| 參考文獻 |
1. Wold, F. (1981) In vivo chemical modification of proteins (post-translational modification). Annu Rev Biochem 50, 783-814
2. Walsh, C. T., Garneau-Tsodikova, S., and Gatto, G. J., Jr. (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 44, 7342-7372
3. Harding, J. J. (1985) Nonenzymatic covalent posttranslational modification of proteins in vivo. Adv Protein Chem 37, 247-334
4. Davies, M. J. (2005) The oxidative environment and protein damage. Biochim Biophys Acta 1703, 93-109
5. Morrison, D. K. (2009) The 14-3-3 proteins: integrators of diverse signaling cues that impact cell fate and cancer development. Trends Cell Biol 19, 16-23
6. Kilpatrick, D. C. (2002) Animal lectins: a historical introduction and overview. Biochim Biophys Acta 1572, 187-197
7. Sparvero, L. J., Asafu-Adjei, D., Kang, R., Tang, D., Amin, N., Im, J., Rutledge, R., Lin, B., Amoscato, A. A., Zeh, H. J., and Lotze, M. T. (2009) RAGE (Receptor for Advanced Glycation Endproducts), RAGE ligands, and their role in cancer and inflammation. J Transl Med 7, 17
8. Muller, F. L., Lustgarten, M. S., Jang, Y., Richardson, A., and Van Remmen, H. (2007) Trends in oxidative aging theories. Free Radic Biol Med 43, 477-503
9. Ray, P. D., Huang, B. W., and Tsuji, Y. (2012) Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling. Cell Signal 24, 981-990
10. Martin, K. R., and Barrett, J. C. (2002) Reactive oxygen species as double-edged swords in cellular processes: low-dose cell signaling versus high-dose toxicity. Hum Exp Toxicol 21, 71-75
11. Jang, Y. Y., and Sharkis, S. J. (2007) A low level of reactive oxygen species selects for primitive hematopoietic stem cells that may reside in the low-oxygenic niche. Blood 110, 3056-3063
12. Shacter, E. (2000) Quantification and significance of protein oxidation in biological samples. Drug Metab Rev 32, 307-326
13. Xu, G., and Chance, M. R. (2007) Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem Rev 107, 3514-3543
14. Tainer, J. A., Roberts, V. A., and Getzoff, E. D. (1991) Metal-binding sites in proteins. Curr Opin Biotechnol 2, 582-591
15. Regan, L. (1993) The design of metal-binding sites in proteins. Annu Rev Biophys Biomol Struct 22, 257-287
16. Uchida, K., and Kawakishi, S. (1994) Identification of oxidized histidine generated at the active site of Cu,Zn-superoxide dismutase exposed to H2O2. Selective generation of 2-oxo-histidine at the histidine 118. J Biol Chem 269, 2405-2410
17. Lewisch, S. A., and Levine, R. L. (1995) Determination of 2-oxohistidine by amino acid analysis. Anal Biochem 231, 440-446
18. Traore, D. A., El Ghazouani, A., Jacquamet, L., Borel, F., Ferrer, J. L., Lascoux, D., Ravanat, J. L., Jaquinod, M., Blondin, G., Caux-Thang, C., Duarte, V., and Latour, J. M. (2009) Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein. Nat Chem Biol 5, 53-59
19. Davies, M. J., Fu, S., Wang, H., and Dean, R. T. (1999) Stable markers of oxidant damage to proteins and their application in the study of human disease. Free Radic Biol Med 27, 1151-1163
20. Huang, C. F., Liu, Y. H., and Tai, H. C. (2015) Synthesis of peptides containing 2-oxohistidine residues and their characterization by liquid chromatography-tandem mass spectrometry. J Pept Sci 21, 114-119
21. Chen, C. S., Korobkova, E., Chen, H., Zhu, J., Jian, X., Tao, S. C., He, C., and Zhu, H. (2008) A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 5, 69-74
22. Team, R. C. (2015) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing
23. Warnes, G. R., Bolker, B., Bonebakker, L., Gentleman, R., Huber, W., Liaw, A., Lumley, T., Maechler, M., Magnusson, A., and Moeller, S. (2009) gplots: Various R programming tools for plotting data. R package version 2
24. Andres Leon, E., Ezkurdia, I., Garcia, B., Valencia, A., and Juan, D. (2009) EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res 37, D629-635
25. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504
26. Carbon, S., Ireland, A., Mungall, C. J., Shu, S., Marshall, B., Lewis, S., Ami, G. O. H., and Web Presence Working, G. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289
27. Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C. Y., and Wei, L. (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39, W316-322
28. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29
29. Kanehisa, M., and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30
30. Frith, M. C., Saunders, N. F., Kobe, B., and Bailey, T. L. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol 4, e1000071
31. Rajashankar, K. R., Kniewel, R., Solorzano, V., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (2004) Crystal Structure of 2-methylcitrate dehydratase.
