研究生: |
林敬宭 Lin, Jing-Cyun |
---|---|
論文名稱: |
生物素衍生化蛋白開關於細胞膜表面小分子偵測之應用 Biotin-Derived Protein Switch for Signal-On Detection of Small Molecules on Cell Surface |
指導教授: |
陳貴通
Tan, Kui-Thong |
口試委員: |
許馨云
Hsu, Hsin-Yun 黃郁棻 Huang, Yu-Fen |
學位類別: |
碩士 Master |
系所名稱: |
理學院 - 化學系 Department of Chemistry |
論文出版年: | 2023 |
畢業學年度: | 111 |
語文別: | 中文 |
論文頁數: | 136 |
中文關鍵詞: | 蛋白質開關 、生物素化 、半合成 |
外文關鍵詞: | Protein Switch, Biotinylated, Semisynthetic |
相關次數: | 點閱:62 下載:0 |
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隨著醫療資源的發展,大腦的疾病仍然沒有明確的診斷方案或可量化的化學生物標記物質,因此在治療上增加了一定的難易度。許多研究指出,神經傳導物質在這方面影響甚深。常見的神經傳導物質,如興奮性的Glutamate和抑制性的GABA,亦或作為調節劑的Acetylcholine,這些分子的濃度和分佈都會影響訊號的變化,因此瞭解它們與大腦之間的時空關係,有助於生物醫學的發展。目前已有許多基於小分子和基因編碼的螢光感測器用於檢測各式的神經活動,其中,合成蛋白質開關是一項具有前瞻性的方法,因此我們欲延伸其技術來擴大對這領域的應用,在此研究中,我們提出一系列可調控生物素化蛋白開關來偵測細胞膜表面之小分子,其原理為藉由改變生物素周圍的空間障礙作為螢光訊號的開關。在未存在小分子的狀態下,生物素會因被包覆在結合蛋白與目標蛋白之間,呈現封閉構型,使其無法與Streptavidin結合;當加入小分子後,其會與探針之配體端進行競爭,使生物素呈現開放構型,同時活化了與Streptavidin的作用力,並透過修飾在Streptavidin上的染料Cy5來達標記的效果。我們預期能將此設計應用在不同的神經傳導物質偵測上,以及最後能順利引入到生物體內進行相關實驗。
With the development of medical resources, there are still no clear diagnostic schemes or quantifiable chemical biomarkers for brain disorders, which increase the difficulty of treatment. Researches have pointed out that most of them are affected by neurotransmitters. There are several excitatory, inhibitory, and modulatory neurotransmitters, such as Glu, GABA and ACh, respectively, will impact the change of signal by their concentration and distribution. Thus, determining the spatiotemporal relationship between these chemical signals and the brain is beneficial for biomedical development. Nowadays, numerous small-molecule based and genetically encoded sensors have been developed to track neural activity. Synthetic protein switch is one of the prospective methods in this field. Hence, we refer to these techniques to expand the applications. In this thesis, we introduce a series of tunable biotin-derived protein switch to detect small molecules on cell surface. The principle of this design is switching the fluorescent signal on and off by altering the steric hindrance of biotin. In the absence of analyte, the protein switch forms a closed conformation, and the biotin, meanwhile, will be trapped between the binding proteins causing it is unable to interact with streptavidin. While adding the analyte will let the analyte compete with the ligand of the probe, and lead the protein switch to form an open conformation activating the interaction between biotin and streptavidin. Consequently, the exposing biotin binds to streptavidin-Cy5 and generates the fluorescent turn-on signal. Based on the design, we expect these kinds of protein switch can be applied to detect different kinds of neurotransmitters, and be also expressed in vivo.
1. Loewi, O. Über humorale übertragbarkeit der Herznervenwirkung. Pflügers Archiv. 1921, 189, 239-242.
2. Leopold, A. V.; Shcherbakova, D. M.; Verkhusha, V. V. Fluorescent Biosensors for Neurotransmission and Neuromodulation: Engineering and Applications. Front. Cell. Neurosci. 2019, 13, 474.
3. Pereda, A. E. Electrical synapses and their functional interactions with chemical synapses. Nat. Rev. Neurosci. 2014, 15, 250-263.
4. Da, Y.; Luo, S.; Tian, Y. Real-Time Monitoring of Neurotransmitters in the Brain of Living Animals. ACS Appl. Mater. Interfaces 2023, 15, 138-157.
