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研究生:呂文翔
研究生(外文):Lu, Wen-Shiang
論文名稱:雞細胞激素介白素-1beta之高解析度結晶學結構顯示與人類介白素-1beta在受體結合上的差異
論文名稱(外文):High-Resolution Crystal Structure of Chicken Cytokine Interleukin-1 beta Reveals Differences in Receptor Binding Compared to Human Interleukin-1 beta
指導教授:殷献生
指導教授(外文):Yin, Hsien-Sheng
學位類別:碩士
校院名稱:國立清華大學
系所名稱:生物資訊與結構生物研究所
學門:生命科學學門
學類:生物訊息學類
論文種類:學術論文
論文出版年:2010
畢業學年度:98
語文別:英文
論文頁數:51
中文關鍵詞:介白素-1 beta分子動態模擬細胞激素
外文關鍵詞:chickeninterleukin-1 betamolecular dynamics simulationcytokine
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人類的介白素-1 beta (interleukin-1 beta, IL-1 beta) 為免疫系統中一個已被廣泛研究的細胞激素,其所涉及的反應除發炎外也包含了細胞增生、分化以及細胞凋亡等生理現象。五種禽類 (雞、鴨、鵝、火雞、鴿子) 的介白素-1 beta 對於哺乳類 (人類、鼠科) 在蛋白質序列上具有 31-35% 的相似度,然而至今尚未經過完整的研究。在本研究中,我們彙報了解析度達 1.58 埃 (angstrom) 的雞介白素-1 beta 重組蛋白質的結晶學結構,這個蛋白質在結構上包含了 12 個 beta-摺板 (beta-strand) 與 1 個 alpha-螺旋 (alpha-helix) 等二級結構,並進一步形成一個圓桶狀的構型。雞介白素-1 beta 對於其受體的模型建立與受體結合運算,在交互作用的位置上與人類介白素-1 beta 比較後顯示出了一些不同處。分子動態 (Molecular dynamics, MD) 模擬則顯示出經過與受體結合,在結構動態變化範圍上的顯著改變。雞介白素-1 beta 在結構上的 3 號與 9 號圈環 (loop) 在與受體結合前具有顯著的波動,一旦發生結合,這些圈環的可變動性則因為與受體的直接結合而明顯地降低。總結而論,這些結果說明與受體結合後所導致的不僅傾向於合適的焓值 (enthalpy) 同時也包括在結構上較低的熵值 (entropy).
Human interleukin-1 beta (IL-1 beta) is an important cytokine in the immune system which involves in inflammatory response, cell proliferation, differentiation and apoptosis, has been studied extensively. Five avian (chicken, duck, goose, turkey and pigeon) IL-1 betas share 31-35% protein sequence identity to mammal (human and murine) and are less well understood. In this study, we report the crystal structure of recombinant chicken IL-1 beta, to 1.58 angstrom resolution. The protein structure is comprised of 12 beta-strands and 1 alpha-helix, which form a barrel-shaped conformation. Modeling ligand docking of chicken IL-1 beta to its receptor reveals some differences at the site of interaction compared to human IL-1 beta. Molecular dynamics (MD) simulations reveal significant changes in the dynamic range of motion on receptor binding. The Loops 3 and 9 of chicken interleukin-1 beta have the most significant fluctuation before receptor binding. Upon binding, the flexibility of these loops, which are in direct contact with the receptor, markedly decreases. Taken together, these results suggest that receptor binding leads to not only favorable enthalpy but lower conformational entropy.
Chapter 1............................................................................1
Introduction ......................................................................1
1.1 Interleukin-1..............................................................1
Chapter 2............................................................................5
Materials and Methods..............................................................5
2.1 Materials..................................................................5
2.2 Expression and Purification of Chicken IL-1 beta...........................5
2.3 Functional Assay of the Recombinant Chicken IL-1 beta......................6
2.4 Biophysical Properties of Recombinant Chicken IL-1 beta....................7
2.5 Crystallization of Recombinant Chicken IL-1 beta...........................8
2.6 Structure Determination and Refinement.....................................8
2.7 Structure Analysis........................................................10
2.8 Molecular Modeling and Receptor Docking of Chicken IL-1 beta................11
2.9 MD Simulations for the IL-1 beta/IL-1R Type I Complex.....................11
Chapter 3...........................................................................14
Results and Discussion............................................................14
3.1 Functional Assay and Biophysical Properties of Recombinant IL-1 beta......14
3.2 Structure Determination...................................................15
3.3 Temperature Factors and HB Interactions...................................17
3.4 Electrostatic Potential Surface Map.......................................18
3.5 Hydrophobic Cavity........................................................19
3.6 Molecular Modeling of Chicken IL-1R type I................................21
3.7 Molecular Docking of Chicken IL-1 beta to its Receptor, IL-1R type I......22
3.8 MD simulations............................................................24
Chapter 4...........................................................................28
Conclusions......................................................................28
Figures and Figure Lengends.........................................................30
Table...............................................................................46
References..........................................................................47
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