32. Mittl, P. R., Berry, A., Scrutton, N. S., Perham, R. N., and Schulz, G. E. (1994) Anatomy of an engineered NAD-binding site. Protein Sci 3, 1504-1514
33. Gallagher, D. T., Gilliland, G. L., Xiao, G., Zondlo, J., Fisher, K. E., Chinchilla, D., and Eisenstein, E. (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6, 465-475
34. Dock-Bregeon, A. C., Rees, B., Torres-Larios, A., Bey, G., Caillet, J., and Moras, D. (2004) Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution. Mol Cell 16, 375-386
35. Wright, N. T., Varney, K. M., Ellis, K. C., Markowitz, J., Gitti, R. K., Zimmer, D. B., and Weber, D. J. (2005) The three-dimensional solution structure of Ca(2+)-bound S100A1 as determined by NMR spectroscopy. J Mol Biol 353, 410-426
36. Wilson, M. A., Ringe, D., and Petsko, G. A. (2005) The atomic resolution crystal structure of the YajL (ThiJ) protein from Escherichia coli: a close prokaryotic homologue of the Parkinsonism-associated protein DJ-1. J Mol Biol 353, 678-691
37. Fullerton, S. W., Griffiths, J. S., Merkel, A. B., Cheriyan, M., Wymer, N. J., Hutchins, M. J., Fierke, C. A., Toone, E. J., and Naismith, J. H. (2006) Mechanism of the Class I KDPG aldolase. Bioorg Med Chem 14, 3002-3010
38. Green, A. R., Hayes, R. P., Xun, L., and Kang, C. (2012) Structural understanding of the glutathione-dependent reduction mechanism of glutathionyl-hydroquinone reductases. J Biol Chem 287, 35838-35848
39. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res 28, 235-242
40. Sayle, R. A., and Milner-White, E. J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 20, 374
41. Zhou, J., and Rudd, K. E. (2013) EcoGene 3.0. Nucleic Acids Res 41, D613-624
42. Xu, D., and Zhang, Y. (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80, 1715-1735
43. Uchida, K., and Kawakishi, S. (1993) 2-Oxo-histidine as a novel biological marker for oxidatively modified proteins. FEBS Lett 332, 208-210
44. Lewisch, S. A., and Levine, R. L. (1999) Determination of 2-oxohistidine by amino acid analysis. Methods Enzymol 300, 120-124
45. Atwood, C. S., Huang, X., Khatri, A., Scarpa, R. C., Kim, Y. S., Moir, R. D., Tanzi, R. E., Roher, A. E., and Bush, A. I. (2000) Copper catalyzed oxidation of Alzheimer Abeta. Cell Mol Biol (Noisy-le-grand) 46, 777-783
46. Schoneich, C. (2000) Mechanisms of metal-catalyzed oxidation of histidine to 2-oxo-histidine in peptides and proteins. J Pharm Biomed Anal 21, 1093-1097
47. Gunther, M. R., Peters, J. A., and Sivaneri, M. K. (2002) Histidinyl radical formation in the self-peroxidation reaction of bovine copper-zinc superoxide dismutase. J Biol Chem 277, 9160-9166
48. Hovorka, S. W., Biesiada, H., Williams, T. D., Huhmer, A., and Schoneich, C. (2002) High sensitivity of Zn2+ insulin to metal-catalyzed oxidation: detection of 2-oxo-histidine by tandem mass spectrometry. Pharm Res 19, 530-537
49. Schoneich, C., and Williams, T. D. (2002) Cu(II)-catalyzed oxidation of beta-amyloid peptide targets His13 and His14 over His6: Detection of 2-Oxo-histidine by HPLC-MS/MS. Chem Res Toxicol 15, 717-722
50. Schiewe, A. J., Margol, L., Soreghan, B. A., Thomas, S. N., and Yang, A. J. (2004) Rapid characterization of amyloid-beta side-chain oxidation by tandem mass spectrometry and the scoring algorithm for spectral analysis. Pharm Res 21, 1094-1102
51. Inoue, K., Garner, C., Ackermann, B. L., Oe, T., and Blair, I. A. (2006) Liquid chromatography/tandem mass spectrometry characterization of oxidized amyloid beta peptides as potential biomarkers of Alzheimer′s disease. Rapid Commun Mass Spectrom 20, 911-918
