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作者(中文):游奇縉
作者(外文):Yu, Chi-Ching
論文名稱(中文):結合聚脯胺酸胜肽與自組裝胜肽之水解酶設計和其催化效率探討
論文名稱(外文):Design of Polyproline Based Peptides and Self-Assembling Structures as Catalysts for Ester Hydrolysis
指導教授(中文):洪嘉呈
指導教授(外文):Horng, Jia-Cherng
口試委員(中文):江昀緯
吳淑褓
口試委員(外文):Chiang, Yun-Wei
Wu, Shu-Pao
學位類別:碩士
校院名稱:國立清華大學
系所名稱:化學系
學號:107023517
出版年(民國):109
畢業學年度:108
語文別:中文
論文頁數:93
中文關鍵詞:胜肽聚脯胺酸自組裝催化酯類水解立體電子效應
外文關鍵詞:peptidepolyprolineself-assemblingcatalysisesterstereoelectronic
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近幾年來,許多研究將胜肽設計為人工水解酶,並期望能模擬天然水解酶的活 性及選擇性,然而設計出高活性水解酶的仍然是一大挑戰。在本研究中,我們利用 催化二聯體以及自組裝的概念來設計一系列人工水解酶,同時也合成聚脯胺酸衍生 物,試圖研究胜肽結構與催化效率間的關聯。我們以 CD 光譜鑑定所設計胜肽的 結構以及穩定性,並利用 UV-Vis 光譜以及酯類受質研究人工水解酶的催化能力。 在第一部分實驗中,利用簡單的聚脯胺酸短胜肽作為人工水解酶,我們發現 PPII 結構的完整性對於人工水解酶的催化效率有很重要的影響,並且催化二聯體內官能 基的間距也是影響催化效率的重要因素。在第二部分的實驗中,以自組裝胜肽作為 人工水解酶,我們發現催化效率有顯著提升,並且催化效率與 β-sheet 結構的穩定 度以及受質結合環境相關,另外我們也發現,自組裝胜肽的碳氮端置換會對酵素的 轉換率(turnover rate)造成很大的改變。在第三部分的實驗中,我們以自組裝胜肽對 甲基對氧磷水解反應進行催化,以探討磷酯水解的催化,實驗結果說明由於自組裝 胜肽所營造的受質結合環境不適用於甲基對氧磷,因此自組裝胜肽並不能有效的進 行催化。本研究說明在人工水解酶中,維持穩定的二級結構以形成有效的催化中心 才能使人工水解酶作為有效的催化劑,並且在本研究中人工水解酶的催化效率有不 俗的表現,對於未來在催化較具挑戰性的酯類水解反應有很大的進展。
Recently, a number of peptide-based enzymes have been designed to mimic the activity and selectivity of natural hydrolysis. But, creating catalysts with great catalytic activity is still challenging. In this study, we designed a series of peptide as artificial enzymes and utilize the concept of catalytic dyad and assembly strategy. We also synthesized proline derivatives in an attempt to study the relationship between the structure and catalytic efficiency of peptides. The secondary structures of peptides were characterized by circular dichroism spectroscopy, and their catalytic efficiency were evaluated by UV-Vis spectroscopy using p-nitrophenyl ester assay. In the first part, the results indicate the higher catalytic efficiency could be attributed to well-defined polyproline II (PPII) structure. In addition, the distance between catalytic dyad is also important for catalytic efficiency. In the second part, the results demonstrate the assembled structure could enhance the catalytic activity on ester hydrolysis significantly. According to the kinetic parameters, the catalytic efficiency lies in the extent of β-sheet structure, as well as a suitable binding pocket for substrates. Furthermore, reversing the sequence within a peptide may dramatically affect the turnover rate of catalyst. In the third part, we carried out the experiments of phosphoester hydrolysis, and self-assembling peptides were used as catalysts for methyl-paraoxon hydrolysis. We find out that self- assembling peptides are incapable of catalyzing methyl-paraoxon hydrolysis effectively, because its binding pocket may not apply to methyl-paraoxon. Our investigation has revealed the necessity of maintaining a stable secondary structure for effective peptide- base enzymes, and promising catalytic efficiency of assembling peptides makes inroads in designing artificial enzymes for challenging substrates.
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 聚脯胺酸 (Polyproline) 1
1-2 PPII (polyproline II) 結構 2
1-3 立體電子效應 (stereoelectronic effect) 3
1-4 β-sheet 結構 5
1-5 酯類水解反應 (Ester hydrolysis reaction) 6
1-6 天然水解酶作用機制 8
1-7 人工水解酶的設計 10
1-8 研究動機 14
第二章 實驗部分 15
2-1 實驗儀器 15
2-2 實驗藥品 16
2-3 脯胺酸衍生物合成 19
2-3-1 合成步驟 19
2-3-2 合成方法 21
2-4 圓二色光譜儀 (Circular dichroism spectrometer, CD) 26
2-5 固相胜肽合成法 (Solid phase peptide synthesis, SPPS) 30
2-5-1 酯化 (esterification)、醯胺化反應 (amidation) 31
2-5-2 去保護(deprotection) 32
2-5-3 活化(activation) 32
2-5-4 耦合(coupling) 33
2-5-5 切除(cleavage) 33
2-6 胜肽的合成、純化與鑑定 34
2-7 光譜測量 36
2-7-1 UV 光譜測量胜肽濃度 36
2-7-2 CD 光譜測量( Far-UV 光譜) 36
2-7-3 ATR-FTIR 光譜測量 36
2-7-4 催化水解活性實驗 37
2-8 催化活性實驗數據處理 40
2-9 電子顯微鏡 42
2-9-1 穿透式電子顯微鏡(transmission electron microscopy, TEM) 42
2-9-2 原子力顯微鏡(atomic force microscope, AFM) 42
2-10 計算模擬聚脯胺酸結構之研究方法 42
第三章 結果與討論 43
第一部分 聚脯胺酸短胜肽作為人工水解酶 43
3-1 聚脯胺酸短胜肽及其替換骨架衍生物設計 43
3-2 胜肽結構之鑑定 44
3-3 PPII 結構穩定性對酯類水解催化效率探討 46
3-4 計算模擬聚脯胺酸結構 47
第二部分 自組裝胜肽與聚脯胺酸結合作為人工水解酶 50
3-5 含聚脯胺酸片段的自組裝人工水解酶設計 50
3-6 自主裝胜肽二級結構之鑑定 52
3-7 胜肽自組裝結構之鑑定 56
3-7-1 穿透式電子顯微鏡(TEM) 56
3-7-2 原子力顯微鏡(AFM) 60
3-7-3 霍式轉換紅外光譜(FTIR) 64
3-8 自組裝胜肽對酯類水解催化效率探討 65
3-8-1 不同 pH 值下自組裝結構對酯類水解催化效率探討 65
3-8-2 自組裝胜肽內聚脯胺酸片段對酯類水解催化效率探討 70
3-8-3 自組裝胜肽碳氮端置換對酯類水解催化影響探討 72
3-8-4 自組裝胜肽與相關研究的酯類水解催化效率比較 74
第三部分 自組裝人工水解酶對磷酯水解催化探討 76
第四章 結論與展望 79
參考文獻 81
附錄 87
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