5. Zhou, Y.; Danbolt, N. C. Glutamate as a neurotransmitter in the healthy brain. J. Neural Transm. (Vienna) 2014, 121, 799-817.
6. Owens, D. F.; Kriegstein, A. R. Is there more to GABA than synaptic inhibition? Nat. Rev. Neurosci. 2002, 3, 715-727.
7. Baganz, N. L.; Blakely, R. D. A dialogue between the immune system and brain, spoken in the language of serotonin. ACS Chem. Neurosci. 2013, 4, 48-63.
8. Wang, H.; Jing, M.; Li, Y. Lighting up the brain: genetically encoded fluorescent sensors for imaging neurotransmitters and neuromodulators. Curr. Opin. Neurobiol. 2018, 50, 171-178.
9. Ou, Y.; Buchanan, A. M.; Witt, C. E.; Hashemi, P. Frontiers in Electrochemical Sensors for Neurotransmitter Detection: Towards Measuring Neurotransmitters as Chemical Diagnostics for Brain Disorders. Anal. Methods 2019, 11, 2738-2755.
10. Konig, M.; Thinnes, A.; Klein, J. Microdialysis and its use in behavioural studies: Focus on acetylcholine. J. Neurosci. Methods 2018, 300, 206-215.
11. Takeda, S.; Sato, N.; Ikimura, K.; Nishino, H.; Rakugi, H.; Morishita, R. Novel microdialysis method to assess neuropeptides and large molecules in free-moving mouse. Neuroscience 2011, 186, 110-119.
12. Liang, R.; Broussard, G. J.; Tian, L. Imaging chemical neurotransmission with genetically encoded fluorescent sensors. ACS Chem. Neurosci. 2015, 6, 84-93.
13. Kostyuk, A. I.; Demidovich, A. D.; Kotova, D. A.; Belousov, V. V.; Bilan, D. S. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Int. J. Mol. Sci. 2019, 20, 4200.
14. Sun, F.; Zeng, J.; Jing, M.; Zhou, J.; Feng, J.; Owen, S. F.; Luo, Y.; Li, F.; Wang, H.; Yamaguchi, T.; et al. A Genetically Encoded Fluorescent Sensor Enables Rapid and Specific Detection of Dopamine in Flies, Fish, and Mice. Cell 2018, 174, 481-496.
15. Feng, J.; Zhang, C.; Lischinsky, J. E.; Jing, M.; Zhou, J.; Wang, H.; Zhang, Y.; Dong, A.; Wu, Z.; Wu, H.; et al. A Genetically Encoded Fluorescent Sensor for Rapid and Specific In Vivo Detection of Norepinephrine. Neuron 2019, 102, 745-761.
16. Iismaa, T. P.; Shine, J. G protein-coupled receptors. Curr. Opin. Cell Biol. 1992, 4, 195-202.
17. Jing, M.; Zhang, P.; Wang, G.; Feng, J.; Mesik, L.; Zeng, J.; Jiang, H.; Wang, S.; Looby, J. C.; Guagliardo, N. A.; et al. A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies. Nat. Biotechnol. 2018, 36, 726-737.
18. Sabatini, B. L.; Tian, L. Imaging Neurotransmitter and Neuromodulator Dynamics In Vivo with Genetically Encoded Indicators. Neuron 2020, 108, 17-32.
19. Dwyer, M. A.; Hellinga, H. W. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 2004, 14, 495-504.
20. Marvin, J. S.; Borghuis, B. G.; Tian, L.; Cichon, J.; Harnett, M. T.; Akerboom, J.; Gordus, A.; Renninger, S. L.; Chen, T. W.; Bargmann, C. I.; et al. An optimized fluorescent probe for visualizing glutamate neurotransmission. Nat. Methods 2013, 10, 162-170.
21. Marvin, J. S.; Scholl, B.; Wilson, D. E.; Podgorski, K.; Kazemipour, A.; Muller, J. A.; Schoch, S.; Quiroz, F. J. U.; Rebola, N.; Bao, H.; et al. Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR. Nat. Methods 2018, 15, 936-939.