52. Boyer, R. F. (2005) Concepts in Biochemistry, 3 edition Ed., Wiley
53. Jensen, P. R., and Michelsen, O. (1992) Carbon and energy metabolism of atp mutants of Escherichia coli. J Bacteriol 174, 7635-7641
54. Dewick, P. M. (2009) Secondary Metabolism: The Building Blocks and Construction Mechanisms. Medicinal Natural Products, pp. 7-38, John Wiley & Sons, Ltd
55. Lundblad, J. R., Laurance, M., and Goodman, R. H. (1996) Fluorescence polarization analysis of protein-DNA and protein-protein interactions. Mol Endocrinol 10, 607-612
56. Jameson, D. M., and Seifried, S. E. (1999) Quantification of protein-protein interactions using fluorescence polarization. Methods 19, 222-233
57. Allen, M., Reeves, J., and Mellor, G. (2000) High throughput fluorescence polarization: a homogeneous alternative to radioligand binding for cell surface receptors. J Biomol Screen 5, 63-69
58. Parker, G. J., Law, T. L., Lenoch, F. J., and Bolger, R. E. (2000) Development of high throughput screening assays using fluorescence polarization: nuclear receptor-ligand-binding and kinase/phosphatase assays. J Biomol Screen 5, 77-88
59. Moerke, N. J. (2009) Fluorescence Polarization (FP) Assays for Monitoring Peptide-Protein or Nucleic Acid-Protein Binding. Curr Protoc Chem Biol 1, 1-15
60. Kim, H. Y., and Gladyshev, V. N. (2007) Methionine sulfoxide reductases: selenoprotein forms and roles in antioxidant protein repair in mammals. Biochem J 407, 321-329
61. Martinez-Ruiz, A., Araujo, I. M., Izquierdo-Alvarez, A., Hernansanz-Agustin, P., Lamas, S., and Serrador, J. M. (2013) Specificity in S-nitrosylation: a short-range mechanism for NO signaling? Antioxid Redox Signal 19, 1220-1235
62. Mittl, P. R., and Schulz, G. E. (1994) Structure of glutathione reductase from Escherichia coli at 1.86 A resolution: comparison with the enzyme from human erythrocytes. Protein Sci 3, 799-809
63. Nishimura, K., Nakayashiki, T., and Inokuchi, H. (1993) Cloning and sequencing of the hemE gene encoding uroporphyrinogen III decarboxylase (UPD) from Escherichia coli K-12. Gene 133, 109-113
64. Henard, C. A., Bourret, T. J., Song, M., and Vazquez-Torres, A. (2010) Control of redox balance by the stringent response regulatory protein promotes antioxidant defenses of Salmonella. J Biol Chem 285, 36785-36793
65. Lim, S. J., Jung, Y. M., Shin, H. D., and Lee, Y. H. (2002) Amplification of the NADPH-related genes zwf and gnd for the oddball biosynthesis of PHB in an E. coli transformant harboring a cloned phbCAB operon. J Biosci Bioeng 93, 543-549
66. Shi, F., Li, K., Huan, X., and Wang, X. (2013) Expression of NAD(H) kinase and glucose-6-phosphate dehydrogenase improve NADPH supply and L-isoleucine biosynthesis in Corynebacterium glutamicum ssp. lactofermentum. Appl Biochem Biotechnol 171, 504-521
67. Xiong, X., Yang, L., Han, X., Wang, J., and Zhang, W. (2010) [Knockout and function analysis of pqqL gene in Escherichia coli]. Wei Sheng Wu Xue Bao 50, 1380-1384
68. Misra, H. S., Khairnar, N. P., Barik, A., Indira Priyadarsini, K., Mohan, H., and Apte, S. K. (2004) Pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria. FEBS Lett 578, 26-30
69. Le, H. T., Gautier, V., Kthiri, F., Malki, A., Messaoudi, N., Mihoub, M., Landoulsi, A., An, Y. J., Cha, S. S., and Richarme, G. (2012) YajL, prokaryotic homolog of parkinsonism-associated protein DJ-1, functions as a covalent chaperone for thiol proteome. J Biol Chem 287, 5861-5870
