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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 楊?伸 | |
| dc.contributor.author | Hong-Syuan Lin | en |
| dc.contributor.author | 林宏軒 | zh_TW |
| dc.date.accessioned | 2021-06-17T04:29:21Z | - |
| dc.date.available | 2023-08-18 | |
| dc.date.copyright | 2018-08-18 | |
| dc.date.issued | 2018 | |
| dc.date.submitted | 2018-08-13 | |
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J., Dennis, P. P., Omer, A. D., Ebhardt, H., Lowe, T. M., Liang, P., Riley, M., Hood, L. & DasSarma, S. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 97, 12176-12181, (2000). 17 Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F. & Oesterhelt, D. The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics 7:169, (2006). 18 Falb, M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J. & Oesterhelt, D. Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res 15, 1336-1343, (2005). 19 Oesterhelt, D. & Stoeckenius, W. Functions of a new photoreceptor membrane. Proc Natl Acad Sci U S A 70, 2853-2857, (1973). 20 Spudich, J. L., Yang, C. S., Jung, K. H. & Spudich, E. N. Retinylidene proteins: structures and functions from archaea to humans. Annu Rev Cell Dev Biol 16, 365-392, (2000). 21 Rao, V. R. & Oprian, D. D. Activating mutations of rhodopsin and other G protein-coupled receptors. Annu Rev Biophys Biomol Struct 25, 287-314, (1996). 22 Hoffmann, M., Wanko, M., Strodel, P., Konig, P. H., Frauenheim, T., Schulten, K., Thiel, W., Tajkhorshid, E. & Elstner, M. Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 128, 10808-10818, (2006). 23 Matsuno-Yagi, A. & Mukohata, Y. Two possible roles of bacteriorhodopsin; a comparative study of strains of Halobacterium halobium differing in pigmentation. Biochem Biophys Res Commun 78, 237-243, (1977). 24 Pfisterer, C., Gruia, A. & Fischer, S. The mechanism of photo-energy storage in the Halorhodopsin chloride pump. J Biol Chem 284, 13562-13569, (2009). 25 Ishchenko, A., Round, E., Borshchevskiy, V., Grudinin, S., Gushchin, I., Klare, J. P., Remeeva, A., Polovinkin, V., Utrobin, P., Balandin, T., Engelhard, M., Buldt, G. & Gordeliy, V. New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex. Sci Rep 7, 41811, (2017). 26 Klare, J. P., Bordignon, E., Engelhard, M. & Steinhoff, H. J. Transmembrane signal transduction in archaeal phototaxis: the sensory rhodopsin II-transducer complex studied by electron paramagnetic resonance spectroscopy. Eur J Cell Biol 90, 731-739, (2011). 27 Hoff, W. D., Jung, K. H. & Spudich, J. L. Molecular mechanism of photosignaling by archaeal sensory rhodopsins. Annu Rev Biophys Biomol Struct 26, 223-258, (1997). 28 Spudich, J. L. The multitalented microbial sensory rhodopsins. Trends Microbiol 14, 480-487, (2006). 29 Ernst, O. P., Lodowski, D. T., Elstner, M., Hegemann, P., Brown, L. S. & Kandori, H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 114, 126-163, (2014). 30 Oesterhelt, D. & Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233, 149-152, (1971). 31 Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E. & Downing, K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213, 899-929, (1990). 32 Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P. & Lanyi, J. K. Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol 291, 899-911, (1999). 33 Lanyi, J. K. Proton transfers in the bacteriorhodopsin photocycle. Biochim Biophys Acta 1757, 1012-1018, (2006). 