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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/55706完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 鄭原忠(Yuan-Chung Cheng) | |
| dc.contributor.author | Yu-Chun Chou | en |
| dc.contributor.author | 周俞均 | zh_TW |
| dc.date.accessioned | 2021-06-16T04:18:35Z | - |
| dc.date.available | 2015-09-03 | |
| dc.date.copyright | 2014-09-03 | |
| dc.date.issued | 2014 | |
| dc.date.submitted | 2014-08-19 | |
| dc.identifier.citation | [1] A. E. Blaurock and W. Stoeckenius. Structure of the purple membrane. Nat. New Biol., 233:152–154, 1971.
[2] F. Kienberger, C. Stroh, G. Kada, R. Moser, W. Baumgartner, V. Pastushenko, C. Rankl, U. Schmidt, H. Mu ̈ller, E. Orlova, C. LeGrimellec, D. Drenckhahn, D. Blaas, and P. Hinterdorfer. Dynamic force microscopy imaging of native mem- branes. Ultramicroscopy, 97:229–237, 2003. [3] H. Luecke, B. Schobert, H. T. Richter, J. P. Cartailler, and J. K. Lanyi. Structure of bacteriorhodopsin at 1.55 angstrom resolution. J. Mol. Biol., 291:899–911, 1999. [4] A. E. Blaurock. Bacteriorhodopsin:a trans0membrane pump containing α-helix. J. Mol. Biol., 93:139–158, 1975. [5] R. Henderson. The purple membrane from halobacterium halobium. Annu. Rev. Biophys. Bioeng., 6:87–109, 1977. [6] R. Henderson. The structure of the purple membrane from halobacterium halo- bium:analysis of the x-ray diffraction pattern. J. Mol. Biol., 93:123–138, 1975. [7] R. Henderson and P. N. T. Unwin. Three-dimensional model of purple membrane obtained by electron microscopy. Nature, 257:28–32, 1975. [8] G. I. King, P. C. Mowery, W. Stoeckenius, H. I. Crespi, and B. P. Schoenborn. Loca- tion of the chromophore in bacteriorhodopsin. Proc Natl. Acad. Sci., 77:4726–4730, 1980. [9] S. Trivedi, O. P. Chouhary, and J. Gharu. Different proposed applications of bacte- riorhodopsin. Rencent Pat DNA Gene, 5:35–40, 2011. [10] B. Becher and T. G. Ebrey. Evidence for chromophore-chromophore(exciton) inter- action in the purple membrane of halobacterium halobium. Biochem. Biophys. Res. Commun., 69:1–6, 1976. [11] M. P. Heyn, P. J. Bauer, and N. A. Dencher. A natural cd label to probe the structure of the purple membrane from halobacterium halobium by means of exciton coupling effects. Biochem. Biophys. Res. Commun., 67:897–903, 1975. [12] E. Karnaukhova, C. Vasileiou, A. Wang, N. Berona, K. Nakanishi, and B. Borhan. Circular dichroism of heterochromophoric and partially regenerated purple mem- brane: Search for exciton coupling. Chirality, 18:72–83, 2006. [13] J. Y. Cassim. Unique biphasic band shape of the visible circular dichroism of bac- teriorhodopsin in purple membrane. Biophys. J., 63:1432–1442, 1992. [14] D. D. Muccio and J. Y. Cassim. Interpretation of the absorption and circular dichroic spectra of oriented purple membrane films. Biophys. J., 26:427–440, 1979. [15] JR. Ignacio Tinoco. Theoretical aspects of optical activity, part two:polymers. Adv. Chem. Phys., 4:113–160, 1962. [16] S. Wu and M. A. El-Sayed. Cd spectrum of bacteriorhodopsin, best evidence against exciton model. Biophys.J., 60:190–197, 1991. [17] J. Frenkel. On the transformation of light inte heat in solids. i. Phys. Rev., 37:17–44, 1931. [18] C. N. Rafferty, J. Y. Cassim, and D. G. McConnell. Circular dichroism, optical rota- tory dispersion and absorption studier in the conformational of bovine rhodopsin in situ and solubilized with detergent. Biophys. Struct. Mechanism., 2:277–320, 1997. [19] B. Becher and T. G. Ebrey. Evidence for chromophore-chromophore (exciton) inter- action in the purple membrane of halobacterium halobium. Biochem. Biophys. Res. Commun., 69:1–6, 1976. [20] J. Reynolds and W. Stoeckenius. Molecular weight of bacteriorhosopsin solubilized in triton x-100. Proc. Natl. Acad. Sci., 74:2803–2804, 1977. [21] D.Rhinow,M.Imhof,I.Chizhik,R.P.Baumann,andN.Hampp.Structuralchanges in bacteriorhodopsin caused by