70. Bonifati, V., Rizzu, P., van Baren, M. J., Schaap, O., Breedveld, G. J., Krieger, E., Dekker, M. C., Squitieri, F., Ibanez, P., Joosse, M., van Dongen, J. W., Vanacore, N., van Swieten, J. C., Brice, A., Meco, G., van Duijn, C. M., Oostra, B. A., and Heutink, P. (2003) Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Science 299, 256-259
71. Lopes, J. M., and Lawther, R. P. (1989) Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon. Gene 76, 255-269
72. Wu, J., Fan, Y., and Ling, J. (2014) Mechanism of oxidant-induced mistranslation by threonyl-tRNA synthetase. Nucleic Acids Res 42, 6523-6531
73. Murray, E. L., and Conway, T. (2005) Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli. J Bacteriol 187, 991-1000
74. Brock, M., Maerker, C., Schutz, A., Volker, U., and Buckel, W. (2002) Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur J Biochem 269, 6184-6194
75. Lenarcic Zivkovic, M., Zareba-Koziol, M., Zhukova, L., Poznanski, J., Zhukov, I., and Wyslouch-Cieszynska, A. (2012) Post-translational S-nitrosylation is an endogenous factor fine tuning the properties of human S100A1 protein. J Biol Chem 287, 40457-40470
76. Wright, N. T., Cannon, B. R., Zimmer, D. B., and Weber, D. J. (2009) S100A1: Structure, Function, and Therapeutic Potential. Curr Chem Biol 3, 138-145
77. Perrin, R. J., Craig-Schapiro, R., Malone, J. P., Shah, A. R., Gilmore, P., Davis, A. E., Roe, C. M., Peskind, E. R., Li, G., Galasko, D. R., Clark, C. M., Quinn, J. F., Kaye, J. A., Morris, J. C., Holtzman, D. M., Townsend, R. R., and Fagan, A. M. (2011) Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer′s disease. PLoS One 6, e16032
78. Curtain, C. C., Ali, F., Volitakis, I., Cherny, R. A., Norton, R. S., Beyreuther, K., Barrow, C. J., Masters, C. L., Bush, A. I., and Barnham, K. J. (2001) Alzheimer′s disease amyloid-beta binds copper and zinc to generate an allosterically ordered membrane-penetrating structure containing superoxide dismutase-like subunits. J Biol Chem 276, 20466-20473
79. Schoneich, C., and Williams, T. D. (2003) CU(II)-catalyzed oxidation of Alzheimer′s disease beta-amyloid peptide and related sequences: remarkably different selectivities of neurotoxic betaAP1-40 and non-toxic betaAP40-1. Cell Mol Biol (Noisy-le-grand) 49, 753-761
80. Kuchibhotla, K. V., Goldman, S. T., Lattarulo, C. R., Wu, H. Y., Hyman, B. T., and Bacskai, B. J. (2008) Abeta plaques lead to aberrant regulation of calcium homeostasis in vivo resulting in structural and functional disruption of neuronal networks. Neuron 59, 214-225
81. Garcia-Alloza, M., Dodwell, S. A., Meyer-Luehmann, M., Hyman, B. T., and Bacskai, B. J. (2006) Plaque-derived oxidative stress mediates distorted neurite trajectories in the Alzheimer mouse model. J Neuropathol Exp Neurol 65, 1082-1089
82. Du Yan, S., Zhu, H., Fu, J., Yan, S. F., Roher, A., Tourtellotte, W. W., Rajavashisth, T., Chen, X., Godman, G. C., Stern, D., and Schmidt, A. M. (1997) Amyloid-beta peptide-receptor for advanced glycation endproduct interaction elicits neuronal expression of macrophage-colony stimulating factor: a proinflammatory pathway in Alzheimer disease. Proc Natl Acad Sci U S A 94, 5296-5301 |
[Endnote RIS 格式]
[相關文章]
[文章引用]
[完整記錄]
[館藏目錄]
[檢視]
plurk
funp
live
udn
HD
myshare
netvibes
friend
youpush
delicious
baidu
Google bookmarks
del.icio.us
hemidemi
facebook
twitter
google
reddit