34 Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P. & Lanyi, J. K. Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science 286, 255-261, (1999). 35 Lanyi, J. K. Bacteriorhodopsin. Annu Rev Physiol 66, 665-688, (2004). 36 Klare, J. P., Chizhov, I. & Engelhard, M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 45, 73-122, (2008). 37 Chizhov, I., Schmies, G., Seidel, R., Sydor, J. R., Luttenberg, B. & Engelhard, M. The photophobic receptor from Natronobacterium pharaonis: temperature and pH dependencies of the photocycle of sensory rhodopsin II. Biophys J 75, 999-1009, (1998). 38 Stenrup, M., Pieri, E., Ledentu, V. & Ferre, N. pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin. Phys Chem Chem Phys 19, 14073-14084, (2017). 39 Tamogami, J., Iwano, K., Matsuyama, A., Kikukawa, T., Demura, M., Nara, T. & Kamo, N. The effects of chloride ion binding on the photochemical properties of sensory rhodopsin II from Natronomonas pharaonis. J Photochem Photobiol B 141, 192-201, (2014). 40 Hayashi, S., Tajkhorshid, E. & Schulten, K. Structural determinants of spectral tuning in the rhodopsin family of proteins. Biophysical Journal 82, 226a, (2002). 41 Luecke, H., Schobert, B., Lanyi, J. K., Spudich, E. N. & Spudich, J. L. Crystal structure of sensory rhodopsin II at 2.4 angstroms: Insights into color tuning and transducer interaction. Science 293, 1499-1503, (2001). 42 Krebs, M. P. & Khorana, H. G. Mechanism of light-dependent proton translocation by bacteriorhodopsin. J Bacteriol 175, 1555-1560, (1993). 43 Mogi, T., Stern, L. J., Marti, T., Chao, B. H. & Khorana, H. G. Aspartic acid substitutions affect proton translocation by bacteriorhodopsin. Proc Natl Acad Sci U S A 85, 4148-4152, (1988). 44 Greenhalgh, D. A., Farrens, D. L., Subramaniam, S. & Khorana, H. G. Hydrophobic amino acids in the retinal-binding pocket of bacteriorhodopsin. J Biol Chem 268, 20305-20311, (1993). 45 Mogi, T., Marti, T. & Khorana, H. G. Structure-function studies on bacteriorhodopsin. IX. Substitutions of tryptophan residues affect protein-retinal interactions in bacteriorhodopsin. J Biol Chem 264, 14197-14201, (1989). 46 Mogi, T., Stern, L. J., Hackett, N. R. & Khorana, H. G. Bacteriorhodopsin mutants containing single tyrosine to phenylalanine substitutions are all active in proton translocation. Proc Natl Acad Sci U S A 84, 5595-5599, (1987). 47 Marti, T., Otto, H., Mogi, T., Rosselet, S. J., Heyn, M. P. & Khorana, H. G. Bacteriorhodopsin mutants containing single substitutions of serine or threonine residues are all active in proton translocation. J Biol Chem 266, 6919-6927, (1991). 48 Subramaniam, S., Greenhalgh, D. A., Rath, P., Rothschild, K. J. & Khorana, H. G. Replacement of leucine-93 by alanine or threonine slows down the decay of the N and O intermediates in the photocycle of bacteriorhodopsin: implications for proton uptake and 13-cis-retinal----all-trans-retinal reisomerization. Proc Natl Acad Sci U S A 88, 6873-6877, (1991). 49 Hackett, N. R., Stern, L. J., Chao, B. H., Kronis, K. A. & Khorana, H. G. Structure-function studies on bacteriorhodopsin. V. Effects of amino acid substitutions in the putative helix F. J Biol Chem 262, 9277-9284, (1987). 50 Ahl, P. L., Stern, L. J., During, D., Mogi, T., Khorana, H. G. & Rothschild, K. J. Effects of amino acid substitutions in the F helix of bacteriorhodopsin. Low temperature ultraviolet/visible difference spectroscopy. J Biol Chem 263, 13594-13601, (1988). 