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| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| dc.contributor.advisor | 楊?伸(Chii Shen, Yang) | |
| dc.contributor.author | Yi-Chung Shen | en |
| dc.contributor.author | 沈宜中 | zh_TW |
| dc.date.accessioned | 2021-06-16T13:39:45Z | - |
| dc.date.available | 2018-07-31 | |
| dc.date.copyright | 2013-07-31 | |
| dc.date.issued | 2013 | |
| dc.date.submitted | 2013-07-15 | |
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Hampp, N., Bacteriorhodopsin as a Photochromic Retinal Protein for Optical Memories. Chem Rev, 2000. 100(5): p. 1755-1776. 21. Dunn, R.J., et al., Structure-function studies on bacteriorhodopsin. I. Expression of the bacterio-opsin gene in Escherichia coli. J Biol Chem, 1987. 262(19): p. 9246-54. 22. Krebs, M.P., R. Mollaaghababa, and H.G. Khorana, Gene replacement in Halobacterium halobium and expression of bacteriorhodopsin mutants. Proc Natl Acad Sci U S A, 1993. 90(5): p. 1987-91. 23. Henderson, R., et al., Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol, 1990. 213(4): p. 899-929. 24. Luecke, H., et al., Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol, 1999. 291(4): p. 899-911. 25. Sudo, Y. and J.L. Spudich, Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc Natl Acad Sci U S A, 2006. 103(44): p. 16129-34. 26. Sasaki, J., et al., Conversion of bacteriorhodopsin into a chloride ion pump. Science, 1995. 269(5220): p. 73-5. 27. Lozier, R.H., R.A. Bogomolni, and W. Stoeckenius, Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium. Biophys J, 1975. 15(9): p. 955-62. 28. Lanyi, J.K., Proton transfers in the bacteriorhodopsin photocycle. Biochim Biophys Acta, 2006. 1757(8): p. 1012-8. 29. Schobert, B., et al., Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. J Mol Biol, 2002. 321(4): p. 715-26. 30. Birge, R.R., et al., Revised assignment of energy storage in the primary photochemical event in bacteriorhodopsin. J Am Chem Soc, 1991. 113(11): p. 4327-4328. 31. Lanyi, J.K. and B. Schobert, Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of the K, L, M1, M2, and M2' intermediates of the photocycle. J Mol Biol, 2003. 328(2): p. 439-50. 32. Luecke, H., et al., Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin. J Mol Biol, 2000. 300(5): p. 1237-55. 33. Luecke, H., Atomic resolution structures of bacteriorhodopsin photocycle intermediates: the role of discrete water molecules in the function of this light-driven ion pump. Biochim Biophys Acta, 2000. 1460(1): p. 133-56. 34. Zimanyi, L., et al., The two consecutive M substates in the photocycle of bacteriorhodopsin are affected specifically by the D85N and D96N residue replacements. Photochem Photobiol, 1992. 56(6): p. 1049-55. 35. Varo, G. and J.K. Lanyi, Kinetic and spectroscopic evidence for an irreversible step between deprotonation and reprotonation of the Schiff base in the bacteriorhodopsin photocycle. Biochemistry, 1991. 30(20): p. 5008-15. 36. Balashov, S.P., et al., Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release. Biophys J, 1996. 70(1): p. 473-81. 37. Richter, H.T., et al., A linkage of the pKa's of asp-85 and glu-204 forms part of the reprotonation switch of bacteriorhodopsin. Biochemistry, 1996. 35(13): p. 4054-62. 38. Lanyi, J. and B. Schobert, Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. J Mol Biol, 2002. 321(4): p. 727-37. 39. Freier, E., S. Wolf, and K. Gerwert, Proton transfer via a transient linear water-molecule chain in a membrane protein. Proc Natl Acad Sci U S A, 2011. 108(28): p. 11435-9. 40. Schobert, B., L.S. Brown, and J.K. Lanyi, Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol, 2003. 330(3): p. 553-70. 41. Rouhani, S., et al., Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate. J Mol Biol, 2001. 313(3): p. 615-28. 42. Shen, Y., et al., Stabilization of the membrane protein bacteriorhodopsin to 140 C in two-dimensional films. Nature, 1993. 366(6450): p. 48-50. 43. Taneva, S.G., et al., Electrokinetic charge of the anesthetic-induced bR480 and bR380 spectral forms of bacteriorhodopsin. Biochim Biophys Acta, 1995. 1236(2): p. 331-7. 44. Eisenbach, M. and S.R. Caplan, Interaction of purple membrane with solvents. II. Mode of interaction. Biochim Biophys Acta, 1979. 554(2): p. 281-92. 