臺灣博碩士論文加值系統

老化和神經退化等疾病皆與蛋白質的氧化極為相關。在生物體中，活性氧化物質的存在是導致蛋白質氧化的主因。在蛋白質上，與金屬離子螯合能力佳的組胺酸為常見的氧化傷害目標之一。近期研究中發現，組胺酸氧化所形成的產物為2-氧基組胺酸，雖然其物理性質和生化特性尚未被了解透徹，但有機會作為蛋白質氧化受損的生物標記物。
我們發展了能有效合成胜肽中含有2-氧基組胺酸殘基方法，並且將合成的三條含有2-氧基組胺酸殘基的胜肽接上螢光染料作為蛋白質微陣列晶片分析E. coli K12蛋白質體的探針。我們的目標是找出在細胞中能辨識2-氧基組胺酸殘基的潛在蛋白。利用三條胜肽探針、螢光偏振和解離常數的測量成功驗證十個交互作用的蛋白。這十種蛋白質中有九個似乎參與細胞的氧化還原相關功能。我們亦利用生物資訊分析得到可能的結合模體位置。並以生物資訊來預測出人體蛋白質體中也存在具有相似結合模體之蛋白為S100A1。後續也驗證了S100A1確實能與三條含有2-氧基組胺酸殘基胜肽之間產生交互作用。存在細菌及人類蛋白質中的可能結合模體恰好皆為裸露在蛋白質外部的一段α螺旋，這意味著該模體有機會與其它蛋白質相互作用。
為了後續證明蛋白質中的結合模體與2-氧基組胺酸殘基之間交互作用的真實性，我們合成了hemE和yqjG這兩個蛋白質的螺旋構型結合模體胜肽，並對於模體胜肽和2-氧基組胺酸分別接合上螢光共振能量轉移螢光對以進行分子之間的交互作用分析。結果顯示這兩種胜肽之間並沒有交互作用產生，而圓二色光譜顯示模體胜肽之二級結構無形成α螺旋，可能為交互作用失敗的主因。結合區域亦可能不僅是一小段α螺旋，因此我們尚未得知此交互作用所需要的結構條件。

Protein oxidation has been associated with aging and neurodegenerative disorders. Histidine is a major target for metal-catalyzed oxidation due to its metal chelating property. 2-Oxohistidine, the major products of histidine oxidation, respectively, have been recently identified as markers of oxidative damage in biological systems, but their biophysical and biochemical properties are understudied.
We developed efficient methods to generate 2-oxohistidine side chains, from peptides. The 2-oxohistidine-containing peptides were conjugated with DyLight fluorophores to make probes for protein microarray analysis against E.coli proteomes. Our goal is to identify cellular proteins that potentially interact with oxidized peptides. Ten interacting proteins were successfully validated using a three peptide probes, fluorescence polarization assay as well as binding constant measurements. We discovered that 9 out of 10 identified proteins seemed to be involved in redox-related cellular functions, and we found a putative consensus binding motif by bioinformatic analysis. A similar binding motif was also identified on human protein S100A1 by bioinformatic prediction. And we validated that S100A1 could interact with all three 2-oxohistidine containing peptides that we synthesized. These putative binding motifs in both bacteria and human were located within α-helices and faced the outside of proteins, which meant that they had the chance to interact with the other proteins.
To identify the interaction between consensus binding motifs and 2-oxohitidine peptide, helical binding motifs from hemE and yqjG were synthesized as individual peptide probes. Binding motif peptides and 2-oxohistidine peptides were labeled with different fluorophores to construct FRET pairs for molecular interaction assays. However, there were no detectable interactions by FRET assays, and CD spectra showed a lack of alpha helical content in the secondary structure of binding motif peptides, which may be the main reason for non-interaction. It may suggest that the functional binding domain was probably larger than just a single helix, and we still do not understand its structural requirements.