51 Mogi, T., Stern, L. J., Chao, B. H. & Khorana, H. G. Structure-function studies on bacteriorhodopsin. VIII. Substitutions of the membrane-embedded prolines 50, 91, and 186: the effects are determined by the substituting amino acids. J Biol Chem 264, 14192-14196, (1989). 52 Kalisky, O., Feitelson, J. & Ottolenghi, M. Photochemistry and fluorescence of bacteriorhodopsin excited in its 280-nm absorption band. Biochemistry 20, 205-209, (1981). 53 Becher, B., Tokunaga, F. & Ebrey, T. G. Ultraviolet and visible absorption spectra of the purple membrane protein and the photocycle intermediates. Biochemistry 17, 2293-2300, (1978). 54 Trivedi, S., Choudhary, O. P. & Gharu, J. Different proposed applications of bacteriorhodopsin. Recent Pat DNA Gene Seq 5, 35-40, (2011). 55 Chu, L. K., Yen, C. W. & El-Sayed, M. A. Bacteriorhodopsin-based photo-electrochemical cell. Biosens Bioelectron 26, 620-626, (2010). 56 Hsu, M. F., Fu, H. Y., Cai, C. J., Yi, H. P., Yang, C. S. & Wang, A. H. Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity. J Biol Chem 290, 29567-29577, (2015). 57 Tamogami, J., Kikukawa, T., Miyauchi, S., Muneyuki, E. & Kamo, N. A tin oxide transparent electrode provides the means for rapid time-resolved pH measurements: application to photoinduced proton transfer of bacteriorhodopsin and proteorhodopsin. Photochem Photobiol 85, 578-589, (2009). 58 Alexiev, U. & Farrens, D. L. Fluorescence spectroscopy of rhodopsins: Insights and approaches. Bba-Bioenergetics 1837, 694-709, (2014). 59 Garcia-Martinez, J., Brunk, M., Avalos, J. & Terpitz, U. The CarO rhodopsin of the fungus Fusarium fujikuroi is a light-driven proton pump that retards spore germination. Sci Rep 5, 7798, (2015). | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/70490 | - |
| dc.description.abstract | 微生物視紫蛋白質 (microbial rhodopsin) 是一種廣泛分布在各種微生物細胞膜上的一種感光蛋白，此類蛋白質結構上含有七個穿膜的α螺旋，並在中心有一個視黃醛 (retinal) 與蛋白質第七穿膜區上離胺酸 (lysine) 鍵結形成希夫鹼 (Schiff base) ，構成發光基團 (chromophore)，而周邊接觸視黃醛並用以穩定發光基團結構的胺基酸稱為視黃醛結合口袋 (retinal binding pocket)，此微環境影響了不同蛋白質的吸收波長。在古生菌中，氫視紫質 (Bacteriorhodopsin, BR)是一種光驅動氫離子運輸蛋白，吸收特定波長光後，會將氫離子運輸至細胞膜外，提供ATP合成酶質動勢來產能。氫視紫質研究中最廣為了解的為Halobacterium salinarum的氫視紫質 (HsBR)，先前在HsBR的點突變研究中指出在視黃醛結合袋，會對發光基團的穩定性產生影響的胺基酸中，有相當高比例的色胺酸 (tryptophan)，也提出這些色胺酸在與視黃醛的交互作用中，扮演重要的角色。而在本實驗室中，有一種來自Haloquadratum walsbyi的氫視紫質 (HwBR)，相較與HsBR，在酸性環境下，發光基團穩定且可正常運輸氫離子。然而兩種BR在視黃醛結合袋的序列卻完全保守，卻對酸性環境有完全不同的穩定性。本研究想要去探討一樣的結構與序列卻有著如此之特性差異，是否包圍發光基團中保守的胺基酸，對於不同蛋白質而言其實扮演了不一樣的角色？本研究以先前研究指出有著重要性的色胺酸為對象，探討其在視紫質功能或是光學性質上所扮演的角色。本實驗中在HsBR和HwBR相同結構位置的的色胺酸做突變，並進行光學上與功能上的測量與分析，發現兩種BR序列保守的色胺酸對於蛋白質的光學和功能特性具有不一樣的影響，並提供色胺酸在可耐酸氫視紫質HwBR可能的功能，為往後發光基團對酸穩定性研究，提供一些基礎與線索。本實驗結果更顯示，對於序列分析為高度保守的胺基酸，仍需以更多和其他胺基酸交互作用來討論其作用。 | zh_TW |
| dc.description.abstract | Rhodopsins belong to a family of retinal-binding protein (RBP) which are widely distributed in different light sensitive organs. In microbes, rhodopsin are distributed on cell membrane, and they respond to light stimuli to mediate various physical functions. This protein family has a conserved seven-transmembrane domain with a retinal binding to a conserved lysine on the seventh helix. Retinal is further stabilized by highly conserved surrounding aromatic amino acids to form a retinal binding pocket, RBP. Bacteriorhodopsin (BR) is a light-driven outward proton pump found in haloarchaea, Upon light activation, BR pump a proton out of cell per photocycle to provide proton gradient to further ATP via F1Fo ATP synthase. Previous mutagenesis