近年來，有許多研究致力於使用合成胜肽作為人工水解酶，以模擬天然水解酶的催化活性與選擇性，然而設計出高催化活性的胜肽水解酶仍是一大挑戰。在本研究中，我們利用聚脯胺酸骨架與催化二聯體的概念，合成聚脯胺酸水解酶，同時利用自組裝的概念，將聚脯胺酸與具自組裝能力的胜肽耦合，以製備含有β褶板結構的自組裝水解酶。藉由改變脯胺酸骨架與催化二聯體位置等，我們設計出一系列的人工水解酶，以探討不同因素對於結構與催化效率的影響。比較本實驗室過去所研究i→i+3位置的催化二聯體，此篇研究致力於i→i+2位置催化二聯體，並統整相似的人工水解酶以進行比較。我們以理論計算模擬可能的胜肽結構與催化二聯體的距離，以CD光譜儀鑑定結構與穩定性，利用穿透式電子顯微鏡觀測大型結構，並利用UV-Vis光譜追蹤酯類水解反應的進行，以評估人工水解酶之催化活性。我們發現結構的穩定性對於催化效果有重要的影響，而催化二聯體的距離、立體障礙、合適的活性中心等也會影響催化效率。除此之外我們的人工水解酶對於較難水解的磷酯類受質與醯胺類受質，也有些微的水解能力。整體來說，本研究合成高催化活性的胜肽為基底之人工水解酶，並探討結構與催化二聯體位置等因素所帶來的影響，有助於設計更具催化活性的人工水解酶。

Recently, several studies have been devoted to synthesizing artificial hydrolases to mimic catalytic activity and selectivity of natural hydrolases. However, it is challenging to design artificial hydrolases with high catalytic activity. In this study, we used polyproline scaffold and the concept of catalytic dyad to synthesize peptide-based hydrolases. Additionally, we used the concept of self-assembly to conjugate polyproline peptides into the self-assembly β-sheets to design hydrolases. By changing proline scaffold and position of the catalytic dyad, we designed a series of artificial hydrolases to study the influences on structure and catalytic efficiency. Comparing to the catalytic dyad at the i→i+3 position which was previously studied in our laboratory, this research is focused on the catalytic dyad at the i→i+2 position. We also integrated similar artificial hydrolases for comparison. We used theoretical calculations to simulate possible peptide structures and the distances between catalytic dyads. We characterized the peptide structures and stability with CD spectroscopy, and examine the assembled structures with electron microscopy. Finally, we used UV-Vis spectroscopy to track the progress of the ester hydrolysis reaction for evaluating the catalytic activities of our designed artificial hydrolases. We find that the stability of the structure plays an important role on catalytic efficiency. Besides, the distances of the catalytic dyad, steric effects, suitable binding pockets, etc. also affect catalytic efficiency. Furthermore, our peptide-based hydrolases also have slight abilities to hydrolyze phosphate ester substrates and amide substrates which are much more difficult to hydrolyze than ester substrates. In conclusion, we synthesized peptides based artificial hydrolases with high catalytic activities, and studied the influences of structure and catalytic dyad positions, which is helpful to design more efficient artificial hydrolases.

中文摘要 I
Abstract II
誌謝辭 III
目錄 IV
圖目錄 VII
表目錄 X
第一章 緒論 1
1-1 蛋白質結構 1
1-2 β褶板結構 1
1-3 聚脯胺酸(Polyproline) 2
1-4 PPII結構 4
1-5 立體電子效應(Stereoelectronic effect) 5
1-6 水解反應(Hydrolysis reaction) 7
1-7 天然水解酶作用機制 11
1-8 人工水解酶的設計 13
1-9 實驗室人工水解酶先例 16
1-10 研究動機 18
第二章 實驗部分 19
2-1 實驗儀器 19
2-2 實驗藥品 20
2-3 脯胺酸衍生物合成 24
2-3-1 合成步驟 24
2-3-2 合成方法 26
2-4 固相胜肽合成法 (Solid phase peptide synthesis, SPPS) 32
2-4-1 酯化反應(esterification)或醯胺化反應(amidation) 33
2-4-2 去保護(deprotection) 34
2-4-3 活化(activation) 34
2-4-4 耦合(coupling) 35
2-4-5 切除(cleavage) 35
2-5 胜肽合成、純化與鑑定 36
2-6 圓二色光譜儀(Circular dichroism spectrometer, CD) 39
2-7 光譜測量 44
2-7-1 UV光譜測量胜肽濃度 44
2-7-2 Far-UV CD光譜測量 44
2-7-3 催化水解反應實驗 45
2-8 催化活性實驗數據處理 50
2-9 穿透式電子顯微鏡(Transmission electron microscopy) 52
2-10 理論計算模擬胜肽 52
2-10-1 使用Gaussian 16模擬聚脯胺酸胜肽 52
2-10-2 使用Discovery studio模擬自組裝胜肽 53
第三章 結果與討論 54
第一部分 以聚脯胺酸為骨架之人工水解酶 54
3-1 聚脯胺酸胜肽之設計 54
3-2 理論計算聚脯胺酸胜肽結構 56
3-3 聚脯胺酸胜肽之二級結構鑑定 59
3-4 聚脯胺酸胜肽對酯類水解催化測定 60
第二部分 β褶板與聚脯胺酸序列結合之自組裝胜肽水解酶 63
3-5 自組裝胜肽之設計 63
3-6 理論計算自組裝胜肽結構 66
3-7 自組裝胜肽之二級結構鑑定 68
3-8 自組裝胜肽之TEM鑑定 75
3-9 自組裝胜肽對酯類水解催化測定 80
3-9-1 自組裝胜肽在pH 7.4下催化酯類水解效率 80
3-9-2 自組裝胜肽在pH 9.0下催化酯類水解效率 82
3-9-3 自組裝胜肽在pH 10.0下催化酯類水解效率 85
3-9-4 相關研究p-NPA水解催化效率比較 88
第三部分 自組裝胜肽對磷酯類與醯胺類受質之催化測定 89
3-10 自組裝人工水解酶對磷酯類受質水解催化測定 89
3-11 自組裝人工水解酶對醯胺類受質水解催化測定 92
第四章 結論與展望 96
參考文獻 98
附錄 104

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