請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/1330
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 鄭原忠 | |
dc.contributor.author | Shou-Ting Hsieh | en |
dc.contributor.author | 謝守庭 | zh_TW |
dc.date.accessioned | 2021-05-12T09:36:32Z | - |
dc.date.available | 2018-08-21 | |
dc.date.available | 2021-05-12T09:36:32Z | - |
dc.date.copyright | 2018-08-21 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-08-18 | |
dc.identifier.citation | [1] Govindjee. Adventures with cyanobacteria: a personal perspective. Front. Plant Sci., 2:1–17, 2011.
[2] Robert E. Blankenship. Molecular mechanisms of photosynthesis. Blackwell Science Ltd, Oxford, UK, 2008. [3] Jon Nield and James Barber. Refinement of the structural model for the Photosystem II supercomplex of higher plants. Biochim. Biophys. Acta - Bioenerg., 1757:353– 361, 2006. [4] Xuepeng Wei, Xiaodong Su, Peng Cao, Xiuying Liu, Wenrui Chang, Mei Li, Xinzheng Zhang, and Zhenfeng Liu. Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution. Nature, 534:69–74, 2016. [5] X. Pan, Z. Liu, M. Li, and W. Chang. Architecture and function of plant light-harvesting complexes II. Curr. Opin. Struct. Biol., 23:515–525, 2013. [6] Doran I.G. Bennett, Kapil Amarnath, and Graham R. Fleming. A structure-based model of energy transfer reveals the principles of light harvesting in photosystem II supercomplexes. J. Am. Chem. Soc., 135:9164–9173, 2013. [7] S Vasil’ev, P Orth, A Zouni, T G Owens, and D Bruce. Excited-state dynamics in photosystem II: insights from the x-ray crystal structure. Proc Natl Acad Sci U S A, 98:8602–8607, 2001. [8] Grzegorz Raszewski, Wolfram Saenger, and Thomas Renger. Theory of optical spectra of photosystem II reaction centers: Location of the triplet state and the identity of the primary electron donor. Biophys. J., 88:986–998, 2005. [9] Stefano Caffarri, Tania Tibiletti, Robert Jennings, and Stefano Santabarbara. A comparison between plant Photosystem I and Photosystem II architecture and functioning. Curr. Protein Pept. Sci., 15:296–331, 2014. [10] Allison M L van de Meene, Martin F Hohmann-Marriott, Wim F J Vermaas, and Robert W Roberson. The three-dimensional structure of the cyanobacterium Synechocystis sp. PCC 6803. Arch. Microbiol., 184:259–270, 2006. [11] Jacqueline Olive, Ghada Ajlani, Chantal Astier, Michel Recouvreur, and Claudie Vernotte. Ultrastructure and light adaptation of phycobilisome mutants of Synechocystis PCC 6803. Biochim. Biophys. Acta (BBA)-Bioenergetics, 1319:275–282, 1997. [12] Tihana Mirkovic, Evgeny E. Ostroumov, Jessica M. Anna, Rienk Van Grondelle, Govindjee, and Gregory D. Scholes. Light absorption and energy transfer in the antenna complexes of photosynthetic organisms. Chem. Rev., 117:249–293, 2017. [13] Yasufumi Umena, Keisuke Kawakami, Jian Ren Shen, and Nobuo Kamiya. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9Å. Nature, 473:55– 60, 2011. [14] Lu Zhang, Daniel Adriano Silva, Houdao Zhang, Alexander Yue, Yijing Yan, and Xuhui Huang. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre. Nat. Commun., 5:1–9, 2014. [15] Elisabet Romero, Ivo H M Van Stokkum, Vladimir I. Novoderezhkin, Jan P. Dekker, and Rienk Van Grondelle. Two different charge separation pathways in photosystem II. Biochemistry, 49:4300–4307, 2010. [16] Vladimir I Novoderezhkin, Elisabet Romero, Jan P Dekker, and Rienk van Grondelle. Multiple charge-separation pathways in Photosystem II: Modeling of transient absorption kinetics. ChemPhysChem, 12:681–688, 2011. [17] Elisabet Romero, Bruce A Diner, Peter J Nixon, Wiliam J Coleman, and Jan P Dekker. Mixed exciton–charge-transfer states in photosystem II: Stark spectroscopy on site-directed mutants. Biophys. J., 103:185–194, 2012. [18] Bart Van Oort, Marieke Alberts, Silvia De Bianchi, Luca Dall’Osto, Roberto Bassi, Gediminas Trinkunas, Roberta Croce, and Herbert Van Amerongen. Effect of antenna-depletion in photosystem II on excitation energy transfer in Arabidopsis thaliana. Biophys. J., 98:922–931, 2010. [19] Emilie Wientjes, Herbert van Amerongen, and Roberta Croce. Quantum yield of charge separation and fluorescence in photosystem II of green plants. J. Phys. Chem. B, 117:11200–11208, 2013. [20] Nathan Nelson and Wolfgang Junge. Structure and energy transfer in photosystems of oxygenic photosynthesis. Annu. Rev. Biochem., 84(1):659–683, 2015. [21] William W. Adams, Barbara Demmig-Adams, Klaus Winter, and Ulrich Schreiber. The