抗菌胜肽資料庫分析及利用分子動態模擬法探討抗菌胜肽Indolicidin於生物膜上的行為

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姓名

蕭裕謙(Yu-chien Hsiao) 查詢紙本館藏

畢業系所

化學學系

論文名稱

抗菌胜肽資料庫分析及利用分子動態模擬法探討抗菌胜肽Indolicidin於生物膜上的行為
(Analysis of Antimicrobial Peptide Database and Molecular Dynamics Simulation of Antimicrobial Peptide, indolicidin in a water-membrane environment)

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摘要(中)

摘要
為了研究抗菌胜肽 (antimicrobial peptide) 的抗菌作用機制，我們的研究分別從三個不同方式進行: 抗菌蛋白資料庫的分析、全原子分子動態模擬Indolicidin (IL) 和膜的交互作用及利用平行淬煉分子動態法 (replica-exchange molecular dynamics, REMD)搭配implicit membrane model (GBSW model) 模擬Indolicidin及其類似物折疊及穿膜的機制。
從抗菌蛋白資料庫的分析中顯示，自然界中鹼性抗菌蛋白大都具有高密度淨正電荷的特性。分析的結果顯示，鹼性抗菌蛋白演化非完全增加帶正電荷胺基酸(Arg、Lys)的propensity，相反地是降低帶負電荷胺基酸(Asp、Glu)的propensity。此外，Trp的propensity也相當的高，這也暗示著Trp可能在抗菌胜肽的功能上扮演重要的角色。我們也依抗菌胜肽的二級結構，分析20種胺基酸的propensity，可供改善抗菌胜肽的研究作為參考。
利用全原子分子動態模擬法，我們探討IL-F89和POPC膜的交互作用，發現IL-F89對膜擾亂的程度較IL輕微，其中包括對膜厚的干擾以及秩序參數的改變，這些結果暗示為何IL-F89溶血性較IL的低; 溶血實驗顯示相同的趨勢。
利用REMD/GBSW的演算法，進行IL-A與IL-analogs (IL、IL-F89、IL-K7F89)單體系統的模擬，發現所有的系統皆無法單獨穿入膜內，都以吸附在膜上的形態存在，然而二級結構的生成(IL-A)也無助於穿膜。根據IL-analogs模擬的結果，我們也排除了幾種抗菌胜肽穿膜的可能路徑，例如:抗菌胜肽會直接穿入膜內而於膜內進行聚集。

摘要(英)

Abstract
To understand the action mechanism of antimicrobial peptides (AMP), our study employed three different means: (i). database analysis of antimicrobial peptides, (ii). all-atom molecular dynamics (MD) simulation of the interaction between Indolicidin (IL) and membrane and (iii). folding and membrane insertion of IL and its analogues by replica-exchange molecular dynamics (REMD) simulation using implicit membrane model (GBSW model).
Database analysis reveals that most naturally-occurring AMPs are cationic and own high density of net positive charges. However, the propensities of positively charged residues (Arg & Lys) are not particularly high; in contrast, the propensities of negatively charged residues (Asp & Glu) are significantly reduced. Moreover, the propensity of Trp is particularly high implying for the critical role of Trp in the antimicrobial action. In addition, we also analyzed the propensities of 20 amino acids in terms of available secondary structures giving the reference of AMP engineering research.
In all-atom MD simulation, we studied the interaction of IL-F89 peptide and POPC membrane. The result showed that IL-F89 has less impact on disordering the POPC membrane (e.g. membrane thickness and order parameter). This result hints for the lower hemolytic activity of IL-F89 than Il which is consistent with the trend of experimental observations.
Using REDM/GBSW, we simulated the folding and membrane insertion of IL, IL-A, IL-F89 & IL-K7F89 monomers. Simulation results showed that these peptides mainly stay at water-lipid interfaces. Moreover, the formation of ?-helix (IL-A) does not enhance its membrane insertion. These results exclude one possible pathway of IL-membrane insertion: IL is not able to insert into membrane alone and aggregates inside the membrane.

關鍵字(中)

★ 抗菌胜肽
★ 分子動態模擬

關鍵字(英)

★ molecular dynamics simulation
★ antimicrobial peptide

論文目次

總目錄
摘要 I
Abstract II
誌謝 III
總目錄 IV
圖目錄 VII
表目錄 IX
第一章緒論 1
1-1 抗菌胜肽簡述 1
1-1-1 抗菌胜肽的發展 1
1-1-2 抗菌胜肽的特色 2
1-1-3 抗菌胜肽的作用機制 3
1-2 Indolicidin的生物活性與作用機制 6
1-2-1 Indolicidin簡述 6
1-2-2 Indolicidin結構特性 7
1-2-3 Indolicidin抗菌與溶血的機制 7
1-2-4 Indolicidin的類似物對於抗菌與溶血的影響 8
1-2-5 結構(structure)的改變 9
1-2-6 疏水性(hydrophobicity)的改變 11
1-2-7 IL及IL-F89的生物活性 13
1-3 蛋白質結構與序列分析背景簡述 16
1-3-1 蛋白質結構特性 16
1-3-1-1 二級結構-螺旋狀結構 17
1-3-1-2 二級結構-平板狀結構 17
1-3-2 胺基酸序列特性 18
1-3-3 蛋白質結構與胺基酸序列來源 19
1-4 抗菌胜肽資料庫 20
1-5 研究動機 20
第二章計算方法 22
2-1 分子動態模擬 22
2-1-1 分子動態模擬的簡介與應用 22
2-1-2 分子力場 23
2-1-3 分子動態模擬原理 27
2-1-4 模擬系統初始設定 29
2-1-4-1 Periodic Boundary Conditions 29
2-1-4-2 Generalized Born Solvent Model ( GB model ) 30
2-1-4-3 Replica-exchange Molecular dynamics method 32
2-1-4-4 模擬系統概述 33
2-3 方向秩序參數(Order parameter) 36
2-4 Define Secondary Structure of Proteins (DSSP) 36
第三章結果與討論:抗菌胜肽資料庫的序列分析 40
3-1 抗菌胜肽資料庫的建立 40
3-2 抗菌胜肽長度及電荷分佈 42
3.3 胺基酸Propensity的計算 44
第四章結果與討論： 53
利用分子動態模擬探討IL衍生物於生物膜上的行為機制 53
4-1 IL-F89與生物膜交互作用行為的探討 55
4-1-1 IL-F89與生物膜的吸附行為 55
4-1-2 IL-F89與生物膜的穿膜行為 57
4-1-4 生物膜頭基分佈 61
4-1-4 膜排列整齊度探討 63
4-2 IL-A單體行為的探討 65
4-2-1 IL-A各種胺基酸於膜上的位置分佈 65
4-2-2 IL-A於膜環境的二級結構 67
4-2-3 IL-A於模擬與實驗環境中結構差異度 69
4-2-4 IL-A於水相與膜環境的位向 71
4-2-5 IL-A穿膜機制探討 72
4-2-6 IL-analogs與IL-A系統穿膜行為的差異 74
第五章總結 79
參考文獻 81
附錄：抗菌資料庫總覽(結構部分) 85
附錄：抗菌資料庫總覽(序列部分) 88

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指導教授

蔡惠旭(Hui-Hsu Tsai)

審核日期

2009-8-10

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