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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/54321完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 王勝仕(Sheng-Shih Wang) | |
| dc.contributor.author | Chih-Kai Chang | en |
| dc.contributor.author | 張智凱 | zh_TW |
| dc.date.accessioned | 2021-06-16T02:50:23Z | - |
| dc.date.available | 2025-12-31 | |
| dc.date.copyright | 2015-09-30 | |
| dc.date.issued | 2015 | |
| dc.date.submitted | 2015-07-14 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/54321 | - |
| dc.description.abstract | 近期研究顯示約50%的失明是白內障(cataract)所造成，而白內障是由於水晶體蛋白聚集(aggregation)使水晶體混濁(opacification)造成視力衰退。水晶體中含有豐富，高濃度的水晶體蛋白使光線能夠順利通過並聚焦於視網膜。然而，許多環境因素如暴露於紫外光環境及酸性環境都會引發水晶體蛋白去摺疊產生聚集，進而造成水晶體混濁。人類γD型水晶體蛋白(HγDC)富含於水晶體核心處，俱有173個殘基，並由兩結構對稱的區域所組成(N端及C端區域)。過去研究發現酸性環境能夠誘導HγDC形成類澱粉纖維(amyloid fibril)，且認為其聚集途徑可能與老化核型白內障(nuclear cataract)的形成有關，然而，其類澱粉纖維形成的機制目前尚不明確。 本研究利用分子動力學模擬(molecular dynamics simulations)及生物資訊預測軟體(bioinformatics tools)探討HγDC於酸性環境下的結構變化及可能的類澱粉纖維形成途徑。根據吾人結果，HγDC在酸性環境下出現顯著的結構擾動，尤其以C端區域之擾動較為明顯；主成分分析(principal components analysis, PCA)之結果顯示HγDC在酸性環境下出現較為明顯之與觸發區域置換(domain swapping)聚集機制相關的區域間旋轉現象；在酸性環境下，吾人發現C端區域上的原態鹽橋對(native salt-bridge)Asp96-Arg151由於Asp96的質子化因素減弱其間的鹽橋作用力；此外，模擬過程中HγDC的二級結構在殘基N160至G164出現延伸之β-strand結構，其與Glu119-Arg162間的靜電作用力減弱與Asp107-Arg168的原態鹽橋作用力隨模擬時間之變化有相當明顯的關聯性；而透過分子對接模擬，吾人發現motif-4參與了許多分子間作用力。吾人相信此研究之結果可讓研究者更了解HγDC之結構轉變及類澱粉纖維形成，並且期望能夠啟發研究人員發展更有效之預防白內障方法。 | zh_TW |
| dc.description.abstract | Recent evidence indicates that approximately 50% of blindness is caused by cataract, a well-known disease of the eye lens related to protein aggregation. The high concentration of well-ordered crystallin proteins distributed throughout the entire eye lens retains the transparency of the lens. Unfortunately, several factors including the exposure of ultraviolet irradiation and possibly acidic conditions may induce the unfolding and/or aggregation of the crystallin proteins, eventually leading to lens opacification. Human γD-crystallin (HγDC), a 173 residue structural protein com-posed of two structurally homologous domains (N-terminal and C-terminal domains), is abundant in the nucleus of the human eye lens. Previous studies have demonstrated that acidic conditions may induce the formation of amyloid fibrils in HγDC and that this aggregation pathway is likely to be related to the initiation of age-related nuclear cataract. However, the detailed mechanism of fibril formation remains elusive. In this work, the structural alteration and the possible amyloid-fibril formation pathway of HγDC at acidic condition was examined on the molecular level by molecular dynamics (MD) sim-ulations and bioinformatics tools. According to our results, a significant structural fluctuation was found in HγDC under acidic conditions, especially in the C-terminal domain. Principal components analysis (PCA) revealed a stronger inter-domain rotation under acidic condition, which supports the hypothesis of the domain-swapping aggregation mechanism. Furthermore, the native salt-bridge interaction between Asp96-Arg151 on the C-terminal domain was found to diminish under the acidic conditions due to the protonation of Asp96. In addition, the weakening of electrostatic inter-action between Glu119-Arg162 and the regaining of Asp107-Arg168 native salt-bridge interaction after 100 ns simulation time were coincided with an extention of beta-strand from the region en-compassing residues N160 to G164. The docking simulation results suggest that motif-4 is mainly involved in the inter-molecular interaction. We believe the outcome from this work provides detailed insights into the structural transition leading to amyloid-fibril formation of HγDC. Moreover, the information obtained herein would definitely contribute to the development of effective ways to prevent cataract. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T02:50:23Z (GMT). No. of bitstreams: 1 ntu-104-R02524027-1.pdf: 17869252 bytes, checksum: c4c9d8b85ff328a5de752e872e1971c5 (MD5) Previous issue date: 2015 | en |
