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研究生:朱文淵
研究生(外文):Wen-yuan Chu
論文名稱(外文):Alanine Scanning Mutagenesis of Aβ(17-42) Amyloid Fibril Stability by Molecular Dynamics Simulations
指導教授:蔡惠旭
指導教授(外文):Hui-Hsu Gavin Tsai
學位類別:碩士
校院名稱:國立中央大學
系所名稱:化學學系
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2015
畢業學年度:103
語文別:英文
論文頁數:78
中文關鍵詞:類澱粉蛋白分子動態模擬纖維穩定性丙胺酸
外文關鍵詞:amyloidMolecular dynamicsFibrillationstabilityalanine
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阿茲罕默症(Alzheimer’s disease)的主要特色是腦中有斑塊聚集沉澱,然後堆積在神經細胞膜上造成神經死亡。而這些斑塊聚集物主要是由乙型-類澱粉蛋白(Amyloid-)所組成。乙型-類澱粉蛋白纖維(Amyloid-fibril)因為錯誤折疊而自組裝聚集形成。由於目前並不完全清楚知道乙型-類澱粉蛋白聚集和穩定纖維的機制,所以找出穩定乙型-類澱粉蛋白纖維的因素是相當重要的議題。
我們利用生物實驗上常用的丙氨酸突變掃描法去探討乙型-類澱粉蛋白纖維穩定要素並使用全原子分子動態模擬來達成此實驗。為了探討胜肽之間的作用力,我們把各個胺基酸有系統性的突變為丙氨酸並藉由分子動態模擬做此實驗。我們分析二級結構,鹽橋(D23-K28)維持傾向,還有跟固態NMR解出結構做偏差比較的RMSD和RMSF數值。
我們模擬結果為野生型(wild type)和突變物(mutants)在C端都會翹起。普遍來說,變異物的strands 2 相較於strands 1是穩定的。甘氨酸是-sheet結構的破壞者,在甘氨酸突變為丙氨酸的試驗中發現,大部分結果顯示出丙氨酸會增加突變區域二級結構的穩定性。另外在我們胺基酸交換位於strands 1和strands 2配對的實驗中發現,其模擬結果顯示和野生型一樣是穩定,因此我們認為胺基酸位於strands 1和strands 2配對的作用力可能是穩定乙型-類澱粉蛋白纖維的關鍵因素之一。在本研究中,系統性調查每個胺基酸側鏈的作用力和乙型-類澱粉蛋白纖維穩定的關係。

Alzheimer’s disease (AD) is characterized by the extracellular deposit of senile plaques in the brain. Senile plaques are mainly composed of the aggregated amyloid beta (Aβ) protein called amyloid. Amyloid fibrils are semi-ordered nanostructures as the result of self-assembly of proteins when they are misfolded under critical conditions. Due to the complexity of Aβ amyloids, the underlying biophysical mechanisms of formation and stability of amyloid fibril are still unclear. Therefore, it is crucial to determine the factors in stabilizing Aβ amyloid fibrils.
Motivated by Ala mutagenesis in biochemical research, we employed all-atom molecular dynamics simulations to investigate the relative stability of Aβ-fibril like oligomer and its mutants by alanine mutagenesis. To investigate the intra-peptide interactions, we simulated the structures of Aβ-fibril like oligomer with one of its residue is systemically mutated to Alanine by MD simulations. The secondary structure, salt-bridge between D23 and K28, RMSF and RMSD deviated from the solid-state NMR determined structure are analyzed.
Our results show wild type as well as most mutants have their C-terminal residues bent. In general, the strands 2 are less stable and strands 1 are relatively more stable. Gly residues are -sheet breaker. Ala mutagenesis of Gly residues generally enhances the -sheet propensity locally. Swapping the two packed residues on strands1 and 2 does not cause the instability of amyloid fibril indicating that the packing interactions are important in stabilizing amyloid fibril. Our study systemically investigates the roles of side chain of each residue on the stability of amyloid fibrils.

摘要 i
Abstract iii
致謝 v
Table of contents vi
List of Figures vi
List of Tables ix
Chapter 1 – Introduction 1
Chapter 2 – Computational Methods 7
Chapter 3 – Results and Discussion 11
3.1 Wild Type 15
3.2 Ala Mutagenesis of Odd-numbered Residues of Strands β1 18
3.3 Ala Mutagenesis of Even-numbered Residues of Strands β1 25
3.4 Ala Mutagenesis of Residues of Turn 30
3.5 Ala Mutagenesis of Even-numbered Residues of Strand β2 36
3.6 Ala Mutagenesis of Odd-numbered Residues of Strand β2 41
3.7 Mutants F19G/G38F and A21V/V36A: Swap the packed residues within β-sheet 48
Chapter 4 – Conclusion and Summary 54
References 56
Appendix A 62
Appendix B 63


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