目錄
口試委員會審定書 #
誌謝 i
中文摘要 ii
ABSTRACT iii
目錄 v
圖片清單 viii
表格清單 x
縮寫表 xi
第1章、 緒論 1
1.1 活性氧化物種 1
1.2 蛋白質氧化 3
1.3 胺基酸殘基的氧化 6
1.4 老化與疾病的自由基理論 13
1.5 組胺酸的生物功能 14
1.6 組胺酸的金屬催化氧化反應 16
1.7 2-氧基組胺酸的生物研究 17
1.8 微陣列蛋白質晶片 20
1.9 螢光共振能量轉移原理 21
1.10 圓二色光譜儀 23
1.11 研究目標 24
第2章、 結果與討論 26
2.1 胜肽中組胺酸殘基的氧化 26
2.1.1 含組胺酸胜肽的序列設計 26
2.1.2 反應條件與液相層析質譜分析 26
2.1.3 利用液相層析串聯式質譜儀鑑定含組胺酸胜肽的氧化位置 30
2.2 以微陣列蛋白質晶片分析胜肽探針的交互作用蛋白質 33
2.2.1 胜肽探針的合成 33
2.2.2 胜肽探針與其交互作用蛋白質分析 36
2.2.3 交互作用蛋白質的功能探討 40
2.2.4 交互作用蛋白質的晶體結構探討 42
2.3 結合模體辨識2-氧基組胺酸鑑定 44
2.3.1 交互作用蛋白質的胜肽序列設計 44
2.3.2 胜肽探針的合成 45
2.3.3 交互作用鑑定 48
2.3.4 圓二色光譜鑑定結合模體之二級結構 51
第3章、 結論 52
3.1 氧化胜肽的合成產率提升 52
3.2 初步的生物發現 52
3.3 結合模體之鑑定 52
第4章、 實驗材料與方法 54
4.1 實驗一般說明與儀器裝置 54
4.2 實驗方法 54
4.2.1 含組胺酸胜肽的氧化 54
4.2.2 以LC-MS/MS鑑定胜肽的實驗方法 55
4.2.3 胜肽與Dylight染料的接合 55
4.2.4 微陣列蛋白質晶片實驗與數據處理 56
4.2.5 胜肽與Alexa fluor染料的接合 56
4.2.6 胜肽與Cy3染料的接合 56
4.2.7 以螢光光譜儀鑑定交互作用的實驗方法 57
4.2.8 以圓二色光譜儀鑑定胜肽之二級結構 57
附錄 58
參考文獻 62

圖片清單
圖 1 1 在粒線體中活性氧化物質的生成與粒線體防衛機制 2
圖 1 2 不同生物系統中所含生物分子組成 3
圖 1 3 蛋白質骨架的氧化與斷裂 4
圖 1 4 蛋白質的氧化交聯 6
圖 1 5 活性氧化物質生成、氧化傷害與細胞防衛機制 14
圖 1 6 銅/鋅超氧化物歧化酶的活性部位 15
圖 1 7 組胺酸的金屬催化氧化反應 16
圖 1 8 Cu,Zn-SOD與自身產物過氧化氫的反應 18
圖 1 9 PerR轉錄因子 19
圖 1 10 微陣列技術上比較蛋白質（或基因）組學的分析 21
圖 1 11 有效發生螢光共振能量轉移的條件。 22
圖 1 12 兩種螢光共振能量轉移實驗類型。 23
圖 1 13 圓二色光譜對於蛋白質二級結構類型在遠紫外光譜區上的表現 24
圖 1 14 研究目標和策略 25
圖 2 1 胜肽模型的氧化概述流程圖 27
圖 2 2 含組胺酸胜肽氧化反應的液相層析圖 28
圖 2 3 含組胺酸胜肽氧化的液向層析質譜圖 29
圖 2 4 氧化AG胜肽的串聯式質譜圖 30
圖 2 5 氧化SE胜肽的串聯式質譜圖 31
圖 2 6 氧化IA胜肽的串聯式質譜圖 32
圖 2 7 螢光染料DyLight的結構 33
圖 2 8 以質譜偵測合成的胜肽探針 35
圖 2 9 胜肽探針合成與微陣列蛋白質晶片分析的整體實驗流程 36
圖 2 10 E. coli蛋白質體晶片的代表性圖像（以SE*和SE為探針） 37
圖 2 11 2-氧基組胺酸胜肽與交互作用蛋白質的解離常數長條圖 40
圖 2 12 十個驗證蛋白質的共通模體 42
圖 2 13 E. coli K12蛋白質體中之互動蛋白與人類S100A1蛋白的三維晶體結構圖 43
圖 2 14 螢光染料Alexa fluor 488和Cy3的結構 45
圖 2 15 以質譜偵測合成的胜肽探針 47
圖 2 16 胜肽混合實驗配對流程圖 48
圖 2 17 利用波長480 nm激發來觀察是否有FRET效應 49
圖 2 18 利用波長480 nm激發來觀察是否有FRET效應 50
圖 2 19 HE、YQ兩條模擬胜肽之圓二色光譜圖 51

表格清單
表格 1 1 胺基酸殘基的氧化產物結構及質量變化 8
表格 2 1 胜肽與螢光染料DyLight的接合 34
表格 2 2 2-氧基組胺酸胜肽與交互作用蛋白質的解離常數 39
表格 2 3 交互作用蛋白質的功能介紹 41
表格 2 4 胜肽與螢光染料Alexa fluor 488和Cy3的接合 46
表格 2 5 利用CONTILL軟體分析二級結構比例 51

1.Lanciano, P. et al. Molecular mechanisms of superoxide production by complex III: a bacterial versus human mitochondrial comparative case study. Biochim. Biophys. Acta 1827, 1332-1339 (2013).