| dc.description.tableofcontents | 誌謝 I 中文摘要 II Abstract III 目錄 V 圖目錄 VIII 表目錄 XI 第一章 緒論 1 1.1 研究動機 1 1.2 章節概述 2 第二章 文獻回顧 3 2.1 蛋白質聚集(Protein aggregation) 3 2.1.1 蛋白質聚集途徑 8 2.1.2 蛋白質聚集形態(morphology) 9 2.1.3 以區域置換(domain swapping)方式產生蛋白質聚集 11 2.2 白內障(Cataract) 14 2.2.1 水晶體 14 2.2.2 白內障成因 16 2.2.3 白內障種類 19 2.2.4 白內障治療方法 22 2.3 水晶體蛋白(crystallin) 24 2.3.1 α型水晶體蛋白 25 2.3.2 βγ型水晶體蛋白 26 2.3.3 人類γD型水晶體蛋白(Human γD crystallin，HγDC) 28 2.4 電腦模擬(computer simulations) 37 2.4.1 分子動力學模擬(molecular dynamics simulations) 37 2.4.2 蛋白質對接模擬(protein docking simulations) 43 2.4.3 生物資訊軟體 50 2.5 模擬分析方法原理介紹 54 2.5.1 方均根變異(Root mean square deviation, RMSD)分析 54 2.5.2 方均根擾動(Root mean square fluctuation, RMSF)分析 54 2.5.3 原態接觸(Native contact)分析 55 2.5.4 蛋白質二級結構分析(Dictionary of protein secondary structure, DSSP) 55 2.5.5 主成分分析(Principal components analysis, PCA) 57 2.5.6 區域間旋轉分析(Inter-domain rotation analysis) 59 第三章 實驗儀器與步驟 62 3.1 模擬系統與軟體 62 3.1.1 模擬系統 62 3.1.2 模擬軟體 62 3.2 分子動力學模擬及數據分析 63 3.2.1 HγDC原態結構取得 63 3.2.2 Gromacs模擬流程 63 3.2.3 Root Mean Square Deviation (RMSD)分析 64 3.2.4 Root Mean Square Fluctuation (RMSF)分析 65 3.2.5 Native Contact分析 65 3.2.6 離子與蛋白質間交互作用分析 66 3.2.7 氫鍵作用力分析 66 3.2.8 鹽橋作用力(Salt-bridge interaction)分析 67 3.2.9 DSSP二級結構預測分析 67 3.2.10 主成分分析(Principal components analysis) 68 3.2.11 區域間旋轉分析(Inter-domain rotation analysis) 68 3.3 生物資訊預測軟體(Bioinformatics prediction tools) 71 3.4 蛋白質－蛋白質對接模擬(Protein-protein docking simulations) 73 3.4.1 ZDOCK[133] 73 3.4.2 RDOCK[140] 73 3.4.3 FiberDock[132, 138] 74 3.4.4 RosettaDock[131] 75 3.4.5 分子對接動力學模擬 78 3.4.6 蛋白質分子間作用力分析 78 第四章 實驗結果與討論 80 4.1 HγDC在中性及酸性環境下的整體結構變化 80 4.1.1 RMSD分析結果 80 4.1.2 原態接觸分析結果 81 4.1.3 主成分分析結果 82 4.2 探討HγDC結構不穩定區域及其不穩定原因 84 4.2.1 HγDC個別區域之原態接觸分析 84 4.2.2 離子與蛋白質間交互作用分析 87 4.2.3 鹽橋作用力於酸性環境下對HγDC結構穩定性之影響 89 4.2.4 HγDC結構擾動分析 97 4.2.5 以生物資訊軟體預測HγDC的類澱粉聚集熱點區域 98 4.2.6 HγDC二級結構分析 99 4.3 推測HγDC可能的聚集機制 102 4.3.1 區域間旋轉分析 102 4.3.2 剛體對接 104 4.3.3 剛體對接結果修飾 105 4.3.4 對接結構作用力分析 106 第五章 結論與建議 109 5.1 結論 109 5.2 建議 112 Reference 113 | |
| dc.language.iso | zh-TW | |
| dc.subject | 人類γD型水晶體蛋白 | zh_TW |
| dc.subject | 類澱粉纖維 | zh_TW |
| dc.subject | 酸性環境 | zh_TW |
| dc.subject | 蛋白質聚集 | zh_TW |
| dc.subject | 分子動力學模擬 | zh_TW |
| dc.subject | 人類γD型水晶體蛋白 | zh_TW |
| dc.subject | 類澱粉纖維 | zh_TW |
| dc.subject | 酸性環境 | zh_TW |
| dc.subject | 蛋白質聚集 | zh_TW |
| dc.subject | 分子動力學模擬 | zh_TW |
| dc.subject | Human γD-crystallin | en |
| dc.subject | Molecular dynamics (MD) simulations | en |
| dc.subject | Protein aggregation | en |
| dc.subject | Acidic condition | en |
| dc.subject | Amyloid fibril | en |
| dc.subject | Human γD-crystallin | en |
| dc.subject | Molecular dynamics (MD) simulations | en |
| dc.subject | Protein aggregation | en |
| dc.subject | Acidic condition | en |
| dc.subject | Amyloid fibril | en |
| dc.title | 以電腦模擬方式探討人類γD型水晶體蛋白之可能聚集機制 | zh_TW |
| dc.title | Investigating the Possible Aggregation Mechanism of Human γD-Crystallin by Computer Simulations | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 103-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 賴進此(Jinn-Tsyy Lai),林達顯(Ta-Hsien Lin),王孟菊(Meng-Jiy Wang),吳宛儒(Wan-Ru Wu),廖思婷(Shih-Ting Liaw) | |
| dc.subject.keyword | 人類γD型水晶體蛋白,分子動力學模擬,蛋白質聚集,酸性環境,類澱粉纖維, | zh_TW |
| dc.subject.keyword | Human γD-crystallin,Molecular dynamics (MD) simulations,Protein aggregation,Acidic condition,Amyloid fibril, | en |
| dc.relation.page | 126 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2015-07-14 | |
| dc.contributor.author-college | 工學院 | zh_TW |
| dc.contributor.author-dept | 化學工程學研究所 | zh_TW |
| 顯示於系所單位： | 化學工程學系 | |
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