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標題: | 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 Investigating the Possible Aggregation Mechanism of Human γD-Crystallin by Computer Simulations |
作者: | Chih-Kai Chang 張智凱 |
指導教授: | 王勝仕(Sheng-Shih Wang) |
關鍵字: | 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, Human γD-crystallin,Molecular dynamics (MD) simulations,Protein aggregation,Acidic condition,Amyloid fibril, |
出版年 : | 2015 |
學位: | 碩士 |
摘要: | 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。 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. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/54321 |
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顯示於系所單位: | 化學工程學系 |
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