X光晶體繞射應用於幽門螺旋桿菌蛋白質的結構基因體研究

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研究生：	蔡佳吟 Tsai, Jia-Yin
論文名稱：	X光晶體繞射應用於幽門螺旋桿菌蛋白質的結構基因體研究 Structural genomic study of Helicobacter pylori proteins by X-ray Crystallography
指導教授：	孫玉珠 Sun, Yuh-Ju
口試委員:
學位類別：	博士 Doctor
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2007
畢業學年度：	95
語文別：	中文
論文頁數：	86
中文關鍵詞：	幽門螺旋桿菌、假設性蛋白、結構基因體
外文關鍵詞：	Helicobacter pylori, hypothetical protein, structural genomics
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本篇論文主要是利用X光晶體繞射來進行幽門螺旋桿菌的結構基因體研究。幽門螺旋桿菌是一種革蘭氏陰性細菌，被認為與十二指腸潰瘍及胃潰瘍等胃腸相關的疾病有關，甚至與胃癌的發生也有著密切的關係。在1994年國際癌症研究署將幽門螺旋桿菌歸類為人類致癌物。全世界約有一半的人口受到幽門螺旋桿菌的感染，台灣地區的感染率約55%。兩個菌株J99及26695基因序列於1997年定序完成，而我們研究的對象菌株26695基因組具有1,667,867鹼基對，其中1,590有預測的編碼順序，在這些編碼順序中有34%是功能未知及結構未知的蛋白質。我們將由已知幽門螺旋桿菌的全部基因序列，針對生物功能未知的假設性蛋白質，利用X光晶體繞射的多波長異常色散法來解決相位問題以進行立體結構的研究，並利用結構特性探討可能的生物功能。在本篇論文中，我們挑選了三個分別對於酸刺激有反應或鞭毛相關的蛋白質進行結構分析，並利用DALI演算法進行三度空間結構的同源分析進而推測其功能。在已解出的蛋白質結構中；一個為新的摺疊蛋白質，折疊成包含四個螺旋的三角形結構；而另二個被報導與鞭毛的生合成及調控有關聯性的蛋白質，其中一個是長桿狀的螺旋結構具有類似鞭毛的多元體形成特性；而另一個結構則比對到DNA結合蛋白質，我們的實驗結果或許可以給予將來進行生物功能研究的一個方向。

Helicobacter pylori (hereafter H. pylori) is a gram-negative bacterium, which colonizes the gastric mucosa of humans, causing gastritis and peptic ulcer disease, and is associated with certain types of gastric cancers. In 1994, the International Agency for Cancer Research announced that H. pylori is a carcinogen of humans. Two complete genome sequences of the gastric pathogen H. pylori, 26695 and J99, have been determined in 1997. We chose H. pylori strain 26695 as the target genome of the structural genomics study by X-ray crystallography method. The major goal is to provide the significant and detailed structural information of the low homologous proteins in H. pylori. Another goal is to discovery the new structural folds. Three low homologous proteins were selected based on the criteria: acid induced or flagella associated. A structure-based homology analysis with the DALI algorithm was applied to the structure analysis. One of the solved structures is a new fold with four helices folded into a triangle. The other two proteins reported in flagella assembly or regulatory in which one structure demonstrates the characteristics in flagella assembly feature and the other structure matches most of the RNA/DNA binding protein. Our results may shed a light on further functional studies based on their unique protein folding.

中文摘要         i
Abstract         ii
誌謝        iii
Contents        iv
List of Tables        vii
Chapter 1.  Introduction        1
1  Structure genomics         1
2  Helicobacter pylori         2
3  Target selection         3
3.1 Acid-induced Genes        3
3.2 Flagella System        4
4  Aims                          5
5  Figures        6

Chapter 2.  Materials and Methods        10
1 Recombinant protein        10
2 Protein expression and purification        11
3 Protein characterization        12
4 Structure determination        13
5 Table        15

Chapter 3.  Hypothetical Protein Hp0242        16
1 Introduction        16
2 Results        17
2.1 Hp0242 Characterization        17
2.2 Crystallization        17
2.3 MAD Data Collection         18
2.4 Overall Structure        19
2.5 Novel Folding        19
2.6 Oligomeric Structure        20
3 Discussions        21
4 Summary        24
5 Tables and figures        25

Chapter 4.  Putative Flagella Regulatory Protein         36
1 Introduction        36
2 Results        37
2.1 HpFRP Characterization        37
2.2 Crystallization        38
2.3 MAD Data Collection        38
2.4 Overall Structure        39
2.5 Coiled-coil Interaction        40
2.6 Structural Homology Search        40
3 Discussion        41
4 Summary        42
5 Tables and figures        43

Chapter 5.  Polar Flagellin        57
1 Introduction        57
2 Results        58
2.1 HpFlaG Characterization        58
2.2 Crystallization         59
2.3 MAD Data Collection        59
2.4 Sequence Alignment        60
2.5 Overall Structure        60
2.6 Structural Homology Search        61
2.7 Structural Comparison        62
2.8 Oligomeric Structure        63
3 Discussions        63
4 Summary        65
5 Table and Figures        66

Chapter 6.  Conclusion        78
References        80
Research Publications        86

                                

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