45. Bamberg, E., et al., Transmembranous incorporation of photoelectrically active bacteriorhodopsin in planar lipid bilayers. Proc Natl Acad Sci U S A, 1981. 78(12): p. 7502-6. 46. Trivedi, S., O.P. Choudhary, and J. Gharu, Different proposed applications of bacteriorhodopsin. Recent Pat DNA Gene Seq, 2011. 5(1): p. 35-40. 47. Topolancik J, V.F., SYSTEM AND METHOD FOR STRONG PHOTON LOCALIZATION BY DISORDERED PHOTONIC CRYSTAL STRUCTURES (QUASICRYSTALS), 2008, WO Patent WO/2008/151,224. 48. Carmeli, C., et al., PHOTOACTIVE NANOSTRUCTURE AND METHOD OF MANUFACTURING SAME, 2009, Google Patents. 49. Patil, A.V., et al., Engineered bacteriorhodopsin: a molecular scale potential switch. Chemistry, 2012. 18(18): p. 5632-6. 50. Hampp, N., et al., Linker-free covalent coupling of bacteriorhodopsin in purple membrane form, 2005, Google Patents. 51. Walter, J.M., D. Greenfield, and J. Liphardt, Potential of light-harvesting proton pumps for bioenergy applications. Curr Opin Biotechnol, 2010. 21(3): p. 265-70. 52. YACOBY, I., et al., PHOTOCATALYTIC HYDROGEN PRODUCTION AND POLYPEPTIDES CAPABLE OF SAME, 2009, WO Patent WO/2009/013,745. 53. CINQUIN, P. and D. MARTIN, BIOMIMETIC ARTIFICIAL MEMBRANE DEVICE, 2009, WO Patent WO/2009/003,936. 54. Boyden ES, D.K., LIGHT-ACTIVATED CATION CHANNEL AND USES THEREOF, 2007, WO Patent WO/2007/024,391. 55. ABEL, K., ANTIBODIES OPERABLY LINKED TO SELECTED CHEMOATTRACTANTS, 2007, WO Patent WO/2007/001,457. 56. Ostermeier MA, G.G., METHODS FOR MAKING AND USING MOLECULAR SWITCHES INVOLVING CIRCULAR PERMUTATION, 2005, WO Patent WO/2005/072,392. 57. PAN, Z.H., RESTORATION OF VISUAL RESPONSES BY IN VIVO DELIVERY OF RHODOPSIN NUCLEIC ACIDS, 2007, WO Patent WO/2007/131,180. 58. Luecke, H., et al., Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science, 1999. 286(5438): p. 255-61. 59. Hoffmann, M., et al., Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc, 2006. 128(33): p. 10808-18. 60. Jensen RB, K.B., Ward DE, Asato AE., PHOTOCHROMIC MATERIAL COMPRISING A PROTEORHODOPSIN APOPROTEIN AND RETINAL ANALOG, 2005, WO Patent WO/2005/124,230. 61. Baliga, N.S., et al., Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res, 2004. 14(11): p. 2221-34. 62. 傅煦媛, 表現 Haloarcula marismortui 之六個光感受體揭露其獨特的感光特性 碩士論文, 2008, 國立台灣大學. 63. 劉康正, Haloarcula marismortui 中 HmBRI 及 HmBRII 蛋白質特性及功能研究 碩士論文, 2009, 國立台灣大學. 64. 黃敬哲, 以生物科技生產 Haloarcula marismortui HmBRI 蛋白質在生物工業上應用之研究 碩士論文, 2009, 國立台灣大學. 65. 謝祥元, 發展以蛋白質輔助之膜蛋白質大量表現系統 碩士論文, 2011, 國 立台灣大學. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/62302 | - |
| dc.description.abstract | 維他命A 醛結合蛋白質又稱為視紫紅質，結構由七個穿膜的α螺旋組成，並在結構的中央有個活性袋狀區，與具感光功能的視黃醛結合，在生物體中多作為感光受體蛋白質。視紫紅質在吸收一定波長的光源被激發後，分子結構將會從基態進入激發態，在微結構上有連續的改變，而最終能行使一次功能，此過程稱為光週期。本實驗室在嗜鹽古細菌 Haloarucla marismortui 當中分離純化出了六種不同的rhodopsin，並且將其中一種被稱為細菌視紫紅質 (Bacteriorhodopsin,BR)的光驅動外向氫離子幫浦，以點突變的方式建構出了一種具有高的表現量及穩性，且有較緩慢光週期的細菌視紫紅質突變蛋白質，命名為HEBR(Highly-Expressed Bacteriorhodopsin)。我們觀察到 HEBR 在光照下會產生顏色的變化（紫色變為黃色），也發現其變色的程度與溶劑環境的 pH 值正相關。利用光週期測試的方式，我們證實 BR 光週期中一重要的中間態：M 態存在的時間，會隨著 pH 值上升延長而累積；而這個具有不同特徵吸收值的中間態累積，正是 HEBR 在照光時顏色變化的原因。另外，利用化學反應平衡的方法推定光週期反應，解釋 M 態累積與 pH 值的關係，並在 HEBR 變色反應中引進了光照強度這個影響因子，更以時間解析吸收光譜加以證實且進行量化。本研究除確實觀察到 HEBR 蛋白質在不同 pH 值以及不同光照強度下的不同變色情形之外，亦以標準比色卡對真實視覺顏色變化做校正，並以 RGB 數量化所有顏色變化。利用此特殊的變色性質，HEBR 蛋白質的光色特性可被應用在無電池光強度感測系統中，作環境光強度的感測；亦可根據特定光強度下的顏色變化，投入在 pH 量測的應用。 | zh_TW |
| dc.description.abstract | Retinal-binding proteins (RBPs) are composed of seven-transmembrane α helix, which form a binding pocket to secure a photosensing retinal molecule. RBPs response to light illumination after abosorbing maximally at a specific wavelength and exhibit different visual colors. Our laboratory reported six new RBPs from a halophilic archaea, Haloarucla marismortui, and constructed a mutated protein named Highly-Expressed Bacteriorhodopsin (HEBR) from of one of the RBPs, HmBRI, and found it to have exceptional high expression efficiency and high stability, as well as a