22. Helassa, N.; Durst, C. D.; Coates, C.; Kerruth, S.; Arif, U.; Schulze, C.; Wiegert, J. S.; Geeves, M.; Oertner, T. G.; Torok, K. Ultrafast glutamate sensors resolve high-frequency release at Schaffer collateral synapses. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 5594-5599.
23. Marvin, J. S.; Shimoda, Y.; Magloire, V.; Leite, M.; Kawashima, T.; Jensen, T. P.; Kolb, I.; Knott, E. L.; Novak, O.; Podgorski, K.; et al. A genetically encoded fluorescent sensor for in vivo imaging of GABA. Nat. Methods 2019, 16, 763-770.
24. Wang, A.; Feng, J.; Li, Y.; Zou, P. Beyond Fluorescent Proteins: Hybrid and Bioluminescent Indicators for Imaging Neural Activities. ACS Chem. Neurosci. 2018, 9, 639-650.
25. Namiki, S.; Sakamoto, H.; Iinuma, S.; Iino, M.; Hirose, K. Optical glutamate sensor for spatiotemporal analysis of synaptic transmission. Eur. J. Neurosci. 2007, 25, 2249-2259.
26. Okubo, Y.; Sekiya, H.; Namiki, S.; Sakamoto, H.; Iinuma, S.; Yamasaki, M.; Watanabe, M.; Hirose, K.; Iino, M. Imaging extrasynaptic glutamate dynamics in the brain. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 6526-6531.
27. Vilardaga, J. P.; Bunemann, M.; Krasel, C.; Castro, M.; Lohse, M. J. Measurement of the millisecond activation switch of G protein-coupled receptors in living cells. Nat. Biotechnol. 2003, 21, 807-812.
28. Bi, X.; Beck, C.; Gong, Y. Genetically Encoded Fluorescent Indicators for Imaging Brain Chemistry. Biosensors (Basel) 2021, 11, 116.
29. Adams, S. R.; Campbell, R. E.; Gross, L. A.; Martin, B. R.; Walkup, G. K.; Yao, Y.; Llopis, J.; Tsien, R. Y. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc. 2002, 124, 6063-6076.
30. Hoffmann, C.; Gaietta, G.; Bunemann, M.; Adams, S. R.; Oberdorff-Maass, S.; Behr, B.; Vilardaga, J. P.; Tsien, R. Y.; Ellisman, M. H.; Lohse, M. J. A FlAsH-based FRET approach to determine G protein-coupled receptor activation in living cells. Nat. Methods 2005, 2, 171-176.
31. Ziegler, N.; Batz, J.; Zabel, U.; Lohse, M. J.; Hoffmann, C. FRET-based sensors for the human M1-, M3-, and M5-acetylcholine receptors. Bioorg. Med. Chem. 2011, 19, 1048-1054.
32. Brun, M. A.; Griss, R.; Reymond, L.; Tan, K. T.; Piguet, J.; Peters, R. J.; Vogel, H.; Johnsson, K. Semisynthesis of fluorescent metabolite sensors on cell surfaces. J. Am. Chem. Soc. 2011, 133, 16235-16242.
33. Brun, M. A.; Tan, K. T.; Griss, R.; Kielkowska, A.; Reymond, L.; Johnsson, K. A semisynthetic fluorescent sensor protein for glutamate. J. Am. Chem. Soc. 2012, 134, 7676-7678.
34. Xue, L.; Prifti, E.; Johnsson, K. A General Strategy for the Semisynthesis of Ratiometric Fluorescent Sensor Proteins with Increased Dynamic Range. J. Am. Chem. Soc. 2016, 138, 5258-5261.
35. Sakamoto, S.; Yamaura, K.; Numata, T.; Harada, F.; Amaike, K.; Inoue, R.; Kiyonaka, S.; Hamachi, I. Construction of a Fluorescent Screening System of Allosteric Modulators for the GABA(A) Receptor Using a Turn-On Probe. ACS Cent. Sci. 2019, 5, 1541-1553.
36. Wu, C. C.; Huang, S. J.; Fu, T. Y.; Lin, F. L.; Wang, X. Y.; Tan, K. T. Small-Molecule Modulated Affinity-Tunable Semisynthetic Protein Switches. ACS Sens. 2022, 7, 2691-2700.
37. Xue, L.; Karpenko, I. A.; Hiblot, J.; Johnsson, K. Imaging and manipulating proteins in live cells through covalent labeling. Nat. Chem. Biol. 2015, 11, 917-923.
