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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 何孟樵 | zh_TW |
| dc.contributor.advisor | Meng-Chiao Ho | en |
| dc.contributor.author | 葉敏琪 | zh_TW |
| dc.contributor.author | Min-Chi Yeh | en |
| dc.date.accessioned | 2023-06-20T16:22:44Z | - |
| dc.date.available | 2023-11-09 | - |
| dc.date.copyright | 2023-06-20 | - |
| dc.date.issued | 2023 | - |
| dc.date.submitted | 2023-02-09 | - |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/87615 | - |
| dc.description.abstract | 隨著冷凍電子顯微術的發展，許多過去無法利用X射線晶體學或核磁共振光譜學研究的蛋白質得以被解釋，也大大的提升了生物學家的視野。冷凍電子顯微術相較於其他研究蛋白質結構方法學有著四個優點。一，適用於分子量較大且複雜的蛋白聚合物；二，無需結晶；三，無需高濃度蛋白樣品；四，可看到動態變化。因此有越來越多的蛋白質結構藉由冷凍電子顯微術被解出，使其成為現今生物物理學界的主流。
在此篇論文中，我們藉由冷凍電子顯微術解開了兩種核蛋白的結構。其一為無活性的RAD51聚合物，在同源重組中扮演重要的角色。另一為Rpl23聚合物，而Rpl23為核糖體生合成中不可或缺的核糖體蛋白質。在研究RAD51的部分中，我們藉由冷凍電顯得到高解析度的ADP結合的RAD51聚合物，解釋了過去數十年中單分子實驗無法解釋的現象，也提出了當ATP水解時，RAD51聚合物的崩塌機制。而在研究Rpl23的部分中，我們藉由化學交叉鏈結、冷凍電顯和電腦模擬，揭開了Rpl23如何在核糖體生合成過程中被Bcp1和Rkm1保護。 | zh_TW |
| dc.description.abstract | With the development of Cryo-electron microscopy (Cryo-EM), more and more protein structures can be determined, which could not be resolved by X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy in the past, enhancing new insight into biophysical studies. Compared to the other structural determination methods, cryo-EM has four advantages: 1) appropriate for protein complex or marcoprotein, 2) no crystallization, 3) relatively low concentration of protein sample, and 4) the observation of protein dynamics. Hence, more and more structures of proteins or protein complexes can be determined via cryo-EM, leading it to a mainstream method in the biophysical field these days.
In this dissertation, I determined two nucleoprotein structures by cryo-EM. One is RAD51-nucleopfilament, the key player in homologous recombination, the other is Rpl23 protein complex, the essential ribosomal protein (r-protein) during ribosome biogenesis. In the RAD51 section, we determine the high resolution of ADP-bound RAD51 filament to explain the ambiguous phenomena observed in single molecular experiments for decades and propose the collapsing mechanism during ATP hydrolysis. In the Rpl23 section, we combined chemical-crosslinked, cryo-EM, and computational simulation to reveal how Rpl23 is protected by both Bcp1 and Rkm1 during ribosome biogenesis process. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2023-06-20T16:22:44Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2023-06-20T16:22:44Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員會審定書 i
誌謝 ii 中文摘要 iii Abstract iv Chapter 1. Cryo-EM study of the disassembly-competent RAD51-ADP filament unveils a unique two-stranded filament in RAD51 filament dynamics 1 A. 中文摘要 1 B. Abstract 2 C. List of appendixes 4 D. List of figures 5 E. Literature review 7 1. DNA double-strand break (DSB) 7 2. Homologous recombination (HR) 8 3. The initial model of homologous recombination 9 4. The original model of double-strand-break repair (DSBR) recombination 12 5. The synthesis-dependent strain annealing (SDSA) of homologous recombination 14 6. The function of recombinase in homologous recombination 15 7. The function, and activity of RAD51 recombinase 16 8. The regulator of RAD51 18 F. Research introduction 19 G. Results 22 1. Determination of hRAD51-ADP filament structure at 3.1 Å resolution by