臺灣博碩士論文加值系統

1918 年，流行性感冒突然嚴重爆發，在全世界有二千萬到四千萬人因為感染流行性感冒疾病而死亡，造成如此高感染力的原因始終不明，因此JamesStevens 和Scripps 學院的Ian Wilson 在La Jolla 開始著手研究採自阿拉斯加受難者的屍體組織，希望能夠找出原因，他們找出病毒表面蛋白hemagglutinin (HA)的序列並分析其結構，結果顯示，它跟感染鳥的流行性感冒病毒較接近較有關係。對於流行性感冒病毒來說，HA 蛋白是非常重要的，因為它結合到人類的肺細胞表面受器，此時，HA 會改變形態幫助病毒的膜與宿主融合，整個過程在分子層次上是物理化學的交互作用。1918 年造成異常高的傳染性和死亡率的HA 蛋白，在結構上有兩個特別突出的特徵異於一般：(1)一般受器結合位置的範圍是狹小的，然而1918 年流行性感冒病毒的HA 蛋白卻以一個氨基酸突變，使結合位置稍微的變大，這可能會增加傾向於對人類細胞的感染。(2)有兩個之前未被查覺的鹼性小片段(histidine rich)，當病毒融入細胞膜時，可能會提高HA 的感染性，其中一個小片段被發現只有在感染鳥的病毒種類中才有。根據這些線索，我們推論流行性感冒病毒的感染對象，以及禽流感感染人的可能性，應該跟它的HA蛋白質序列所具有的物理化學性質，有很密切的關係。因此，我們利用資料探勘的方法，找出流行性感冒病毒的HA蛋白序列中，感染人與禽類所具備的物理化學性質特徵差異。我們從公開的資料庫(http://www.flu.lanl.gov/)中搜集各種流感病毒的HA蛋白質序列，並分別針對序列上氨基酸的酸鹼性、凡得瓦體積、表面積與疏水性，做與感染事件有關的物理化學性質特徵分析，並找出了一些感染人與禽類的差異點。這些特徵差異點，有助於將來針對病毒的感染以及禽流感感染人類的可能性，發展有效的防制方法。

In 1918, the flu suddenly broke out seriously, 20 million to 40 million people die in infection. The cause of high appeal is still unclear. For the sake of this reason,James Stevens and Ian Wilson who is the faculty of the institute of Scripps studied the structural characters of hemagglutinin (HA) protein that sampled from the victim person in the Alaska.The result revealed that the flu closely relative to the epidemic influenza virus which infects the bird.The HA protein is very important in the event of flu infection,because it bind to the receptor on the cellular surface of human lung specifically, and bring about membrane fusion by the change of conformation. All of the processes are physiochemical interactions in the molecular level.There are two significant physiochemical features for the flu infection which broke out in 1918 may responsible to the high infection and mortality: (1) In general, the size of binding position is narrow, but becoming larger by one amino acid change on the binding position in the flu of 1918, that apt to promote the infection to human. (2) Two histidine-rich segments with basicity may promote the membrane fusion in the infection process.One of the two segments found only in avin flu.According to these clues, we assumed that the infective host and the probability of cross-species infection could be determined by the physiochemical properties of residues in the HA protein sequence.So, we utilized the method of data mining to discover the significant differences in the HA protein sequences between avin and IV human flu. All the HA protein sequences was collected from public database (http://www.flu.lanl.gov/).
The physiochemical properties of residues we studied including hydrophobicity, Van der Waals volume, surface area, and acid-base property. Some important characters have discovered, that may have big help to develop the preventive strategy for the flu infection and cross-species infection, in the future.

第一章 概論.................................................................................................................. 1
1-1 流行性感冒的歷史背景................................................................................ 1
1-1-1 歷史背景............................................................................................. 1
1-1-2 世界上發生禽流感的狀況................................................................. 2
1-1-3 人類感染禽流感的狀況..................................................................... 3
1-2 流行性感冒病毒............................................................................................. 5
1-3 何謂禽流感.................................................................................................... 6
1-4 流行性感冒病毒的組成與結構..................................................................... 7
1-4-1 結構..................................................................................................... 7
1-4-2 核心...................................................................................................... 9
1-4-3 基質蛋白............................................................................................ 10
1-4-4 包膜.................................................................................................... 10
1-4-5 血球凝集素(hemagglutinin) .............................................................. 11
1-4-6 神經氨酸酶(neuraminidase)............................................................. 11
1-4-7 蛋白M2 .............................................................................................. 11
1-5 流行性感冒病毒命名原則........................................................................... 12
1-6 流行性感冒的變異...................................................................................... 12
1-6-1 變異................................................................................................... 12
1-6-2 抗原變化............................................................................................ 13
1-6-3 抗原微變(antigenic drift)................................................................... 13
1-6-4 抗原巨變(antigenic shift)................................................................... 14
1-7 禽流感傳染人的原因................................................................................... 14
1-8 流行性感冒病毒傳播途徑與症狀............................................................... 17
1-9 流行性感冒病毒感染過程與致病性........................................................... 17
第二章 研究背景與動機............................................................................................ 19
2-1 Hemagglutinin (HA)的構造.......................................................................... 19
2-2 研究動機...................................................................................................... 23
第三章 材料與方法.................................................................................................... 25
3-1 資料庫、軟體與分析方法的介紹.............................................................. 25
3-1-1 The Influenza Sequence Database...................................................... 25
3-1-2 ClustalW............................................................................................. 27
3-1-3 S2N ratio ............................................................................................ 29
3-1-4 Permutation test[20-21]...................................................................... 30
3-1-5 SVM (Support Vector Machine)[22].................................................. 30
3-2 研究方法與流程.......................................................................................... 32
VI
3-2-1 蒐集A型流感病毒HA蛋白的基本資料........................................... 33
3-2-2 蒐集A型流感病毒HA蛋白的序列資料........................................... 35
3-2-3 蛋白質序列資料的量化與S2N ratio的計算.................................... 36
3-2-4 利用S2N ratio找出兩群HA蛋白序列中的差異點.......................... 41
第四章 結果與討論.................................................................................................... 46
4-1 結果............................................................................................................... 46
4-1-1 氨基酸出現比例與蛋白質3D結構................................................. 46
4-1-2 以WebLogo方式表現[25]................................................................. 89
4-1-3 以顏色分佈表示............................................................................... 97
4-1-4 利用顯著差異點做為特徵點，使用SVM做分類........................ 105
第五章 結論.............................................................................................................. 108
參考文獻.................................................................................................................... 109

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