Neuroproteomics

Neuroproteomics

Volumn , Issue , 2009, Pages 1-16

  Alzate, Oscar ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85043394075     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (108)

1. Anderson, N. L. and Anderson, N. G. (1998) Proteome and proteomics: New technologies, new concepts, and new words, Electrophoresis 19:1853-61.
2. Creighton, T. E. (1993) Proteins: Structures and molecular properties (New York: W. H. Freeman).
3. Tribl, F., Meyer, H. E. and Marcus, K. (2008) Analysis of organelles within the nervous system: Impact on brain and organelle functions, Expert Rev Proteomics 5:333-51.
4. Fountoulakis, M. (2004) Application of proteomics technologies in the investigation of the brain, Mass Spectrom Rev 23:231-58.
5. Wilson, K. E., Ryan, M. M., Prime, J. E., et al. (2004) Functional genomics and proteomics:Application in neurosciences, J Neurol Neurosurg Psychiatry 75:529-38.
6. Tannu, N. S. and Hemby, S. E. (2006) Methods for proteomics in neuroscience, Prog Brain Res 158:41-82.
7. Becker, M., Schindler, J. and Nothwang, H. G. (2006) Neuroproteomics-The tasks lying ahead, Electrophoresis 27:2819-29.
8. Butcher, J. (2007) Neuroproteomics comes of age, Lancet Neurol 6:850-1.
9. Abul-Husn, N. S. and Devi, L. A. (2006) Neuroproteomics of the synapse and drug addiction, J Pharmacol Exp Ther 318:461-8.
10. Kim, S. I., Voshol, H., van Oostrum, J. et al. (2004) Neuroproteomics: Expression profiling of the brain’s proteomes in health and disease, Neurochem Res 29:1317-31.
11. Tribl, F., Marcus, K., Bringmann, G. et al. (2006) Proteomics of the human brain:Sub-proteomes might hold the key to handle brain complexity, J Neural Transm 113:1041-54.
12. Marcus, K., Schmidt, O., Schaefer, H. et al. (2004) Proteomics-Application to the brain, Int Rev Neurobiol 61:285-311.
13. Boeddrich, A., Lurz, R. and Wanker, E. E. (2003) Huntingtin fragments form aggresomelike inclusion bodies in mammalian cells, Methods Mol Biol 232:217-29.
14. Schubert, D., Herrera, F., Cumming, R. et al. (2009) Neural cells secrete a unique repertoire of proteins, J Neurochem 109:427-35.
15. Liu, J., Liu, M. C. and Wang, K. K. (2008) Physiological and pathological actions of calpains in glutamatergic neurons, Sci Signal 1:tr3.
16. Maurer, M. H. and Kuschinsky, W. (2006) Screening the brain: Molecular fingerprints of neural stem cells, Curr Stem Cell Res Ther 1:65-77.
17. Chen, H. B., Pan, K., Tang, M. K. et al. (2008) Comparative proteomic analysis reveals differentially expressed proteins regulated by a potential tumor promoter, BRE, in human esophageal carcinoma cells, Biochem Cell Biol 86:302-11.
18. Chumbalkar, V., Sawaya, R. and Bogler, O. (2008) Proteomics: The new frontier also for brain tumor research, Curr Probl Cancer 32:143-54.
19. Graner, M. W., Alzate, O., Dechkovskaia, A. M. et al. (2009) Proteomic and immunologic analyses of brain tumor exosomes, FASEB J 23:1541-57.
20. Whittle, I. R., Short, D. M., Deighton, R. F. et al. (2007) Proteomic analysis of gliomas, Br J Neurosurg 21:576-82.
21. Bai, F. and Witzmann, F. A. (2007) Synaptosome proteomics, Subcell Biochem 43:77-98.
22. Cheng, D., Hoogenraad, C. C., Rush, J. et al. (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum, Mol Cell Proteomics 5:1158-70.
23. Emes, R. D., Pocklington, A. J., Anderson, C. N. et al. (2008) Evolutionary expansion and anatomical specialization of synapse proteome complexity, Nat Neurosci 11:799-806.
