臺灣博碩士論文加值系統

硫磺礦硫化葉菌(Sulfolobus solfataricus)擁有耐熱抗性以及耐酸抗性，在攝氏溫度80-85度和酸鹼值2-4的時候生長最為優良，所以硫磺礦硫化葉菌可以在火山和溫泉等地找到。硫磺礦硫化葉菌擁有分子量7kDa、8kDa以及10kDa的去氧核糖核酸結合蛋白質，其中，本篇論文中所使用的Sso7c4正是屬於7kDa裡的其中一個。Sso7c4是一種類組織蛋白(histone-like)的蛋白質二聚體，同樣地，Sso7c4也擁有耐熱抗性以及耐酸抗性。
在本篇論文中，我們建構了一個初始模型，包含了兩個Sso7c4二聚體蛋白質和長度為24個鹼基的雙股去氧核醣核酸，並且我們採用了分子動態模擬來模擬這個系統，研究Sso7c4二聚體蛋白質和去氧核醣核酸之間的交互作用。
在模擬中，我們觀察到，Sso7c4裡的精胺酸(R22/R11′)以及羧基端(C-terminus)都會和去氧核醣核酸的骨架上的磷酸鹽有交互作用，這個觀察結果跟先前的研究結果相符合。除此之外，我們還發現到，除了精胺酸(R22/R11′)以及羧基端之外，Sso7c4裡的帶正電荷的離胺酸(K)也會和去氧核醣核酸的骨架上的磷酸鹽有交互作用，有趣的是，離胺酸在Sso7c4蛋白質序列裡佔了8個(K8，K20，K24，K28，K34，K45，K50，K54)，有6個(K8，K20，K24，K28，K50，K54)有交互作用。
接觸圖(contact map)的分析顯示了兩個Sso7c4蛋白質二聚體之間有重要的分子間作用。特別的是，我們還觀察到了Sso7c4蛋白質二聚體在去氧核醣核酸的骨架上的移動(slide)，正是這些交互作用使去氧核醣核酸結構變形、彎曲。

Sulfolobus solfataricus can be found in volcanoes and hot spring. It grows best at 80-85°C and at the pH level of 2-4. Sso7c4, a member of 7-kDa families of Sulfolobus solfataricus, is a histone-like dimer protein; it can resist to heat and acid. In this study, we employed molecular dynamics simulations to investigate the interactions between Sso7c4 dimers and a double-stranded DNA. We observed that an arginine pair (R22/R11′) and C-terminus of Sso7c4 have significant interactions with the phosphates on the DNA backbone, which are consistent with results of binding assay. In addition, we also observed that six positively charged lysine residues (K8，K20，K24，K28，K50，K54) have interactions with the phosphates on the DNA backbone. Furthermore, the whole Sso7c4 proteins sliding on DNA backbone is observed. Contact map analysis shows the two Sso7c4 dimers have important intermolecular interactions through hydrophobic residues pulling two Sso7c4 dimers closer. These interactions and the sliding of proteins on DNA backbone deform the DNA structure such as bending and shortening the DNA length.

摘要 i
Abstract ii
致謝 iii
Table of contents iv
List of Figures vi
List of Tables ix
Introduction 1
Computational Methods 4
Construction of initial Sso7c4-DNA complex Model 4
Computational details 11
Trajectory Analysis 12
Results and Discussion 13
Structural Change 13
End-to-End Distance of DNA in Complex 15
Dimer to Dimer Distance in Sso7c4-DNA complex System 19
Interactions between Sso7c4 dimers and DNA 21
Lysine-Phosphate Interactions 27
Interactions between two Sso7c4 dimers 41
Conclusion 44
References 46
Appendix A 50
Appendix B 51
Appendix C 52
Appendix D 53
Appendix E 54
Appendix F 55
Appendix G 56
Appendix H 57
Appendix I 58
Appendix J 59
Appendix K 60

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