2.Martin, K.R. & Barrett, J.C. Reactive oxygen species as double-edged swords in cellular processes: Low-dose cell signaling versus high-dose toxicity. Hum. Exp. Toxicol 21, 71-75 (2002).
3.Samoilova, R.I., Crofts, A.R. & Dikanov, S.A. Reaction of superoxide radical with quinone molecules. J. Phys. Chem. A 115, 11589-11593 (2011).
4.Turrens, J.F. Mitochondrial formation of reactive oxygen species. J. Physiol. 552, 335-344 (2003).
5.Chance, B. & Hollunger, G. Energy-linked reduction of mitochondrial pyridine nucleotide. Nature 185, 666-672 (1960).
6.Hansford, R.G., Hogue, B.A. & Mildaziene, V. Dependence of H2O2 formation by rat heart mitochondria on substrate availability and donor age. J. Bioenerg. Biomembr. 29, 89-95 (1997).
7.Wellen, K.E. & Thompson, C.B. Cellular metabolic stress: Considering how cells respond to nutrient excess. Mol. Cell 40, 323-332 (2010).
8.Stadtman, E.R. & Levine, R.L. Protein oxidation. Ann. N.Y. Acad. Sci. 899, 191-208 (2000).
9.Rubbo, H. et al. Nitric oxide regulation of superoxide and peroxynitrite-dependent lipid peroxidation. Formation of novel nitrogen-containing oxidized lipid derivatives. J. Biol. Chem. 269, 26066-26075 (1994).
10.Druzhyna, N.M., Wilson, G.L. & LeDoux, S.P. Mitochondrial DNA repair in aging and disease. Mech. Ageing Dev. 129, 383-390 (2008).
11.Nelson, D.L. & Cox, M.M. Lehninger principles of biochemistry, fifth edition. 708-772 (2008).
12.Davies, M.J. The oxidative environment and protein damage. Biochim. Biophys. Acta, Proteins Proteomics 1703, 93-109 (2005).
13.Grune, T., Shringarpure, R., Sitte, N. & Davies, K. Age-related changes in protein oxidation and proteolysis in mammalian cells. J. Gerontol. A Biol. Sci. Med. Sci. 56, B459-B467 (2001).
14.Zhang, W., Xiao, S. & Ahn, D.U. Protein oxidation: Basic principles and implications for meat quality. Crit. Rev. Food Sci. Nutr. 53, 1191-1201 (2013).
15.Stadtman, E.R. Protein oxidation and aging. Free Radical Res. 40, 1250-1258 (2006).
16.Garrison, W.M. & Weeks, B.M. Radiation chemistry of compounds containing the peptide bond. Radiat. Res. 17, 341-352 (1962).
17.Garrison, W.M. Reaction mechanisms in the radiolysis of peptides, polypeptides, and proteins. Chem. Rev. 87, 381-398 (1987).
18.Lee, J.W. & Helmann, J.D. The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation. Nature 440, 363-367 (2006).
19.Uchida, K. 4-Hydroxy-2-nonenal: a product and mediator of oxidative stress. Progress in Lipid Research 42, 318-343 (2003).
20.Burcham, P.C. & Kuhan, Y.T. Introduction of carbonyl groups into proteins by the lipid peroxidation product, malondialdehyde. Biochem. Biophys. Res. Commun 220, 996-1001 (1996).