24. Jordan, B. A., Fernholz, B. D., Boussac, M. et al. (2004) Identification and verification of novel rodent postsynaptic density proteins, Mol Cell Proteomics 3:857-71.
25. Li, K. W., Hornshaw, M. P., Van Der Schors, R. C. et al. (2004) Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology, J Biol Chem 279:987-1002.
26. Li, K. W. and Jimenez, C. R. (2008) Synapse proteomics: Current status and quantitative applications, Expert Rev Proteomics 5:353-60.
27. Schrimpf, S. P., Meskenaite, V., Brunner, E. et al. (2005) Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry, Proteomics 5:2531-41.
28. Arimon, M., Grimminger, V., Sanz, F. and Lashuel, H. A. (2008) Hsp104 targets multiple intermediates on the amyloid pathway and suppresses the seeding capacity of Abeta fibrils and protofibrils, J Mol Biol 384:1157-73.
29. Fountoulakis, M. and Kossida, S. (2006) Proteomics-driven progress in neurodegeneration research, Electrophoresis 27:1556-73.
30. Herbst, M. and Wanker, E. E. (2006) Therapeutic approaches to polyglutamine diseases:Combating protein misfolding and aggregation, Curr Pharm Des 12:2543-55.
31. Herbst, M. and Wanker, E. E. (2007) Small molecule inducers of heat-shock response reduce polyQ-mediated huntingtin aggregation. A possible therapeutic strategy, Neurodegener Dis 4:254-60.
32. Osorio, C., Sullivan, P. M., He, D. N. et al. (2007) Mortalin is regulated by APOE in hippocampus of AD patients and by human APOE in TR mice, Neurobiol Aging 28:1853-62.
33. Butterfield, D. A. (2004) Proteomics: A new approach to investigate oxidative stress in Alzheimer’s disease brain, Brain Res 1000:1-7.
34. Ding, Q., Dimayuga, E. and Keller, J. N. (2007) Oxidative damage, protein synthesis, and protein degradation in Alzheimer’s disease, Curr Alzheimer Res 4:73-9.
35. Forero, D. A., Casadesus, G., Perry, G. and Arboleda, H. (2006) Synaptic dysfunction and oxidative stress in Alzheimer’s disease: Emerging mechanisms, J Cell Mol Med 10z:796-805.
36. Sultana, R., Perluigi, M. and Butterfield, D. A. (2006) Protein oxidation and lipid peroxidation in brain of subjects with Alzheimer’s disease: Insights into mechanism of neurodegeneration from redox proteomics, Antioxid Redox Signal 8:2021-37.
37. Sultana, R., Perluigi, M. and Butterfield, D. A. (2006) Redox proteomics identification of oxidatively modified proteins in Alzheimer’s disease brain and in vivo and in vitro models of AD centered around Abeta(1-42), J Chromatogr B Analyt Technol Biomed Life Sci 833:3-11.
38. Li, K. W. and Smit, A. B. (2008) Subcellular proteomics in neuroscience, Front Biosci 13:4416-25.
39. Zetterberg, H., Ruetschi, U., Portelius, E. et al. (2008) Clinical proteomics in neurodegenerative disorders, Acta Neurol Scand 118:1-11.
40. Van den Bergh, G. and Arckens, L. (2005) Recent advances in 2D electrophoresis: An array of possibilities, Expert Rev Proteomics 2:243-52.
41. Williams, K., Wu, T., Colangelo, C. and Nairn, A. C. (2004) Recent advances in neuroproteomics and potential application to studies of drug addiction, Neuropharmacology 47 (Suppl 1):148-66.
42. Grant, S. G. (2006) The synapse proteome and phosphoproteome: A new paradigm for synapse biology, Biochem Soc Trans 34:59-63.
43. Jin, M., Bateup, H., Padovan, J. C. et al. (2005) Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multistage mass spectrometry, Anal Chem 77:7845-51.
