利用恆溫滴定微卡計與圓二色光譜儀探討鏈酶卵白素與核適體之鍵結機制

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李芃蓁(Peng-chen Lee) 查詢紙本館藏

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化學工程與材料工程學系

論文名稱

利用恆溫滴定微卡計與圓二色光譜儀探討鏈酶卵白素與核適體之鍵結機制
(Non-classical Thermodynamics, Binding Stoichiometry, and Structural Changes Associated with Streptavidin-Aptamer Binding)

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摘要(中)

本研究利用恆溫滴定微卡計(Isothermal Titration Calorimetry, ITC)與圓二色光譜儀(Circular Dichroism, CD)來探討鏈酶卵白素(Streptavidin, SA)與其核適體(aptamer)之間的作用行為。我們藉由調控SA與其核適體(St-1)結合之環境條件，包含在不同金屬離子種類、鹽濃度及溫度下，期望以ITC獲得熱力學資訊，並結合CD觀測二級結構之變化資訊，探討SA與其核適體(St-1)之間的辨識作用機制。
在熱力學的分析，SA與其核適體(St-1)結合反應的發生是由焓主導，表示此結合反應由靜電作用力主導。藉由鹽類的添加，希望能導致靜電遮蔽的效果，證明SA與St-1之結合反應確實為靜電作用力主導，但從ITC之結果發現，隨著鹽濃度的上升，SA與St-1的結合能力不僅未降低，而且SA與St-1結合之放熱量(焓)是增加的，此結果是與預期的結果相衝突的，因此吾人推測SA與St-1結合過程中，在不同鹽濃度下，應有伴隨著不同程度的SA之構型變化所導致的結果。所以利用CD去分析SA與St-1在結合過程中之二級結構的變化，從實驗結果是SA與St-1在結合過程中是有明顯伴隨著構型的改變，但是構型改變量卻不隨著鹽濃度的添加而有所改變。另外，從SA與St-1結合之熱容量變化(?Cp)之分析，顯示SA與St-1在結合過程中，其三級/四級結構變化量是隨著鹽濃度的添加而明顯增加，表示會造成SA與St-1的結合在不同鹽濃度下會有不同程度的整體構型變化，是由於環境中的水分子的排開程度扮演著很重要的關鍵。本研究還利用CD能觀測二級結構之特點，選擇在特定的波長下，測量不同濃度比之SA與St-1的二級結構變化程度，探討結構變化量與化學劑量比(stoichiometry, N)的關係，結果指出一個SA分子最多能結合兩個核適體分子，此結果與ITC之化學劑量比(N=2)相符。從以上的實驗結果，我們提出一個SA與St-1結合的模型，詳細地解釋兩者之間的辨識行為。更進一步地，藉由SA與St-1之結合機制的了解，本研究利用取代滴定法於ITC實驗，克服了ITC之偵測極限，並得到SA與biotin之結合常數。

摘要(英)

Aptamers are valuable for the discovery and application of new principals and designs of nucleic acid-ligand interactions. This study investigated the thermodynamics and conformational changes associated with the binding between streptavidin (SA) and its DNA aptamer under various temperatures and salt concentrations. The binding was enthalpy-driven with a large entropy cost. The binding association constant (Ka) was independent of the salt concentrations; however, enthalpy increased in conjunction with the salt concentration. The spectroscopic studies indicated that each SA tetramer bound a maximum of 2 aptamer molecules. The binding was accompanied with substantial conformational changes, which were insensitive to the variation of salt concentrations. These non-classical results indicate the prominent involvement of the binding-site hydration water molecules in SA-aptamer binding. We propose a salt-bridge swap model to explain the salt-independent Kd values. To maximize binding affinity, the electrostatic interactions within the proteins and those within the aptamer-Na+ counter ions exchange their partners, resulting in the observed structural changes and the possible release of hydration water molecules.

關鍵字(中)

★ 恆溫滴定微卡計
★ 核適體
★ 圓二色光譜儀
★ 鏈酶卵白素

關鍵字(英)

★ circular dichroism
★ aptamer
★ streptavidin
★ isothermal titration calorimetry

論文目次

目錄
中文摘要 i
Abstract iii
致謝 iv
目錄 v
圖目錄 viii
表目錄 xii
第一章緒論 1
第二章文獻回顧 3
2.1 核適體(aptamer) 3
2.1.1 核適體之介紹 3
2.1.2 Systematic Evolution of Ligands by Exponential Enrichments (SELEX) 5
2.1.3 核適體之應用 7
2.1.4 核適體與目標分子結合機制之研究 10
2.2 鏈酶卵白素(Streptavidin, SA) 17
2.2.1 鏈酶卵白素之介紹 17
2.2.2 鏈酶卵白素之結構 19
2.2.3 鏈酶卵白素和其配體生物素(Biotin)之應用 21
2.2.4 鏈酶卵白素和生物素結合機制之研究 23
2.2.5 鏈酶卵白素之核適體 27
2.3 恆溫滴定微卡計(Isothermal Titration Calorimetry, ITC) 31
2.3.1 恆溫滴定微卡計之介紹 31
2.3.2 恆溫滴定微卡計在生物系統之研究 34
2.3.3 利用取代滴定法改善ITC量測生物系統之極限 36
2.4 圓二色光譜儀(Circular Dichroism, CD) 38
2.4.1 圓二色光譜儀之介紹 38
2.4.2 圓二色光譜儀在生物系統之研究 40
第三章實驗藥品與儀器設備 41
3.1 實驗藥品 41
3.2 實驗儀器 43
3.3 實驗方法 44
3.3.1 緩衝溶液及樣品溶液之配製 44
3.3.2 恆溫滴定微卡計實驗 47
3.3.3 圓二色光譜儀實驗 49
3.3.4 螢光實驗 50
第四章結果與討論 51
4.1 鏈酶卵白素與其核適體之結合常數與熱力學之初步分析 51
4.2 鏈酶卵白素與其核適體結合行為之二級結構分析 57
4.2.1 鏈酶卵白素之核適體二級結構之探討 57
4.2.1.1 不同鹽類及濃度對鏈酶卵白素之核適體二級結構之影響 60
4.2.1.3 不同溫度對於鏈酶卵白素之核適體二級結構之影響 64
4.2.2 鏈酶卵白素二級結構之探討 65
4.2.2.1 鹽濃度對於鏈酶卵白素二級結構之影響 66
4.2.2.2 溫度對於鏈酶卵白素二級結構之影響 67
4.2.3 鏈酶卵白素與其核適體結合之二級結構變化 68
4.3 鏈酶卵白素與核適體結合之化學劑量比(stoichiometry)分析 74
4.4 鏈酶卵白素與其核適體結合之辨識機制探討 77
4.4.1 鹽類效應與一價金屬離子之效應 77
4.4.2 溫度效應與結合熱容量(?Cp)變化之分析 81
4.5 鏈酶卵白素與其核適體結合機制之模型之提出 88
4.6 利用取代滴定法測得鏈酶卵白素與biotin之結合常數 95
第五章結論 98
第六章參考文獻 100

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指導教授

陳文逸(Wen-yih Chen)

審核日期

2012-7-5

推文