21.Tilley, K.A. et al. Tyrosine cross-links:  Molecular basis of gluten structure and function. J. Agric. Food. Chem. 49, 2627-2632 (2001).
22.Martinaud, A. et al. Comparison of oxidative processes on myofibrillar proteins from beef during maturation and by different model oxidation systems. J. Agric. Food. Chem. 45, 2481-2487 (1997).
23.Morzel, M., Gatellier, P., Sayd, T., Renerre, M. & Laville, E. Chemical oxidation decreases proteolytic susceptibility of skeletal muscle myofibrillar proteins. Meat Sci. 73, 536-543 (2006).
24.Xu, G. & Chance, M.R. Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev. 107, 3514-3543 (2007).
25.Shacter, E. Quantification and significance of protein oxidation in biological samples. Drug Metab. Revi. 32, 307-326 (2000).
26.Vogt, W. Oxidation of methionyl residues in proteins: Tools, targets, and reversal. Free Radical Biol. Med. 18, 93-105 (1995).
27.Claiborne, A. et al. Protein-sulfenic acids:  Diverse roles for an unlikely player in enzyme catalysis and redox regulation. Biochemistry 38, 15407-15416 (1999).
28.Boschi-Muller, S., Gand, A. & Branlant, G. The methionine sulfoxide reductases: Catalysis and substrate specificities. Arch. Biochem. Biophys. 474, 266-273 (2008).
29.Pastore, A. & Piemonte, F. S-Glutathionylation signaling in cell biology: Progress and prospects. Eur. J. Pharm. Sci. 46, 279-292 (2012).
30.Jeong, W., Bae, S.H., Toledano, M.B. & Rhee, S.G. Role of sulfiredoxin as a regulator of peroxiredoxin function and regulation of its expression. Free Radical Biol. Med. 53, 447-456 (2012).
31.Giulivi, C., Traaseth, J.N. & Davies, A.K.J. Tyrosine oxidation products: analysis and biological relevance. Amino Acids 25, 227-232 (2003).
32.Berlett, B.S. & Stadtman, E.R. Protein oxidation in aging, disease, and oxidative stress. J. Biol. Chem. 272, 20313-20316 (1997).
33.Amici, A., Levine, R.L., Tsai, L. & Stadtman, E.R. Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions. J. Biol. Chem. 264, 3341-3346 (1989).
34.Jung, T., Höhn, A., Catalgol, B. & Grune, T. Age-related differences in oxidative protein-damage in young and senescent fibroblasts. Arch. Biochem. Biophys. 483, 127-135 (2009).
35.Jung, T., Engels, M., Kaiser, B., Poppek, D. & Grune, T. Intracellular distribution of oxidized proteins and proteasome in HT22 cells during oxidative stress. Free Radical Biol. Med. 40, 1303-1312 (2006).
36.Finley, E.L., Dillon, J., Crouch, R.K. & Schey, K.L. Identification of tryptophan oxidation products in bovine alpha-crystallin. Protein Sci. 7, 2391-2397 (1998).
37.Maskos, Z., Rush, J.D. & Koppenol, W.H. The hydroxylation of tryptophan. Arch. Biochem. Biophys. 296, 514-520 (1992).
38.Pietrucha, K. & Łubis, M. Some reactions of OH radicals with collagen and tyrosine in aqueous solutions. Int. J. Radiat. Appl. Instrum. Part C 36, 155-160 (1990).
39.Morin, B., Davies, M.J. & Dean, R.T. The protein oxidation product 3,4-dihydroxyphenylalanine (DOPA) mediates oxidative DNA damage. Biochem. J. 330, 1059-1067 (1998).
40.Dean, R.T., Wolff, S.P. & McElligott, M.A. Histidine and proline are important sites of free radical damage to proteins. Free Radic. Res. Commun. 7, 97-103 (1989).
41.Uchida, K. & Kawakishi, S. Reaction of a histidyl residue analog with hydrogen peroxide in the presence of copper(II) ion. J. Agric. Food. Chem. 38, 660-664 (1990).
42.Xu, G., Takamoto, K. & Chance, M.R. Radiolytic modification of basic amino acid residues in peptides:  Probes for examining protein−protein interactions. Anal. Chem. 75, 6995-7007 (2003).
43.L. Hawkins, C. & J. Davies, M. EPR studies on the selectivity of hydroxyl radical attack on amino acids and peptides. J. Chem. Soc., Perkin Trans. 2, 2617-2622 (1998).