slower photocycle recovery rate. In addition, HEBR showed purple to yellow color changing when exposure to light, and the degree of such color changing was pH-dependent. Photocycle measurement unveiled that the accumulation of an important intermediate state, M state, is proportional to the increasing of pH value and consequently the color changing. In addition, by chemical reaction equilibrium, we introduced light intensity as another variable to describe such pheromone. Furthermore, this study calibrated the visual color changing with a professional standard color card with software, and quantified them as RGB values. Based on thecorrelation between HEBR color changing, pH value and light intensity, a series of HEBR under different pH was shown to report different light intensity and we proposed to use it as a battery-free light intensity indicator. Furthermore, HEBR also could serve as pH indicator by the color changing under certain light intensity. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T13:39:45Z (GMT). No. of bitstreams: 1 ntu-102-R99b22019-1.pdf: 11116967 bytes, checksum: 2e074df17fde90d9301c5a69f1f7fbe5 (MD5) Previous issue date: 2013 | en |
| dc.description.tableofcontents | 目錄................................................................................................................................. i
圖目錄........................................................................................................................... iv 表目錄........................................................................................................................... vi 摘要.............................................................................................................................. vii Abstract ....................................................................................................................... viii 第一章 緒論.................................................................................................................. 1 第一節 微生物視紫紅質...................................................................................... 1 第二節 細菌視紫紅質.......................................................................................... 4 2.1 細菌視紫紅質光週期與運輸機制.......................................................... 5 2.2 細菌視紫紅質相關應用......................................................................... 9 第三節 Haloarcula marismortui ........................................................................ 11 第四節 HEBR ..................................................................................................... 13 4.1 HEBR 性質研究 ................................................................................... 13 4.2 HEBR 相關應用 ................................................................................... 15 第五節 研究動機與目的.................................................................................... 16 第二章 材料與方法.................................................................................................... 18 第一節 實驗材料與藥品.................................................................................... 18 1.1 菌種....................................................................................................... 18 1.2 質體....................................................................................................... 18 1.3 藥品....................................................................................................... 18 第二節 實驗儀器與設備.................................................................................... 20 2.1 蛋白質電泳與轉印設備....................................................................... 20 2.2 離心機................................................................................................... 20 2.3 光週期測試儀器................................................................................... 20 2.4 其他儀器............................................................................................... 20 2.5 電腦軟體及其他................................................................................... 21 第三節 實驗方法................................................................................................ 22 ii 3.1 蛋白質之表現與純化........................................................................... 22 3.1.1 蛋白質異源表現........................................................................ 22 3.1.2 破菌與蛋白質粗萃取................................................................ 22 3.1.3 膜分離與膜蛋白質回溶............................................................. 22 3.1.4 親和層析法................................................................................ 23 3.1.5 修正後的膜蛋白純化方式........................................................ 23 3.2 蛋白質電泳與基本定性分析............................................................... 24 3.2.1 SDS-PAGE 變性膠體電泳 ......................................................... 