ratio of variable to maximum chlorophyll fluorescence from photosystem II, measured in leaves at ambient temperature and at 77K, as an indicator of the photon yield of photosynthesis. Planta, 180:166–174, 1990. [22] Vladimir I. Novoderezhkin, Elena G. Andrizhiyevskaya, Jan P. Dekker, and Rienk Van Grondelle. Pathways and timescales of primary charge separation in the photosystem II reaction center as revealed by a simultaneous fit of time-resolved fluorescence and transient absorption. Biophys. J., 89:1464–1481, 2005. [23] Yutaka Shibata, Shunsuke Nishi, Keisuke Kawakami, Jian Ren Shen, and Thomas Renger. Photosystem II does not possess a simple excitation energy funnel: Time-resolved fluorescence spectroscopy meets theory. J. Am. Chem. Soc., 135:6903– 6914, 2013. [24] L Konermann and A. R. Holzwarth. Analysis of the absorption spectrum of photosystem II reaction centers: temperature dependence, pigment assignment, and inhomogeneous broadening. Biochemistry, 35:829–42, 1996. [25] Raoul N Frese, Marta Germano, Frank L de Weerd, Ivo H M van Stokkum, Anatoli Ya Shkuropatov, Vladimir a Shuvalov, Hans J van Gorkom, Rienk van Grondelle, and Jan P Dekker. Electric field effects on the chlorophylls, pheophytins, and beta-carotenes in the reaction center of photosystem II. Biochemistry, 42:9205–9213, 2003. [26] ML Groot, JP Dekker, R van Grondelle, FTH Den Hartog, and S Völker. Energy transfer and trapping in isolated photosystem II reaction centers of green plants at low temperature. A study by spectral hole burning. J Phys Chem, 3654:11488–11495, 1996. [27] Gunther H Schatz, Helmut Brock, and Alfred R Holzwarth. Picosecond kinetics of fluorescence and absorbance changes in photosystem II particles excited at low photon density. Proc. Natl. Acad. Sci. U. S. A., 84:8414–8, 1987. [28] Günther H Schatz, Helmut Brock, and Alfred R Holzwarth. Kinetic and energetic model for the primary processes in Photosystem II. Biophys. J., 54:397–405, sep 1988. [29] Jan P. Dekker and Rienk Van Grondelle. Primary charge separation in photosystem ii. Photosynthesis Research, 63:195–208, 2000. [30] Yusuke Yoneda, Tetsuro Katayama, Yutaka Nagasawa, Hiroshi Miyasaka, and Yasufumi Umena. Dynamics of excitation energy transfer between the subunits of Photosystem II dimer. J. Am. Chem. Soc., 138:11599–11605, 2016. [31] Ahmed Mohamed, Ryo Nagao, Takumi Noguchi, Hiroshi Fukumura, and Yutaka Shibata. Structure-based modeling of fluorescence kinetics of photosystem II: relation between its dimeric form and photoregulation. J. Phys. Chem. B, 120:365–376, 2016. [32] Makio Yokono, Ryo Nagao, Tatsuya Tomo, and Seiji Akimoto. Regulation of excitation energy transfer in diatom PSII dimer: How does it change the destination of excitation energy? Biochim. Biophys. Acta (BBA)-Bioenergetics, 1847:1274–1282, 2015. [33] Koen Broess, Gediminas Trinkunas, Chantal D. Van Der Weij-De Wit, Jan P Dekker, Arie Van Hoek, and Herbert Van Amerongen. Excitation energy transfer and charge separation in photosystem II membranes revisited. Biophys. J., 91:3776–3786, 2006. [34] Thomas Renger and Frank Müh. Understanding photosynthetic light-harvesting: a bottom-up theoretical approach. Phys. Chem. Chem. Phys., 15:3348–3371, 2013. [35] Thomas Renger, Volkhard May, and Oliver Ku. Ultrafast excitation energy transfer dynamics in photosynthetic pigment-protein complexes. Phys. Rep., 343:137–254, 2001. [36] A Davydov. Theory of molecular excitons. Springer, 2013. [37] Mino Yang and Graham R Fleming. Influence of phonons on exciton transfer dynamics: comparison of the Redfield, Forster, and modified Redfield equations. Chem. Phys., 275:355–372, 2002. [38] M. E. Madjet, A. Abdurahman, and T. Renger. Intermolecular coulomb couplings from ab initio electrostatic potentials: Application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers. J. Phys. Chem. B, 110:17268–17281, 2006. [39] Julia Adolphs, Frank Müh, Mohamed El Amine Madjet, and Thomas Renger. Calculation of pigment transition energies in the FMO protein: From simplicity to complexity and back. Photosynth. Res., 95:197–209, 2008. [40] J Adolphs, F Muh, Me-a Madjet, Marcel Schmidt am Busch, and Thomas Renger. Structure-based calculation of optical spectra of Photosystem I suggest an asymmetric light-harvesting process. J. Am. Chem. Soc., 132:3331–3343, 2010. [41] M. E. Madjet, A. Abdurahman, and T. Renger. Intermolecular coulomb couplings from ab initio