44.Uchida, K., Kato, Y. & Kawakishi, S. A novel mechanism for oxidative cleavage of prolyl peptides induced by the hydroxyl radical. Biochem. Biophys. Res. Commun. 169, 265-271 (1990).
45.Trelstad, R.L., Lawley, K.R. & Holmes, L.B. Nonenzymatic hydroxylations of proline and lysine by reduced oxygen derivatives. Nature 289, 310-312 (1981).
46.Requena, J.R. & Stadtman, E.R. Conversion of lysine to Nϵ-(carboxymethyl)lysine increases susceptibility of proteins to metal-catalyzed oxidation. Biochem. Biophys. Res. Commun. 264, 207-211 (1999).
47.Davies, M.J. Protein and peptide alkoxyl radicals can give rise to C-terminal decarboxylation and backbone cleavage. Arch. Biochem. Biophys. 336, 163-172 (1996).
48.Xu, G. & Chance, M.R. Radiolytic modification of acidic amino acid residues in peptides:  Probes for examining protein−protein interactions. Anal. Chem. 76, 1213-1221 (2004).
49.Xu, G. & Chance, M.R. Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting. Anal. Chem. 77, 4549-4555 (2005).
50.Gerschman, R., Gilbert, D.L., Nye, S.W., Dwyer, P. & Fenn, W.O. Oxygen poisoning and X-irradiation: A mechanism in common. Science 119, 623-626 (1954).
51.Hempelmann, L.H. & Hoffman, J.G. Practical aspects of radiation injury. Annu. Rev. Nucl. Sci. 3, 369-392 (1953).
52.Harman, D. Aging: A theory based on free radical and radiation chemistry. J. Gerontol. 11, 298-300 (1956).
53.McCord, J.M. & Fridovich, I. Superoxide dismutase: An enzymic function for erythrocuprein (hemocuprein).. J. Biol. Chem. 244, 6049-6055 (1969).
54.Chance, B., Sies, H. & Boveris, A. Hydroperoxide metabolism in mammalian organs. Physiol. Rev. 59, 527-605 (1979).
55.Kujoth, G.C. et al. Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-484 (2005).
56.Yui, R., Ohno, Y. & Matsuura, E.T. Accumulation of deleted mitochondrial DNA in aging drosophila melanogaster. Genes Genet. Syst. 78, 245-251 (2003).
57.Muller, F.L., Lustgarten, M.S., Jang, Y., Richardson, A. & Van Remmen, H. Trends in oxidative aging theories. Free Radical Biol. Med. 43, 477-503 (2007).
58.Kuznetsova, A.A., Kuznetsov, N.A., Ishchenko, A.A., Saparbaev, M.K. & Fedorova, O.S. Step-by-step mechanism of DNA damage recognition by human 8-oxoguanine DNA glycosylase. Biochim. Biophys. Acta, Gen. Subj. 1840, 387-395 (2014).
59.Höhn, A., König, J. & Grune, T. Protein oxidation in aging and the removal of oxidized proteins. J. Proteomics 92, 132-159 (2013).
60.Martínez, A., Portero-Otin, M., Pamplona, R. & Ferrer, I. Protein targets of oxidative damage in human neurodegenerative diseases with abnormal protein aggregates. Brain Pathol. 20, 281-297 (2010).
61.Sultana, R., Perluigi, M. & Butterfield, D.A. Oxidatively modified proteins in Alzheimer’s disease (AD), mild cognitive impairment and animal models of AD: role of Abeta in pathogenesis. Acta Neuropathol. 118, 131-150 (2009).
62.Choi, J. et al. Oxidative Modifications and down-regulation of ubiquitin carboxyl-terminal hydrolase L1 associated with idiopathic Parkinson''s and Alzheimer''s diseases. J. Biol. Chem. 279, 13256-13264 (2004).
63.Sorolla, M.A. et al. Proteomic and oxidative stress analysis in human brain samples of Huntington disease. Free Radical Biol. Med. 45, 667-678 (2008).
64.Lipinski, B. Hydroxyl radical and its scavengers in health and disease. Oxid. Med. Cell. Longevity 2011 (2011).
65.Tainer, J.A., Roberts, V.A. & Getzoff, E.D. Protein metal-binding sites. Curr. Opin. Biotechnol. 3, 378-387 (1992).