24 3.2.2 CBR 膠體染色............................................................................ 24 3.2.3 蛋白質轉印................................................................................ 24 3.2.4 西方墨點法與免疫呈色............................................................ 25 3.3 蛋白質儀器分析................................................................................... 25 3.3.1 特定酸鹼值之蛋白質樣本準備................................................. 25 3.3.2 特徵吸收光譜測定.................................................................... 25 3.3.3 光週期測試................................................................................ 26 3.3.4 傅立葉轉換紅外光譜測試........................................................ 26 3.3.5 酸度係數 (pKa) 測定 ............................................................... 27 3.3.6 三維螢光光譜測定.................................................................... 27 3.3.7 時間解析吸收光譜測試............................................................ 27 3.3.8 不同光強度下蛋白質顏色分析................................................ 28 第三章 結果與討論.................................................................................................... 29 第一節 HEBR 蛋白質表現純化與特性分析 ................................................... 29 1.1 HEBR 蛋白質表現純化、電泳與吸收光譜分析 ............................... 29 1.2 酸度係數測定....................................................................................... 30 第二節 HEBR 的光色特性與光週期測試 ........................................................ 32 2.1 HEBR 基態光週期測試 ....................................................................... 32 2.2 HEBR 激發中間 M 態光週期測試 ................................................... 33 2.3 以平衡反應動力學解釋光週期趨緩與光色特性............................... 36 第三節 顏色變化、pH 值與光強度 ................................................................. 38 iii 3.1 HEBR 變色與光強度之關係 ................................................................ 38 3.2 時間解析吸收光譜測試....................................................................... 38 第四節 以 HEBR 建構生物材料光強度感測系統 ......................................... 42 4.1 不同光強度下蛋白質顏色分析........................................................... 42 第四章 總結................................................................................................................ 45 第五章 未來展望........................................................................................................ 46 第一節 HEBR 應用產品設計預想 ..................................................................... 46 第二節 未來工作目標........................................................................................ 47 附錄 HEBR 蛋白質與 HmBRI WT 生物物理特性比較：生物物理儀器分析 . 48 A.1 三維螢光光譜測定 .............................................................................. 48 A.2 傅立葉轉換紅外光譜測定 .................................................................. 52 參考文獻...................................................................................................................... 55 碩士論文口試問與答.................................................................................................. 61 | |
| dc.language.iso | zh-TW | |
| dc.subject | pH 值-光強度依賴顏色變化 | zh_TW |
| dc.subject | 無電池光強度感測器。 | zh_TW |
| dc.subject | 光週期 | zh_TW |
| dc.subject | Highly-Expressed Bacteriorhodopsin | zh_TW |
| dc.subject | Highly-Expressed Bacteriorhodopsin (HEBR) | en |
| dc.subject | photocycle | en |
| dc.subject | pH-light intensity dependent color changing | en |
| dc.subject | cell-free light intensity indicator | en |
| dc.title | HmBRI 突變設計蛋白質之光學特性與應用研究 | zh_TW |
| dc.title | Photonic properties and application studies of an engineered HmBRI protein | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 101-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 梁國淦,許瑞祥,黃慶璨,李昆達 | |
| dc.subject.keyword | Highly-Expressed Bacteriorhodopsin,光週期,pH 值-光強度依賴顏色變化,無電池光強度感測器。, | zh_TW |
| dc.subject.keyword | Highly-Expressed Bacteriorhodopsin (HEBR),photocycle,pH-light intensity dependent color changing,cell-free light intensity indicator, | en |
| dc.relation.page | 66 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2013-07-15 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科技學系 | zh_TW |
| Appears in Collections: | 生化科技學系 | |
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| ntu-102-1.pdf Restricted Access | 10.86 MB | Adobe PDF |
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