 325 1180-1186.
86. J. Zhang, D.R. Goodlett, E.R. Peskind, J.F. Quinn, Y. Zhou, Q. Wang, C. Pan, E. Yi, J. Eng, R.H. Aebersold and T.J. Montine (2005) Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol. Aging 26 207-227.
87. R. Zhang, C.S. Sioma, S. Wang and F.E. Regnier (2001) Fractionation of isotopically labeled peptides in quantitative proteomics. Anal. Chem. 73 5142-5149.
88. G. Zhou, H. Li, D. DeCamps, S. Chen, H. Shu, Y. Gong, M. Flaig, J.W. Gillespie, N. Hu, P.R. Taylor, M.R. Emmert-Buck, L.A. Liotta, E.F. Petricoin III and Y. Zhao (2002) 2D differential in-gel electrohoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol. Cell. Proteomics 1 117-124.
89. H. Zhou, J.A. Ranish, J.D. Watts and R. Aebersold (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 19 512-515.
90. H. Zhou, J.D. Watts and R. Aebersold (2001) A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol. 19 375-378.