44. Hanger, D. P., Betts, J. C., Loviny, T. L., Blackstock, W. P. and Anderton, B. H. (1998) New phosphorylation sites identified in hyperphosphorylated tau (paired helical filament- tau) from Alzheimer’s disease brain using nanoelectrospray mass spectrometry, J Neurochem 71:2465-76.
45. Wan, J., Roth, A. F., Bailey, A. O. and Davis, N. G. (2007) Palmitoylated proteins:Purification and identification, Nat Protoc 2:1573-84.
46. Yang, J., Gibson, B., Snider, J. et al. (2005) Submicromolar concentrations of palmitoyl-CoA specifically thioesterify cysteine 244 in glyceraldehyde-3-phosphate dehydrogenase inhibiting enzyme activity: A novel mechanism potentially underlying fatty acid induced insulin resistance, Biochemistry 44:11903-12.
47. Barnes, S., Shonsey, E. M., Eliuk, S. M. et al. (2008) High-resolution mass spectrometry analysis of protein oxidations and resultant loss of function, Biochem Soc Trans 36:1037-44.
48. Butterfield, D. A. and Sultana, R. (2007) Redox proteomics identification of oxidatively modified brain proteins in Alzheimer’s disease and mild cognitive impairment: Insights into the progression of this dementing disorder, J Alzheimers Dis 12:61-72.
49. Hutson, S. M., Poole, L. B., Coles, S. and Conway, M. E. (2008) Redox regulation and trapping sulfenic acid in the peroxide-sensitive human mitochondrial branched chain aminotransferase, Methods Mol Biol 476:139-52.
50. Paige, J. S., Xu, G., Stancevic, B. and Jaffrey, S. R. (2008) Nitrosothiol reactivity profiling identifies S-nitrosylated proteins with unexpected stability, Chem Biol 15:1307-16.
51. Pamplona, R., Naudi, A., Gavin, R. et al. (2008) Increased oxidation, glycoxidation, and lipoxidation of brain proteins in prion disease, Free Radic Biol Med 45:1159-66.
52. Kim, H., Eliuk, S., Deshane, J. et al. (2007) 2D gel proteomics: An approach to study age-related differences in protein abundance or isoform complexity in biological samples, Methods Mol Biol 371:349-91.
53. Lubec, G., Krapfenbauer, K. and Fountoulakis, M. (2003) Proteomics in brain research:Potentials and limitations, Prog Neurobiol 69:193-211.
54. Choi, J., Forster, M. J., McDonald, S. R. et al. (2004) Proteomic identification of specific oxidized proteins in ApoE-knockout mice: Relevance to Alzheimer’s disease, Free Radic Biol Med 36:1155-62.
55. Mori, H., Oikawa, M., Tamagami, T. et al. (2007) Oxidized proteins in astrocytes generated in a hyperbaric atmosphere induce neuronal apoptosis, J Alzheimers Dis 11:165-74.
56. Alzate, O., Hussain, S. R., Goettl, V. M. et al. (2004) Proteomic identification of brainstem cytosolic proteins in a neuropathic pain model, Brain Res Mol Brain Res 128:193-200.
57. Jacobs, S., Van de Plas, B., Van der Gucht, E. et al. (2008) Identification of new regional marker proteins to map mouse brain by 2-D difference gel electrophoresis screening, Electrophoresis 29:1518-24.
58. Pinaud, R., Osorio, C., Alzate, O. and Jarvis, E. D. (2008) Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics, Eur J Neurosci 27:1409-22.
59. Swatton, J. E., Prabakaran, S., Karp, N. A., Lilley, K. S. and Bahn, S. (2004) Protein profiling of human postmortem brain using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE), Mol Psychiatry 9:128-43.
60. Riederer, B. M. (2008) Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis, J Proteomics 71:231-44.
61. Scholz, B., Svensson, M., Alm, H. et al. (2008) Striatal proteomic analysis suggests that first L-dopa dose equates to chronic exposure, PLoS ONE 3:e1589.