cryo-EM 22 2. Local conformation changes of the nucleotide-binding pocket result in extension of the hRAD51 filament 24 3. ADP state dislodges L1 and L2 loops from DNA triplet interaction 26 4. Structural transition between one-stranded ATP filament and two-stranded ADP filament monitored by ATP-chase and time-resolved CryoEM 27 5. The proposed collapsing mechanism for ATP-ADP structural transition 30 H. Materials and Methods 33 1. hRAD51 protein engineering, expression, and purification 33 2. Cryo-EM sample preparation and data collection 33 3. Image processing and helical reconstruction 34 4. Structural transition monitored by ATP chase and time-resolved Cryo-EM 35 I. Discussion 37 Chapter 2. Cryo-EM study of the protection mechanism of Bcp1/Rpl23/Rkm1 complex in ribosomal biogenesis 67 A. 中文摘要 67 B. Abstract 68 C. List of appendixes 69 D. List of figures 69 E. List of tables 70 F. Literature review 71 1. Saccharomyces cerevisiae 71 2. The complexity of ribosome and rRNA 72 3. Ribosome Biogenesis 73 4. The processing of precursor rRNA in eukaryotes 74 5. The maturation process of pre-40S subunit from 90S pre-ribosomal particles 75 6. The maturation process of pre-60S subunit from 90S pre-ribosomal particles. 76 7. Nuclear export of pre-ribosomal subunits 77 8. The transport of ribosomal protein by importin 78 9. The functions of r-proteins 79 10. The functions of ribosomal protein L23 (Rpl23) 80 11. The chaperone of ribosomal protein 81 12. The functions of yeast BRCA2 and CDKN1A interacting protein (Bcp1) 82 13. The function of Ribosomal lysine N-methyltransferase 1 (Rkm1) 83 G. Research introduction 84 H. Results 86 1. Bcp1 and Rkm1 coordinate the stability of Rpl23 86 2. The structure of Bcp1/Rpl23 binary complex cannot be determined 87 3. The structure of Bcp1, Rkm1, and Rpl23 ternary complex 88 I. Materials and Methods 90 1. Expression and purification of recombinant His-Bcp1, Rpl23, and His-Rkm1 protein 90 2. Cross-linking reactions of Bcp1/Rpl23/Rkm1 complex 91 3. Cryo-EM sample preparation and data collection 92 4. Image processing 92 5. Computational simulation 93 J. Discussions 94 Reference 116 | - |
| dc.language.iso | en | - |
| dc.subject | Rpl23 | zh_TW |
| dc.subject | 冷凍電子顯微技術 | zh_TW |
| dc.subject | RAD51 | zh_TW |
| dc.subject | 同源重組 | zh_TW |
| dc.subject | 核糖體生合成 | zh_TW |
| dc.subject | RAD51 | en |
| dc.subject | Cryo-EM | en |
| dc.subject | Ribosome biogensis | en |
| dc.subject | Rpl23 | en |
| dc.subject | Homologous recombination | en |
| dc.title | 藉由冷凍電顯技術研究核蛋白結構 | zh_TW |
| dc.title | Structural studies of nucleoproteins by Cryo-EM | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 111-1 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.oralexamcommittee | 蕭超隆;冀宏源;梁博煌;羅凱尹 | zh_TW |
| dc.contributor.oralexamcommittee | Chiao-Long Hsiao;Hung-Yuan Chi;Po-Huang Liang;Kai-Yin Lo | en |
| dc.subject.keyword | 冷凍電子顯微技術,RAD51,同源重組,Rpl23,核糖體生合成, | zh_TW |
| dc.subject.keyword | Cryo-EM,RAD51,Homologous recombination,Rpl23,Ribosome biogensis, | en |
| dc.relation.page | 136 | - |
| dc.identifier.doi | 10.6342/NTU202300298 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2023-02-09 | - |
| dc.contributor.author-college | 生命科學院 | - |
| dc.contributor.author-dept | 生化科學研究所 | - |
| dc.date.embargo-lift | 2028-02-01 | - |
| 顯示於系所單位： | 生化科學研究所 | |
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