38. Clarke, W. ; Sokoll, L. J.; Rai, A. J. Immunoassays. In Contemporary practice in clinical chemistry, 4th ed.; Clarke, W.; Marzinke, M. Eds.; Academic Press, 2020; Chapter 12, pp 201– 214.
39. Fujishima, S. H.; Yasui, R.; Miki, T.; Ojida, A.; Hamachi, I. Ligand-directed acyl imidazole chemistry for labeling of membrane-bound proteins on live cells. J. Am. Chem. Soc. 2012, 134, 3961-3964.
40. Inoue, A.; Ohmuro-Matsuyama, Y.; Kitaguchi, T.; Ueda, H. Creation of a Nanobody-Based Fluorescent Immunosensor Mini Q-body for Rapid Signal-On Detection of Small Hapten Methotrexate. ACS Sens. 2020, 5, 3457-3464.
41. Christopoulos, T. K.; Diamandis, E. P. The biotin-(strept)avidin system: principles and applications in biotechnology. Clinical Chemistry 1991, 37, 625-636.
42. Terai, T.; Kohno, M.; Boncompain, G.; Sugiyama, S.; Saito, N.; Fujikake, R.; Ueno, T.; Komatsu, T.; Hanaoka, K.; Okabe, T.; et al. Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport. J. Am. Chem. Soc. 2015, 137, 10464-10467.
43. Ding, Z.; Fong, R. B.; Long, C. J.; Stayton, P. S.; Hoffman, A. S. Size-dependent control of the binding of biotinylated proteins to streptavidin using a polymer shield. Nature 2001, 411, 59-62.
44. Cherkasov, V. R.; Mochalova, E. N.; Babenyshev, A. V.; Vasilyeva, A. V.; Nikitin, P. I.; Nikitin, M. P. Nanoparticle Beacons: Supersensitive Smart Materials with On/Off-Switchable Affinity to Biomedical Targets. ACS Nano 2020, 14, 1792-1803.
45. Hoelzel, C. A.; Zhang, X. Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies. Chembiochem 2020, 21, 1935-1946.
46. Los, G. V.; Encell, L. P.; McDougall, M. G.; Hartzell, D. D.; Karassina, N.; Zimprich, C.; Wood, M. G.; Learish, R.; Ohana, R. F.; Urh, M.; et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 2008, 3, 373-382.
47. Keppler, A.; Gendreizig, S.; Gronemeyer, T.; Pick, H.; Vogel, H.; Johnsson, K. A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 2003, 21, 86-89.
48. Lindskog, S. Structure and mechanism of carbonic anhydrase. Pharmacol. Ther. 1997, 74, 1-20.
49. Chiaramonte, N.; Romanelli, M. N.; Teodori, E.; Supuran, C. T. Amino Acids as Building Blocks for Carbonic Anhydrase Inhibitors. Metabolites 2018, 8, 36.
50. Baker, D. J.; Beddell, C. R.; Champness, J. N.; Goodford, P. J.; Norrington, F. E.; Smith, D. R.; Stammers, D. K. The binding of trimethoprim to bacterial dihydrofolate reductase. FEBS Lett. 1981, 126, 49-52.
51. Heaslet, H.; Harris, M.; Fahnoe, K.; Sarver, R.; Putz, H.; Chang, J.; Subramanyam, C.; Barreiro, G.; Miller, J. R. Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim. Proteins 2009, 76, 706-717.
52. Wermuth, C. G.; Bourguignon, J. J.; Schlewer, G.; Gies, J. P.; Schoenfelder, A.; Melikian, A.; Bouchet, M. J.; Chantreux, D.; Molimard, J. C.; Heaulme, M.; et al. Synthesis and structure-activity relationships of a series of aminopyridazine derivatives of gamma-aminobutyric acid acting as selective GABA-A antagonists. J. Med. Chem. 1987, 30, 239-249.
53. Yamaura, K.; Kiyonaka, S.; Numata, T.; Inoue, R.; Hamachi, I. Discovery of allosteric modulators for GABAA receptors by ligand-directed chemistry. Nat. Chem. Biol. 2016, 12, 822-830.
54. Reja, S. I.; Minoshima, M.; Hori, Y.; Kikuchi, K. Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications. Chem. Sci. 2020, 12, 3437-3447.