electrostatic potentials: Application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers. J. Phys. Chem. B, 110:17268–17281, 2006. [42] Brent P Krueger, Gregory D Scholes, and Graham R Fleming. Calculation of couplings and energy-transfer pathways between the pigments of LH2 by the ab initio transition density cube method. J. Phys. Chem. B, 102:5378–5386, 1998. [43] Thomas Renger, Mohamed El-Amine Madjet, Marcel Schmidt Am Busch, Julian Adolphs, and Frank Müh. Structure-based modeling of energy transfer in photosynthesis. Photosynth. Res., 116:367–388, 2013. [44] Gregory D Scholes, Carles Curutchet, Benedetta Mennucci, Roberto Cammi, and Jacopo Tomasi. How solvent controls electronic energy transfer and light harvesting. J. Phys. Chem. B, 111:6978–6982, 2007. [45] David Chandler. Introduction to modern statistical mechanics. New York, 1987. [46] Stéphanie Valleau, Alexander Eisfeld, and Alán Aspuru-Guzik. On the alternatives for bath correlators and spectral densities from mixed quantum-classical simulations. J. Chem. Phys., 137, 2012. [47] Vladimir I Novoderezhkin, Danielis Rutkauskas, and Rienk van Grondelle. Dynamics of the emission spectrum of a single LH2 complex: interplay of slow and fast nuclear motions. Biophys. J., 90:2890–2902, 2006. [48] Grzegorz Raszewski and Thomas Renger. Light harvesting in photosystem II core complexes is limited by the transfer to the trap: Can the core complex turn into a photoprotective mode? J. Am. Chem. Soc., 130:4431–4446, 2008. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/handle/123456789/1330 | - |
dc.description.abstract | 光合作用是地球上生物生存裡非常重要的過程。它開始於光合收 光複合體(LHC),收集太陽光並將能量傳給反應中心(RCs)。作為 氧氣生成引擎的光系統 II(PSII)核心複合體是關鍵的光合作用複合 體之一。PSII 核心複合體是一個對稱二聚體,它包含四個天線複合體
(CP43 和 CP47)和兩個反應中心(RC)。要了解這種複雜的光合作用 複合體中的能量傳輸需要有效的理論模型,這樣的模型可以忠實地再 現系統中的激發態能量轉移過程。在這項工作中,我們基於先前的分 子動力學(MD)模擬研究結果提出了 PSII 核心複合體中激發態能量轉 移的有效模型並根據 modified Redfield theory 計算激發態之間能量轉移 的速率常數。它描述了 297 K 時 CP47、CP43 以及 RC 的吸收光譜以及 PSII 中 37 個發色團之間的全激發能量轉移動力學。此外,在我們的模 型中,也考慮了兩種主要電荷分離途徑 PD1 途徑和 ChlD1 途徑。我們 發現在 PSII 核心複合物的單體中,從 CP43(CP47)到 CP47(CP43) 的激發態能傳遞過程最有可能通過 RC。此外,我們發現 CP47 有作為 能量調節器的功能,它可以傳遞單體之間的激發態能量,並且當兩個 RC 中有一個在關閉的狀態時,使得 PSII 核心複合物保持高效率的電 荷轉移。最後,我們發現 CLA625 可能是兩種 PSII 核心複合物單體之 間能量傳遞的橋樑。我們的結果提出了 PSII 核心複合物構建成二聚體 結構的可能原因。此外,也為理解 PSII 核心複合體中的光捕獲提供了 新的見解,並且展示基於分子動力學模擬和量子化學計算的第一種原 理方法可以有效地用於闡明複雜光合複合體中光捕獲的動力學。 | zh_TW |
dc.description.abstract | The Photosystem II (PSII) core complex, the engine for oxygen genera- tion, is an important photosynthetic complex. It is a symmetric dimer that contains four antenna complexes (CP43 and CP47) and two reaction cen- ters (RCs). Understanding energy transport in such complex photosynthetic complexes requires theoretical effective models that can faithfully reproduce excitation energy transfer (EET) dynamics. In this work, we present an effec- tive model for EET in the PSII core complex based on a previous molecular dynamics (MD) simulation study. This model describes absorption spectra of CP47, CP43 and RC at 297 K as well as the full EET dynamics among the 74 chromophores in the PSII. Energy transfer rate constants are modeled based on the modified Redfield theory and two pathways of primary charge separation are treated phenomenologically in our model. We show that in the monomer, EET between two antenna complexes most likely occurs presum- ably through the RC. Also, the CLA625s are a bridge between monomers and cause the CP47s to become an energy regulator, which can transfer the excitation energy between monomers and maintain high efficiency of charge transfer when one of RCs is closed. CP47s as an energy regulator may be the reason for the dimeric structure of PSII core complex. Our model provides new insights towards the understanding of light harvesting in the PSII core complex and shows that a first principle approach based on MD simulations and quantum chemistry calculations can be effectively utilized to elucidate the dynamics of light harvesting in photosynthetic complexes. | en |
dc.description.provenance | Made available in DSpace on 2021-05-12T09:36:32Z (GMT). No. of bitstreams: 1 ntu-107-R05223127-1.pdf: 2265464 bytes, checksum: 6a43d546ea42fcc67026d1b6f9d34abb (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | 口試委員會審定書 iii
