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研究生： 施博閔
Shih, Po-Min
論文名稱： 小角度X光散射在多結構域蛋白Trigger Factor與結蛋白上的應用
Application of Small Angle X-ray Scattering on Multi-domain Protein Trigger Factor and Knotted Proteins
指導教授： 徐邦達
Hsu, Ban-Dar
徐尚德
Hsu, Shang-Te
口試委員: 徐尚德
Hsu, Shang-Te
蘇群仁
Su, Chun-Jen
徐邦達
Hsu, Ban-Dar
學位類別： 碩士
Master
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： 2014
畢業學年度： 102
語文別： 英文
論文頁數： 144
中文關鍵詞： 小角度Ｘ光散射 、蛋白質 、結蛋白
外文關鍵詞： Trigger factor, knotted protein, Flory's theory
相關次數： 點閱：3  下載：0 
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    • 中文摘要
    由於小角度X光散射(SAXS)可以獲得關於結構的整體資訊．這篇論文主要藉由這些資訊進行比較及分析，期望透過SAXS結果輔助解決問題：關於誘導型伴護蛋白(TF) 晶體中結構所表現的不穩定二聚體結構是否同於水溶液中的結構；打結蛋白質在變形條件下的表現是否與一般蛋白不同；及泛素C端水解酶L1 (UCHL1) 晶體結構的局部結構差異是否能由SAXS觀測得知。
    透過ATSAS 套裝軟體提供的剛體模擬的功能，我們發現藉由改變domain 間相對位置，獲得TF在水溶液中的可能結構，相較於晶體結構，這些新結構符合SAXS觀測結果。TF 113-432提供了符合的例子。
    根據Flory的理論與已發表的SAXS實驗數據，我們發現化學變性的蛋白質依循Rg=2.049*L^0.581的規律，而一般蛋白質主要依循Rg=2.078*L^0.446的條件．而打結蛋白YibK在化學變性的條件下，SAXS所測得的平均Rg稍大於預期的結果，透過EOM的分析結果，YibK在變性過程中有多種結構分布產生，而這些結構有著較平均值大的Rg值，去除這些影響後，打結蛋白與一般蛋白的Rg值在化學變性的條件下沒有明顯的差異。
    另外我們以分子動態模擬的方法，模擬UCHL1在水溶液中的行為，我們透過模擬得到了UCHL1在水溶液中的可能結構，而模擬結果相較於經體結構所回推的SAXS結果更貼近實驗值。

    Abstract
    Small angle X-ray scattering (SAXS) is a powerful methods in observing particles’ shapes. To our knowledge, trigger factor (TF) has a non-native dimer form from crystal packinf artifact; Knotted protein YibK conatains the knot in chemically denatured state; UCHL1 wild type (WT) and its mutantion I93M have almost the same crystal structure but the different behaviors.
    We use SAXS to investigate these phenomena with ATSAS programs. Rigid body modeling reveals the reorientational TF domains’ positions to fit experimental data. With mixture and flexibility system, we analyzed the Rg distribution of YibK to understand the structural information in chemically denatured condition. Combination of SAXS and molecular dynamic (MD) simulation reveals how the local structural effect on the global conformation.
    We found that the new orientation of TF individual domains have a better predicted SAXS data than crystal structures. Applied Flory’s theory on experimental SAXS results, knotted proteins have similar global conformation with those unknotted proteins.

    Content 中文摘要 3 Abstract 4 Content 5 List of Figures 7 List of tables 9 List of equations 9 1 Introduction 10 1.1 Multi-domain protein 11 1.1.1 Trigger factor 11 1.2 Knotted protein 16 1.2.1 YbeA 20 1.2.2 YibK 20 1.2.3 HP0242 22 1.2.4 Ubiquitin C-terminal Hydrolase 1 23 2 Background 24 2.1 SAXS 24 2.1.1 Background of SAXS 26 2.1.2 Data processing 27 2.1.3 Experimental SAXS problems 32 2.1.4 SAXS analysis 34 2.1.4.1 Determination of molecular weights of proteins by SAXS 34 2.1.4.2 Protocols of the usage of ATSAS programs 35 2.1.4.3 Assessment of data accuracy 38 2.2 Application of Flory’s theory to study protein folding 41 2.2.1.1 Radius of gyration analysis on existing protein structures 42 2.2.1.2 Intrinsically disorder proteins 43 2.2.1.3 Flory’s theory of chemically denatured proteins 44 2.2.1.4 Flory’s theory of native proteins 45 2.3 Molecular Dynamics Simulation 46 3 Material and Methods 47 3.1 SAXS at NSRRC 49 3.1.1 Introduction of instrument operation procedures 50 3.1.2 Data processing at NSRRC 51 3.2 Data process of ATSAS suite programs 55 3.2.1 Primus 55 3.2.2 Dammif 58 3.2.3 Supcomb 60 3.2.4 Damaver 61 3.2.5 SASREF 63 3.2.6 EOM 64 3.3 Other online servers 65 3.3.1 FoXS 65 3.3.2 BIOISIS 65 4 Results 66 4.1 Results of SAXS analyses 68 4.2 Multi-domain protein 74 4.2.1 TF 76 4.2.1.1 Full length TF 76 4.2.1.2 Individual domains of TF 78 4.2.1.3 Combination of two domains 82 4.2.1.4 Rigid body modeling 85 4.3 Knotted proteins 87 4.3.1 SAXS results of native knotted proteins 87 4.3.1.1 YbeA 87 4.3.1.2 YbeA & YibK 89 4.3.1.3 HP0242 91 4.3.1.4 UCHL1 WT and I93M 93 4.3.2 Chemical denaturation of knotted proteins 96 4.3.2.1 Experimental SAXS data 96 4.3.2.2 Ensemble Optimization Method (EOM) 97 4.4 MD simulations 99 4.4.1 Comparison of SAXS with MD simulations 99 5 Discussion 102 5.1 Comparison of different SAXS parameters 102 5.2 Surveys of Rg values of proteins under native and chemically denaturing conditions 104 5.3 Molecular modeling of TF by SAXS 106 5.4 Knotted protein analysis 108 6 Conclusion 111 7 Supplementary information 112 7.1 Experimental Rg values of proteins 112 7.2 Experimental SAXS parameters 119 7.3 Rg values of knotted proteins as a function of chemical denaturant concentration 121 7.4 Inputs for setting up MD simulations by GROMACS 122 8 Appendix 127 8.1 Guinier equation 127 8.2 Flory’s equation 132 9 Reference 134

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