66.Valentine, J.S., Doucette, P.A. & Zittin Potter, S. Copper-zinc superoxide dismutase and amyotrophic lateral sclerosis. Annu. Rev. Biochem 74, 563-593 (2005).
67.Hengen, P.N. Purification of His-Tag fusion proteins from Escherichia coli. Trends Biochem. Sci 20, 285-286 (1995).
68.Mller, I.M., Rogowska-Wrzesinska, A. & Rao, R.S.P. Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective. J. Proteomics 74, 2228-2242 (2011).
69.Uchida, K. & Kawakishi, S. Ascorbate-mediated specific oxidation of the imidazole ring in a histidine derivative. Bioorg. Chem. 17, 330-343 (1989).
70.Schöneich, C. Mechanisms of metal-catalyzed oxidation of histidine to 2-oxo-histidine in peptides and proteins. J. Pharm. Biomed. Anal. 21, 1093-1097 (2000).
71.Sies, H. Strategies of antioxidant defense. Eur. J. Biochem. 215, 213-219 (1993).
72.Khossravi, M. & Borchardt, R.T. Chemical pathways of peptide degradation. X: Effect of metal-catalyzed oxidation on the solution structure of a histidine-containing peptide fragment of human relaxin. Pharm. Res. 17, 851-858 (2000).
73.Uchida, K. & Kawakishi, S. 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 (1994).
74.Lewisch, S.A. & Levine, R.L. Determination of 2-oxohistidine by amino acid analysis. Anal. Biochem. 231, 440-446 (1995).
75.Atwood, C.S. et al. Copper catalyzed oxidation of Alzheimer Abeta. Cell. Mol. Biol. 46, 777-783 (2000).
76.Sayre, L.M. et al. In situ oxidative catalysis by neurofibrillary tangles and senile plaques in Alzheimer’s disease. J. Neurochem. 74, 270-279 (2000).
77.Curtain, C.C. et al. Alzheimer''s disease Amyloid-β binds copper and zinc to generate an allosterically ordered membrane-penetrating structure containing superoxide dismutase-like subunits. J. Biol. Chem. 276, 20466-20473 (2001).
78.Schöneich, C. & Williams, T.D. Cu(II)-catalyzed oxidation of β-Amyloid peptide targets His13 and His14 over His6:  Detection of 2-oxo-histidine by HPLC-MS/MS. Chem. Res. Toxicol. 15, 717-722 (2002).
79.Dubbs, J.M. & Mongkolsuk, S. Peroxide-sensing transcriptional regulators in bacteria. J. Bacteriol 194, 5495-5503 (2012).
80.Traore, D.A.K. et al. Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein. Nat. Chem. Biol. 5, 53-59 (2009).
81.Smith, M.G. et al. Global analysis of protein function using protein microarrays. Mech. Ageing Dev. 126, 171-175 (2005).
82.Uzoma, I. & Zhu, H. Interactome mapping: Using protein microarray technology to reconstruct diverse protein networks. Genomics Proteomics Bioinformatics 11, 18-28 (2013).
83.Chen, C.-S. et al. Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol. Cell. Proteomics 8, 1765-1776 (2009).
84.Zhu, H. & Qian, J. Chapter Four – Applications of Functional Protein Microarrays in Basic and Clinical Research. Adv. Genet. 79, 123-155 (2012).
85.Chandra, H., Reddy, P.J. & Srivastava, S. Protein microarrays and novel detection platforms. Expert Rev. Proteomics 8, 61-79 (2011).
86.Hall, D.A., Ptacek, J. & Snyder, M. Protein microarray technology. Mech. Ageing Dev. 128, 161-167 (2007).
87.Clegg, R.M. Fluorescence resonance energy transfer. Curr. Opin. Biotechnol. 6, 103-110 (1995).
88.Piston, D.W. & Kremers, G.-J. Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem. Sci 32, 407-414 (2007).
89.Broussard, J.A., Rappaz, B., Webb, D.J. & Brown, C.M. Fluorescence resonance energy transfer microscopy as demonstrated by measuring the activation of the serine/threonine kinase Akt. Nat. Protoc. 8, 265-281 (2013).
90.Citovsky, V., Gafni, Y. & Tzfira, T. Localizing protein–protein interactions by bimolecular fluorescence complementation in planta. Methods 45, 196-206 (2008).