two-photon-induced photobleaching. J. Phys. Chem. B, 116:7455–7462, 2012. [22] K. C. Ng and L. K. Chu. Effects of surfactants on purple membrane and bacte- riorhodopsin: solubilization or aggregation? J. Phys. Chem. B, 117:6241–6249, 2013. [23] G. Pescitelli and R. W. Woody. The exciton origin of the visible circular dichroism spectrum of bacteriorhodopsin. J. Phys. Chem B, 116:6751–6763, 2012. [24] N. Berova, P. L. Polavarapu, K. Nakanishi, and R. W. Woody. Comprehensive chi- roptical spectroscopy. Wiley Press, 2012. [25] N. Berova, K. Nakanishi, and R. W. Woody. Circular dichroism:principle and ap- plications. Wiley Press, 2000. [26] A. Rodger and B. Norden. Circular Dichroism and Linear Dichroism. Oxford Uni- versity Press, 1997. [27] G. D. Fasman. Circular Dichroism and the Conformational Analysis of Biomolecules. Spring Press, 1996. [28] D. A. Lightner and J. E. Gurst. Stereochemistry from Circular Dichroism Spec- troscopy. Wiley Press, 2000. [29] G. R. Loppnow and R. A. Mathies. Photochemicalhole-burning spectroscopy od bovine rhodopsin and bacteriorhodopsin. J. Phys. Chem., 96:737–745, 1992. [30] I.J.LeeandJ.K.Gillie.Photochemicalholeburninginbacteriorhodopsin.Chemical Physics Letters, 156:227–232, 1989. [31] D. Oesterhelt and B. Hess. Reverisble photolysis of the purple complet in the purple membrane of halobecterium halobium. Eur. J. Biochem., 37:316–326, 1973. [32] T. H. Bayburt, Y. V. Grinkova, and S. G. Sligar. Assembly of single bacteri- orhodopsin trimers in bilayer nanodiscs. Arch. Biochem. and Biophys., 450:215–222, 2006. [33] H. Yamashita, K. Voitchovsky, T. Uchihashi, S. Anroranz Contera, J. F. Ryan, and T. Ando. Dynamics of bacteriorhodopsin 2d crystal observed by high-speed atomic force microscopy. J. Struct. Biol., 184:153–158, 2009. [34] H. Yamashita, K. Inoue, M. Shibita, T. Uchihashi, J. Sasaki, H. Kandori, and T. Ando. Role of tirmer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy. J. Struct. Biol., 184:2–11, 2013. [35] L.O. Essen, R. Siegert, W. D. Lehmannn, and D. Oesterhelt. Lipid patches in mem- brane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex. Proc. Natl. Acad. Sci., 95:11673––11678, 1998. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/55706 | - |
| dc.description.abstract | 視紫質蛋白在細胞膜上會以三個單體組成一個擁有三轉軸(C3) 的三聚體單位,而三聚體會依循六角形晶格在二維平面上進行排列, 過去這種滿足前述排列(P3 對稱性)的視紫質蛋白質構造被稱之為紫 膜。在過去的圓二色光譜實驗中發現圓二色譜會對於紫膜結構的變化 十分敏感,由於圓二色譜的測量相較於其他測量結構的方法更方便、 便宜、快速,且實驗環境也更逼近於生物體中的溶液環境,因此我們 想要研究光譜和紫膜結構之間的關係,希望未來在利用光譜回推結構 上有更進一步的發展。
過去的實驗和計算已經証實紫膜在可見光範圍的的圓二色譜峰值 是來自於視紫質中發色團的貢獻,於是一開始的論文中我們便從最簡 單的三聚體單位開始,利用擁有動態微擾和靜態微擾的激子模型去計 算光譜,更同時改變發色團的躍遷偶極矩方向,去探討耦合值與內旋 強度(與圓二色譜成正比)和光譜變化之間的關聯性,在滿足 P3 對稱 性下的排列,我們可以透過比較光譜峰值以及對應的正負號去縮小可 能的視紫質排列構型。接下來我們增加模型中三聚體的數目到七個或 十九個去試圖模擬紫膜的聚集體,我們發現若使用蛋白質資料庫標號 為 1C3W 的 X 光結晶排列做為計算的構型,七個或十九的三聚體計算 光譜所求得的光譜峰值的正負號會恰好和實驗值相反,由於 X 光結晶 所提供的排列方式可能與紫膜實際上在溶液中的排列方式不同,再加 上在文獻上的高速原子力顯微鏡測量中展現了其它滿足 P3 對稱性但為 不同類型的排列方式,我們將計算模型中的三聚體同時進行旋轉來考 慮原子力顯微鏡中所提供的新構型,發現旋轉約 30 度的模型可以解釋 實驗光譜,並可以透過電子結構去探討旋轉角度和光譜變化之間的關 係,最後期許我們的研究可以為未來探討結構排列和光譜的關係提供 一些基礎。 | zh_TW |
| dc.description.abstract | The bacteriorhodopins (BR) assemble into ordered two-dimensional hexagonal crystalline patches called purple membrane (PM). The circular dichroism (CD) spectra is sensitive to its conformational change, and we try to use excitonic model to investigate the relationship between the structures of PM and CD spectra to obtain more information. First, we calculate the spectra of one BR trimer with dynamic disorder and static disorder, and change the angle of transition dipole to see the variation which is determined by rotational strength of each eigenstate and the sign of coupling. We can thus probe the possible angle of transition dipoles. Second, we expand the size of the system to model aggregated PM structure, including models with 7 and 19 bR trimers, respectively. By comparing with the biphasic pattern of experimental results, we propose a PM structure in solution with new arrangement of bR trimers different from the result of x-ray crystallography. We vary the distance between bR trimers and rotate the orientations of trimers, and aim to understand the variation in CD spectra through the electronic structures. We believe our research can provide additional useful viewpoints to construct relationship between molecular structures and CD spectra in PM systems. