臺灣博碩士論文加值系統

在這篇論文中，主要的目的是從序列及結構分析醣苷水解酵素與配體結合的活性位點鄰近胺基酸特性。目前蛋白質有三級結構資訊的數量約有74,300個，蛋白質的三級結構能表示不同蛋白質的折疊方式或是在空間中小分子化合物與蛋白質結合的位置關係。從蛋白質結構分類資料庫，考慮含有催化區塊結構資訊的蛋白質，我們分別對醣苷水解酵素的第1、9、11、22個家族，建立含有配體與三級結構的蛋白質模板，透過配體與蛋白質結合在活性位點的位置關係，對應到序列上的某些胺基酸片段，以及對這些片段作分析。利用我們提出的這個流程，將此家族共同特性，用於判斷具有相似結構的蛋白質是否也具有醣類催化的功能。

In this research, the objective is to analyze the residues, which are around the active site of Glycoside Hydrolases where the ligands bind, from sequence and structure. Currently, there are about 74,300 structures in Structural Classification of Proteins (SCOP)[1]. The structure of the protein can provide the information of different folds and the position where substrates bind with proteins in space. We consider the catalytic domains of the proteins, and construct the templates library which includes ligands and structures. Through mapping the relative positions, where ligands and proteins bind, to the corresponding sequences, there are some segments of the residues, and analysis of these segments. Utilized the flow chart, the analysis of the GH families is used to determine whether the protein with similar structure has the function of catalyzed glycoside or not.

中文摘要 ............................................................................................................................ iii
ABSTRACT ....................................................................................................................... iv
致謝詞 ................................................................................................................................. v
CONTENTS ....................................................................................................................... vi
Chapter 1 - Introduction ................................................................................................... 1
Chapter 2 - Material and Method .................................................................................... 3
2.1 Material ........................................................................................................... 3
2.2 Flow Chart ...................................................................................................... 3
2.3 Templates Construction ................................................................................. 4
2.4 Data Preprocessing ........................................................................................ 5
2.5 Distance Calculation ...................................................................................... 6
2.6 Segments Selection and Ligands Extraction ................................................ 6
2.7 Sequence Analysis .......................................................................................... 7
2.8 Structure Analysis .......................................................................................... 7
2.9 Properties ........................................................................................................ 8
Chapter 3 – Results and Discussion ................................................................................. 9
3.1 Results ............................................................................................................. 9
3.2 Targets Verification ...................................................................................... 10
3.3 Similar Structure but not in Glycoside Hydrolases Family ..................... 21
3.4 Comparison with GH009 3H3K 2RGK ..................................................... 23
Chapter 4 - Conclusion and Future work ...................................................................... 24
4.1 Conclusion .................................................................................................... 24
4.2 Future work .................................................................................................. 24
REFERENCES ................................................................................................................. 26

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