62. Seshi, B. (2007) Proteomics strategy based on liquid-phase IEF and 2-D DIGE:Application to bone marrow mesenchymal progenitor cells, Proteomics 7:1984-99.
63. Haskins, W. E., Kobeissy, F. H., Wolper, R. A. et al. (2005) Rapid discovery of putative protein biomarkers of traumatic brain injury by SDS-PAGE-capillary liquid chromatography- tandem mass spectrometry, J Neurotrauma 22:629-44.
64. Kobeissy, F. H., Warren, M. W., Ottens, A. K. et al. (2008) Psychoproteomic analysis of rat cortex following acute methamphetamine exposure, J Proteome Res 7:1971-83.
65. Ottens, A. K., Kobeissy, F. H., Wolper, R. A. et al. (2005) A multidimensional differential proteomic platform using dual-phase ion-exchange chromatography-polyacrylamide gel electrophoresis/reversed-phase liquid chromatography tandem mass spectrometry, Anal Chem 77:4836-45.
66. Andrade, E. C., Krueger, D. D. and Nairn, A. C. (2007) Recent advances in neuroproteomics, Curr Opin Mol Ther 9:270-81.
67. Chen, H. and Fan, Z. H. (2009) Two-dimensional protein separation in microfluidic devices, Electrophoresis 30:758-65.
68. Moon, H., Wheeler, A. R., Garrell, R. L., Loo, J. A. and Kim, C. J. (2006) An integrated digital microfluidic chip for multiplexed proteomic sample preparation and analysis by MALDI-MS, Lab Chip 6:1213-9.
69. Fung, E. (2004) Protein arrays: Methods and protocols (Totowa, NJ: Humana Press).
70. Dickson, C. (2008) Protein techniques: Immunoprecipitation, in vitro kinase assays, and Western blotting, Methods Mol Biol 461:735-44.
71. Gallagher, S. and Chakavarti, D. (2008) Immunoblot analysis, J Vis Exp Jun 20.
72. Barnouin, K. (2004) Two-dimensional gel electrophoresis for analysis of protein complexes, Methods Mol Biol 261:479-98.
73. Ehlers, M. D. (2003) Activity level controls postsynaptic composition and signaling via the ubiquitin-proteasome system, Nat Neurosci 6:231-42.
74. Persson, A., Hober, S. and Uhlen, M. (2006) A human protein atlas based on antibody proteomics, Curr Opin Mol Ther 8:185-90.
75. Saerens, D., Ghassabeh, G. H. and Muyldermans, S. (2008) Antibody technology in proteomics, Brief Funct Genomic Proteomic 7:275-82.
76. Schachman, H. K. (1959) Ultracentrifugation in biochemistry (New York: Academic Press).
77. Van Holde, K. E. (1975) Sedimentation analysis of proteins (New York: Academic Press).
78. Creeth, J. M. and Knight, C. G. (1967) The macromolecular properties of bloodgroup substances. Sedimentation-velocity and viscosity measurements, Biochem J 105:1135-45.
79. Creeth, J. M. and Pain, R. H. (1967) The determination of molecular weights of biological macromolecules by ultracentrifuge methods, Prog Biophys Mol Biol 17:217-87.
80. Teller, D. C. (1973) Characterization of proteins by sedimentation equilibrium in the analytical ultracentrifuge, Methods Enzymol 27:346-441.
81. Geerlof, A., Brown, J., Coutard, B. et al. (2006) The impact of protein characterization in structural proteomics, Acta Crystallogr D Biol Crystallogr 62:1125-36.
82. Stafford, W. F., 3rd (2009) Protein-protein and ligand-protein interactions studied by analytical ultracentrifugation, Methods Mol Biol 490:83-113.
83. Ahmed, F. E. (2008) Mining the oncoproteome and studying molecular interactions for biomarker development by 2DE, ChIP and SPR technologies, Expert Rev Proteomics 5:469-96.
84. Jonsson, U., Fagerstam, L., Ivarsson, B. et al. (1991) Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology, Biotechniques 11:620-7.