91.Miyawaki, A. et al. Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388, 882-887 (1997).
92.Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906-918 (2002).
93.Johnson, W.C. Protein secondary structure and circular dichroism: A practical guide. Proteins: Struct. Funct. Bioinf. 7, 205-214 (1990).
94.Greenfield, N.J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876-2890 (2006).
95.Kelly, S.M., Jess, T.J. & Price, N.C. How to study proteins by circular dichroism. Biochim. Biophys. Acta, Proteins Proteomics 1751, 119-139 (2005).
96.Huang, C.F., Liu, Y.H. & Tai, H.C. Synthesis of peptides containing 2‐oxohistidine residues and their characterization by liquid chromatography‐tandem mass spectrometry. J. Pept. Sci. 21, 114-119 (2015).
97.Wu, J., Fan, Y. & Ling, J. Mechanism of oxidant-induced mistranslation by threonyl-tRNA synthetase. Nucleic Acids Res. 42, 6523-6531 (2014).
98.Green, A.R., Hayes, R.P., Xun, L. & Kang, C. Structural understanding of the glutathione-dependent reduction mechanism of glutathionyl-hydroquinone reductases. J. Biol. Chem. 287, 35838-35848 (2012).
99.Le, H.-T. et al. YajL, Prokaryotic homolog of parkinsonism-associated protein DJ-1, functions as a covalent chaperone for thiol proteome. J. Biol. Chem. 287, 5861-5870 (2012).
100.Nishimura, K., Nakayashiki, T. & Inokuchi, H. Cloning and sequencing of the hemE gene encoding uroporphyrinogen III decarboxylase (UPD) from Escherichia coli K-12. Gene 133, 109-113 (1993).
101.Lopes, J.M. & Lawther, R.P. Physical identification of an internal promoter, ilvAp, in the distal portion of the ilvGMEDA operon. Gene 76, 255-269 (1989).
102.Henard, C.A., Bourret, T.J., Song, M. & Vázquez-Torres, A. Control of redox balance by the stringent response regulatory protein promotes antioxidant defenses of salmonella. J. Biol. Chem. 285, 36785-36793 (2010).
103.Lim, S.-J., Jung, Y.-M., Shin, H.-D. & Lee, Y.-H. 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 (2002).
104.Shi, F., Li, K., Huan, X. & Wang, X. 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 (2013).
105.Murray, E.L. & Conway, T. Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli. J. Bacteriol. 187, 991-1000 (2005).
106.Mittl, P.R.E. & Schulz, G.E. Structure of glutathione reductase from Escherichia coli at 1.86 Å resolution: Comparison with the enzyme from human erythrocytes. Protein Sci. 3, 799-809 (1994).
107.Xiong, X., Yang, L., Han, X., Wang, J. & Zhang, W. Knockout and function analysis of pqqL gene in Escherichia coli. Acta Microbiol. Sin. 50, 1380-1384 (2010).
108.Misra, H.S. et al. Pyrroloquinoline‐quinone: a reactive oxygen species scavenger in bacteria. FEBS Lett. 578, 26-30 (2004).
109.Brock, M., Maerker, C., Schütz, A., Völker, U. & Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Eur. J. Biochem. 269, 6184-6194 (2002).
110.Lenarčič Živković, M. et al. Post-translational S-nitrosylation is an endogenous factor fine tuning the properties of human S100A1 protein. J. Biol. Chem. 287, 40457-40470 (2012).
111.Wright, N.T., Cannon, B.R., Zimmer, D.B. & Weber, D.J. S100A1: Structure, function, and therapeutic potential. Curr. Chem. Biol. 3, 138-145 (2009).
112.Perrin, R.J. et al. Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer''s disease. PLoS ONE 6, e16032 (2011).
113.Kuchibhotla, K.V. et al. Aβ plaques lead to aberrant regulation of calcium homeostasis in vivo resulting in structural and functional disruption of neuronal networks. Neuron 59, 214-225 (2008).
114.Garcia-Alloza, M., Dodwell, S.A., Meyer-Luehmann, M., Hyman, B.T. & Bacskai, B.J. Plaque-Derived oxidative stress mediates distorted neurite trajectories in the Alzheimer mouse model. J. Neuropath. Exp. Neurol. 65, 1082-1089 (2006).
115.Du Yan, S. et al. Amyloid-β 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 (1997).