摘要 v Abstract vii 1 Introduction 1 1.1 Light harvesting and charge transfer of oxygenic photosynthesis .............. 1 1.1.1 The structure of photosystem II ................................................................ 2 1.1.2 Primary charge separation in the reaction center...................................... 5 1.1.3 Efficient EET and high quantum yield (QY) of charge transfer (CT)........... 6 1.1.4 Two models for energy and electron transfer in the PSII........................... 7 1.2 What is the role of the dimeric PSII core complex?...................................... 9 1.3 The outline of this work................................................................................ 9 2 Theoretical background 13 2.1 Structure-based model for photosynthetic complexes................................ 13 2.1.1 System-bath model and Frenkel exciton Hamiltonian................................ 13 2.1.2 Methods for estimation of the site energy................................................ 16 2.1.3 Methods for estimation of the excitonic coupling..................................... 19 2.2 Quantum correction of classical time correlation function from MD............ 20 2.2.1 Classical time correlation function from MD............................................. 21 2.2.2 Harmonic quantum correction of energy gap auto-correlation function............................................................................................................ 23 2.3 Simulation of the absorption spectrum ..................................................... 24 3 Effective models for RC, CP47 and CP43 29 3.1 Model Hamiltonian...................................................................................... 29 3.1.1 Pigment labels of PSII core complex........................................................ 29 3.1.2 Block Hamiltonians of PSII core complex................................................. 30 3.2 An effective model for RC ......................................................................... 34 3.2.1 Calibration of H_RC ................................................................................ 34 3.2.2 Frenkel exciton Hamiltonian of RC ......................................................... 36 3.3 Effective models for CP47 and CP43......................................................... 39 3.3.1 Calibration of H_CP47 and H_CP43 ........................................................ 39 3.3.2 FrenkelexcitonHamiltonianofCP47.......................................................... 40 3.3.3 FrenkelexcitonHamiltonianofCP43.......................................................... 42 4 Effective model for PSII core complex monomer (C1) 45 4.1 Master equation and rate constant matrix based on MRT.......................... 45 4.2 Exciton states and inter-complex excitonic couplings for PSII core complex monomer(C1)................................................................................................... 47 4.3 Excitation energy transfer dynamics in a monomer of PSII core complex(C1) 50 5 An effective model for PSII core complex (C2) 53 5.1 Exciton states and inter-monomer excitonic couplings for PSII core complex(C2) ................................................................................................... 53 5.2 Excitation energy transfer dynamics in PSII core complex(C2).................. 55 5.3 Mutation and a closed RC for PSII core complex....................................... 57 5.3.1 Excitation energy transfer for PSII core complex without CLA625s........ 58 5.3.2 Excitation energy transfer for PSII core complex with a closed RC........ 61 5.3.3 Excitation energy transfer for mutant PSII core complex with a closed RC................................................................................................................... 63 6 Conclusion 65 Bibliography 67 | |
dc.language.iso | en | |
dc.title | 光系統 II 核心複合體能量傳遞動力學的理論研究 | zh_TW |
dc.title | A Theoretical Study of Energy Transfer Dynamics in the Photosystem II Core Complex | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 許昭萍,朱修安 | |
dc.subject.keyword | 光系統 II 核心複合體,單體間能量傳遞,能量調節器, | zh_TW |
dc.subject.keyword | PSII core complex,inter-monomeric excitation energy transfer,energy regulator, | en |
dc.relation.page | 72 | |
dc.identifier.doi | 10.6342/NTU201802891 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2018-08-18 | |
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 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-107-1.pdf | 2.21 MB | Adobe PDF | 檢視/開啟 |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。