85. Myszka, D. G. (1997) Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors, Curr Opin Biotechnol 8:50-7.
86. Visser, N. F. and Heck, A. J. (2008) Surface plasmon resonance mass spectrometry in proteomics, Expert Rev Proteomics 5:425-33.
87. Yuk, J. S. and Ha, K. S. (2005) Proteomic applications of surface plasmon resonance biosensors: Analysis of protein arrays, Exp Mol Med 37:1-10.
88. Greenfield, N. J. (2006) Using circular dichroism spectra to estimate protein secondary structure, Nat Protoc 1:2876-90.
89. Kahle, P. J. and Haass, C. (2004) How does parkin ligate ubiquitin to Parkinson’s disease? EMBO Rep 5:681-5.
90. Matus, S., Lisbona, F., Torres, M. et al. (2008) The stress rheostat: An interplay between the unfolded protein response (UPR) and autophagy in neurodegeneration, Curr Mol Med 8:157-72.
91. Sahara, N., Maeda, S. and Takashima, A. (2008) Tau oligomerization: A role for tau aggregation intermediates linked to neurodegeneration, Curr Alzheimer Res 5:591-8.
92. Uehara, T. (2007) Accumulation of misfolded protein through nitrosative stress linked to neurodegenerative disorders, Antioxid Redox Signal 9:597-601.
93. Uversky, V. N. (2008) Alpha-synuclein misfolding and neurodegenerative diseases, Curr Protein Pept Sci 9:507-40.
94. Johnson, M. D., Yu, L. R., Conrads, T. P. et al. (2005) The proteomics of neurodegeneration, Am J Pharmacogenomics 5:259-70.
95. Chun, W. and Johnson, G. V. (2007) The role of tau phosphorylation and cleavage in neuronal cell death, Front Biosci 12:733-56.
96. Ferrer, I., Martinez, A., Boluda, S., Parchi, P. and Barrachina, M. (2008) Brain banks:Benefits, limitations and cautions concerning the use of post-mortem brain tissue for molecular studies, Cell Tissue Bank 9:181-94.
97. Gutstein, H. B., Morris, J. S., Annangudi, S. P. and Sweedler, J. V. (2008) Microproteomics:Analysis of protein diversity in small samples, Mass Spectrom Rev 27:316-30.
98. Ogasawara, H., Doi, T. and Kawato, M. (2008) Systems biology perspectives on cerebellar long-term depression, Neurosignals 16:300-17.
99. Routtenberg, A. (2008) The substrate for long-lasting memory: If not protein synthesis, then what? Neurobiol Learn Mem 89:225-33.
100. Sunyer, B., Diao, W. and Lubec, G. (2008) The role of post-translational modifications for learning and memory formation, Electrophoresis 29:2593-2602.
101. Bullmore, E. and Sporns, O. (2009) Complex brain networks: Graph theoretical analysis of structural and functional systems, Nat Rev Neurosci 10:186-98.
102. Grant, S. G. and Husi, H. (2001) Proteomics of multiprotein complexes: Answering fundamental questions in neuroscience, Trends Biotechnol 19:S49-54.
103. Stelzl, U. and Wanker, E. E. (2006) The value of high quality protein-protein interaction networks for systems biology, Curr Opin Chem Biol 10:551-8.
104. Volonte, C., D’Ambrosi, N. and Amadio, S. (2008) Protein cooperation: From neurons to networks, Prog Neurobiol 86:61-71.
105. Venkatesan, K., Rual, J. F., Vazquez, A. et al. (2009) An empirical framework for binary interactome mapping, Nat Methods 6:83-90.
106. Yu, H., Braun, P., Yildirim, M. A. et al. (2008) High-quality binary protein interaction map of the yeast interactome network, Science 322:104-10.
107. Yook, S. H., Oltvai, Z. N. and Barabasi, A. L. (2004) Functional and topological characterization of protein interaction networks, Proteomics 4:928-42.
108. Wuchty, S., Oltvai, Z. N. and Barabasi, A. L. (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network, Nat Genet 35:176-9.