study in a well-studied bacteriorhodopsin, HsBR, showed that some residues in RBP can affect chromophore stability and the maximum absorbance (Abs-max). Among these residues, tryptophan residues were shown to play important roles in interaction with retinal and the Abs-max wavelength. Previously we found HwBR, a bacteriorhodopsin from Haloquadratum walsbyi, to have more stable Abs-max and functionality under acidic condition when compared to HsBR even though they have identical residues in RBP. To investigate such a paradox, this study mutated three corresponding tryptophan residues in both BR proteins and found conserved tryptophans contributed differently to the Abs-max and functionality under acidic conditions in two BR. We concluded further analysis in the interaction between tryptophan and nearby residues or water molecule network essential. This study also provide clear clues for future investigating on the acid-tolerance of RBP in microbial rhodopsin. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-17T04:29:21Z (GMT). No. of bitstreams: 1 ntu-107-R05b22017-1.pdf: 3997559 bytes, checksum: bbdcbf32a99a58ad4c318dce9be42cae (MD5) Previous issue date: 2018 | en |
| dc.description.tableofcontents | 致謝 II
摘要 III ABSTRACT IV 目錄 V 圖目錄 VII 表目錄 VIII 第一章 緒論 1 第一節 嗜鹽古生菌 1 第二節 微生物視紫蛋白質 2 第三節 氫視紫質 4 第四節 視黃醛與發光基團 6 第五節 氫視紫質發光基團之點突變研究 8 第六節 研究與動機 9 第二章 實驗材料與方法 12 第一節 實驗材料與藥品 12 2.1.1 菌種 12 2.1.2 質體 12 2.1.3 蛋白質藥品 12 2.1.4 化學藥品 12 第二節 實驗儀器與設備 14 2.2.1 核酸電泳設備 14 2.2.2 蛋白質電泳與轉印設備 14 2.2.3 離心機 14 2.2.4 光電流量測用儀器 14 2.2.5 光週期實驗用量測儀器 14 2.2.6 其他 15 第三節 實驗方法 16 2.3.1 生物資訊分析 16 2.3.2 HsBR與HwBR 突變株之質體建構 16 2.3.3 HsBR、HwBR及其突變蛋白質表達與純化 18 2.3.4 蛋白質電泳與西方墨點法分析 20 2.3.5 特徵吸收波長光譜掃描 21 2.3.6 光電流訊號測試 21 2.3.7 可見光光譜光週期測試 22 第三章 結果 23 第一節 結構比較與命名法 23 3.1.1 古生菌視黃醛結合袋序列比對 23 3.1.2 視黃醛胺基酸空間命名法 23 第二節 吸收光譜 29 3.2.1 HsBR突變之吸收光譜 29 3.2.2 HwBR突變之吸收光譜 31 3.2.3 HsBR與HwBR D2突變吸收光譜之比較 33 3.2.4 HsBR與HwBR H1突變吸收光譜之比較 35 3.2.5 HsBR與HwBR V2突變吸收光譜之比較 37 第三節 D2、H1、V2氫離子運輸功能性測試 41 3.3.1 光電流訊號 41 3.3.2 HsBR與HwBR D2突變之光電流訊號比較 41 3.3.3 HsBR與HwBR H1突變之光電流訊號比較 43 3.3.4 HsBR與HwBR V2突變之光電流訊號比較 44 第四節 光週期 47 3.4.1 HsBR與其突變之光週期比較 47 3.4.2 HwBR與其突變之光週期比較 49 第四章 總結與討論 52 第一節 保守胺基酸對於蛋白質功能的影響 52 第二節 TRYPTOPHAN的螢光對於光週期的影響 53 第五章 未來展望 55 第六章 參考文獻 56 | |
| dc.language.iso | zh-TW | |
| dc.subject | 色胺酸 | zh_TW |
| dc.subject | 氫視紫質 | zh_TW |
| dc.subject | 視黃醛結合袋 | zh_TW |
| dc.subject | 發光基團 | zh_TW |
| dc.subject | Haloquadratum walsbyi | zh_TW |
| dc.subject | Haloquadratum walsbyi | en |
| dc.subject | bacteriorhodopsin | en |
| dc.subject | retinal binding pocket | en |
| dc.subject | chromophore | en |
| dc.subject | tryptophan | en |
| dc.title | 視黃醛結合袋中保守色胺酸點突變對兩種氫視紫質酸耐受性能力之不同影響 | zh_TW |
| dc.title | Mutations of Conserved Tryptophans in the Retinal Binding Pocket Contribute Differently upon Acid-tolerance in Two Different Bacteriorhodopsins | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 106-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 梁博煌,徐駿森,李昆達,吳?承 | |
| dc.subject.keyword | 氫視紫質,視黃醛結合袋,發光基團,色胺酸,Haloquadratum walsbyi, | zh_TW |
| dc.subject.keyword | bacteriorhodopsin,retinal binding pocket,chromophore,tryptophan,Haloquadratum walsbyi, | en |
| dc.relation.page | 63 | |
| dc.identifier.doi | 10.6342/NTU201802830 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2018-08-13 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科技學系 | zh_TW |
| 顯示於系所單位： | 生化科技學系 | |
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