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研究生:吳盈清
研究生(外文):Yng-Ching Wu
論文名稱:蛋白質結構基本單元之物理性質研究
論文名稱(外文):Investigation on physical properties of basic structural unit of protein
指導教授:黃吉川黃吉川引用關係
指導教授(外文):Chi-Chuan Hwang
學位類別:碩士
校院名稱:國立成功大學
系所名稱:工程科學系碩博士班
學門:工程學門
學類:綜合工程學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:141
中文關鍵詞:蛋白質
外文關鍵詞:protein
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基因是製造蛋白質的藍圖,蛋白質才是執行生命現象的主角,但是蛋白質活性的表現並不完全由基因來決定,而是與環境變化有著高度的關聯性。因此,蛋白質結構與生化功能的研究即成為了現在生物科技研發的重點。另外,由於蛋白質結構過於複雜且具有多樣性,故本論文希望藉由分子動力學模擬的研究,先來了解氨基酸的物理性質,並進一步利用模組化概念將每一種氨基酸設計為單一模組程式,以做為日後研究蛋白質巨分子之先前準備,並做為爾後探討生化病理機制和開發新藥的重要參考。
The paper is presented to investigate the folding characteristics of amino acids in the aqueous solution. The folding characteristics of amino acids obtained using molecular dynamics simulations method here is provided a preliminary study for the long-term project of the protein folding characteristics, composing by many basic amino acids. The molecular model of amino acids includes the potentials used to simulate the interactions between carbon, hydrogen, oxygen and nitrogen etc. In addition, the bonding behaviors of the molecule includes bond stretching, bond bending and bond-angle torsion behaviors are also included. The polar effect of the water molecule is simulated by using Simple Point Charge (SPC) model. The folding characteristics under the influence of the water molecule of its hydrogen bonding effect are investigated. The results of this study show that the polar effect of the water molecule has an insignificant influence on the bond length and bond-bending angle. The bond torsion angle located around at a hydrogen atom is more influenced by this polar effect.
頁次
目錄………………………………………………………………………..I
圖目錄…………………………………………………………………....V
表目錄………………………………………………………………...VIII
符號說明………………………………………………………………...IX
中文摘要………………………………………………………………...XI
誌謝………………………………………………………………......XII

第一章 緒論…………………………………………………………….1
1-1 研究動機、目的與背景……………………………………….1
1-2 文獻回顧……………………………………………………….4
1-2-1 蛋白質資訊…………………………………………………......6
1-2-2 決定蛋白質結構的實驗方法……………………………….....12
1-2-3決定蛋白質結構的理論模擬方法…………………………......14
1-2-3-A 同源模擬法……………………………………………….15
1-2-3-B 折疊辨識法………………..……..……………………....17
1-2-3-C 從頭起算法…………………..………………………......19
1-2-3-C-I 晶格模型……………………………………………......20
1-2-3-C-II蒙地卡羅…………………………………………….......26
1-2-3-C-III分子動力學………………………………………........27
1-3 本文架構………………………………………………..…......29

第二章 蛋白質分子結構………………………………………….…31
2-1 前言…………………………………………………….…….32
2-2 基本單元:氨基酸…………………………………….….…33
2-3 氨基酸側鏈之物理化學性質分類……………………….….39
2-4 蛋白質一級結構
2-4-1胜肽鍵…………………………………………..….……….....46
2-4-2胜肽鏈………………………………………………………......48
2-5 蛋白質二級結構………………………………………….…......49
2-5-1 α螺旋…………………………………………………..…......50
2-5-2 β螺旋……………………………………………………........51
2-5-3 轉折…………………………………………………..…….....52
2-6 蛋白質三級結構…………………………………………..….....54
2-7 蛋白質四級結構…………………………………………….......56


第三章 蛋白質分子的生化功能………………………….…………57
3-1前言………………………………………………….……….......58
3-2 生物分子之一般特性………………………………..……….....59
3-3 生命的簡單物質……………………………………..……….....61
3-4 酸鹼概念 & …………………………………………...........62
3-5 蛋白質的分類…………………………………………….…......66
3-6 酵素……………………………………………………..….......69
3-7 肌紅蛋白與血紅蛋白……………………………………….......73

第四章 分子動力學數值模擬
4-1 分子間作用力與勢能函數…………………………………...77
4-2物理參數與無因次化……………….…..…………………….....81
4-3 時間步階選取………………………….……………………......84
4-4 節省模擬時間之方法…………………..…………………….....85
4-4-1 截斷半徑法……………………………………………........86
4-4-2 Verlet表列法…………………………………………........87
4-4-3 Cell link表列法………………………….…….…….......90
4-4-4 Verlet表列結合Cell link表列法………………….........92
4-5 預測修正計算法…………………………………………….......93

第五章 結果與討論………………………………………………….97
5-1 甘氨酸模擬結果……………………………………………...100
5-2 苯丙氨酸模擬結果…………………………………………...107
第六章 結論與建議
6-1 結論…………………………………………………………......111
6-2 建議…………………………………………………………......112
參考文獻………………………………………………………………..114
附錄 A-1 鏈分子鍵結力推導:鍵角作用力………………………..125
附錄 A-2 鏈分子鍵結力推導:鍵結扭轉角作用力………………..128
附錄 B 蛋白質分子動力學模擬的參數對照表……………………..132
附錄 C Prion氨基酸序列…………………………………………...139
自述……………………………………………………………………..141
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