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T04:18:35Z (GMT). No. of bitstreams: 1 ntu-103-R01223167-1.pdf: 11852715 bytes, checksum: 6ddcf0a6d66df8173c18c3b1defb739d (MD5) Previous issue date: 2014 | en |
| dc.description.tableofcontents | 1 Introduction 1
1.1 Purple membrane ...................................................................... 1 1.2 Motivation.................................................................................. 3 2 Disordered exciton model for absorption and circular dichroism spectrum 5 2.1 Exciton model............................................................................ 5 2.2 Absorption spectrum ................................................................. 7 2.3 Circular dichroism ..................................................................... 8 3 BR Trimer 12 3.1 Structure and Chromophore arrangement.................................. 12 3.2 CD spectra and absorption spectra of trimer ..............................16 3.3 Orientation of transition dipole.................................................. 17 3.4 Dynamic disorder and static disorder......................................... 20 3.5 Lifetime broadening effect ........................................................ 21 3.6 Conclusion ................................................................................ 21 4 Cluster model of PM 25 4.1 Model........................................................................................ 25 4.2 CD spectrum and absorption spectrum...................................... 26 4.3 Conclusion ................................................................................ 27 5 Geometrical effect in CD spectra of PM 30 5.1 Introduction............................................................................... 30 5.2 Model......................................................................................... 31 5.3 CD spectrum ............................................................................. 32 5.4 Correlation diagram of inter-trimeric distance ............................32 5.5 Correlation diagram of orientation angle.................................... 34 5.6 Conclusion ................................................................................ 34 6 Conclusion 42 Bibliography 44 | |
| dc.language.iso | en | |
| dc.subject | 視紫質 | zh_TW |
| dc.subject | 紫膜 | zh_TW |
| dc.subject | P3 對稱性 | zh_TW |
| dc.subject | 聚集體 | zh_TW |
| dc.subject | 圓二色譜 | zh_TW |
| dc.subject | 內旋強度 | zh_TW |
| dc.subject | bacteriorhodopin | en |
| dc.subject | rotational strength | en |
| dc.subject | circular dichroism | en |
| dc.subject | aggregation | en |
| dc.subject | P3 symmetry | en |
| dc.subject | purple membrane | en |
| dc.title | 細菌視紫質的二維紫膜結構和圓二色譜之探討 | zh_TW |
| dc.title | Investigation of the relationship between the structure of purple membrane of bacteriorhodopsin and circular dichroism spectrum | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 102-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 金必耀(Bih-Yaw Jin),陸駿逸(Chun-Yi Lu) | |
| dc.subject.keyword | 視紫質,紫膜,P3 對稱性,聚集體,圓二色譜,內旋強度, | zh_TW |
| dc.subject.keyword | bacteriorhodopin,purple membrane,P3 symmetry,aggregation,circular dichroism,rotational strength, | en |
| dc.relation.page | 47 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2014-08-20 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 化學研究所 | zh_TW |
| 顯示於系所單位： | 化學系 | |
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