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研究生: 周家緯
Chou, Chia-Wei
論文名稱: 探索蛋白質結構變化之整合平台
An integrated platform for exploring conformational change of proteins
指導教授: 張天豪
Chang, Tien-Hao
學位類別: 碩士
Master
系所名稱: 電機資訊學院 - 電機工程學系
Department of Electrical Engineering
論文出版年: 2014
畢業學年度: 102
語文別: 中文
論文頁數: 34
中文關鍵詞: 結構轉變蛋白質結合
外文關鍵詞: conformational changes, protein interaction
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  • 結構變化在各種具有重要生物功能的蛋白質交互作用間廣泛的被觀察到,舉例來說:adenylate kinase (AdK)催化ATP分解成AMP及磷酸的轉移,過程中產生巨大的結構轉變 (從開放狀態轉換至封閉狀態),此結構轉換可能與基質或配體結合與後轉錄調控有關,如:磷酸化。已有許多研究將蛋白質特性可視化,如:將蛋白質每個胺基酸之演化保留度以圖形顯示。但大部份的研究皆著眼於蛋白質本質特性,而非蛋白質結構轉變。
    本研究提供精緻且人性化的使用者介面,使用者可使用互動式圖表與3D立體結構來觀察結構轉變,使用者可以看到蛋白質結合造成的結構轉變,同時,本研究也提供了全面性的資訊,包含:sequence domains、structural domains、phosphorylation sites、catalytic sites、secondary structures、disorder regions、conservation profile以及hydrophathy profile。使用者可以深入探討各種生物特性間的關聯,本篇研究也將有利於各領域的探討,如:protein disorder、secondary structure transition、protein flexibility/plasticity、protein interaction、post-translational modification與molecular dynamics。

    Proteins play important roles in many biological processes. These biological processes are conducted by a series of protein interactions with various molecules like proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions. This work presents the CCProf platform, which provides conformational changes of entire proteins, named conformational change profile (CCP) in the context. CCProf aims to be a platform where users can study potential causes of novel conformational changes. It provides ten biological features, including conformational change, potential binding target site, secondary structure, conservation, disorder propensity, hydropathy propensity, sequence domain, structural domain, phosphorylation site and catalytic site. All these information are integrated into a unified and well aligned view so that researchers can capture important relevance between different biological features visually. CCProf contains 41568 structure pairs for 3638 proteins. In addition, CCProf provides a 3D view in which users can see the structures before and after conformational changes as well as binding targets that induce conformational changes. All information (e.g., CCP, binding targets and structures) shown in CCProf, including intermediate data are available for download to expedite further analyses.

    第 一 章 緒論 1 第 二 章 相關研究 2 2.1生物分子 2 2.1.1蛋白質-protein 2 2.1.2去氧核糖核酸-DNA 3 2.1.3配體-ligand 4 2.1.4離子-ion 6 2.2蛋白質的結構轉變 6 2.2.1蛋白質的二級結構 6 2.2.2蛋白質的非穩定與穩定結構 7 2.3蛋白質的序列轉變 7 2.4相關資料庫 8 2.4.1蛋白質資料庫 8 2.4.2蛋白質域資料庫 9 2.4.3蛋白質結構轉換資料庫 9 第 三 章 資料蒐集與實作方法 11 3.1產生蛋白質結構對 11 3.2蛋白質結構疊合 13 3.2.1 CCProf蛋白質結構疊合 13 3.2.2蛋白質結構形變計算 13 3.3潛在生物分子結合判定 14 3.4蛋白質結構對之二級結構分析 15 3.5序列保留度分析 16 3.6 PDB sites資料蒐集 17 3.7蛋白質域資訊蒐集 19 3.8蛋白質結構穩定性計算 19 3.9親水性/疏水性計算 19 第 四 章 使用介面與個案分析 20 4.1 CCProf使用者介面 20 4.1.1首頁 20 4.1.2搜尋頁 21 4.1.3結果頁 22 4.2個案分析 25 4.2.1 轉譯起始因子(IF2/eIF5B) 25 4.2.2鳥苷酸結合蛋白(GBP1) 28 4.3資料庫比較 30 第 五 章 結論與未來展望 32 5.1結論 32 5.2未來展望 32 參考文獻 33

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