臺灣博碩士論文加值系統

錨蛋白重複域(Ankryrin Repeat Domain, ARD)是由一組序列相似度低但結構極為相似的基本重複單元所組成的蛋白質結構。這類蛋白結構經演化後，基本重複單元的重複數量及重複序列內容存在極大差異性，對多細胞生物的不同細胞訊息調控路徑扮演重要且多樣的特定生物功能。例如透過羥基化作用與抑制缺氧誘導因子(Factor Inhibiting HIF, FIH)酵素結合，降低FIH對細胞內缺氧誘導因子(Hypoxia-Inducible Factor, HIF)轉錄活性的抑制，直接影響血管增生、腫瘤細胞生長及能量代謝等重要功能。為正確預測ARD蛋白質序列及評估不同功能分類，本論文採用序列排比及二級結構特徵的比對技術進行序列自動分析。所建置的線上自動預測分析系統可辨識查詢序列是否為ARD家族、自動切割基本重複單元區段及辨識所有可能結合的羥基化位置。經測試資料集的實驗結果證實本論文所建構的系統對ARD序列的自動辨識可以達到94.9%的敏感度、90.7%的特異度和92.8%的正確率；針對ARD序列之基本重複單元自動切割可以達到94.6%的敏感度、88.6%的特異度和92.7%的正確率。除此之外，本研究同時使用ARD的序列內容、幾何結構及基因本體論的註解資訊進行ARD序列的功能群組分析，結果顯示以基因本體論的功能分群和以序列內容的分群結果較為相關，而且分群結果將具有相同功能的ARD歸類為同一群組。此外，本論文所建構的自動預測分析系統也針對Ensembl資料庫第82版的69個模式物種進行ARD序列預測，結果可以跨物種辨識出17,157條ARD序列，並提供每個ARD序列基本重複單元的位置資訊及所有可能羥基化的結合位點標註資訊。我們相信此線上預測系統及完整ARD資料庫的建置能夠有效協助生物學家進一步了解ARD的交互作用機制及完整的生物功能。

Ankyrin Repeat Domain (ARD) is an alpha-solenoid repeat structure formed by cascading a series of ankyrin repeat units. These fundamental repeat units within a structure possess low sequence similarity but high structural conservation. The number of fundamental repeat unit and sequence contents are diversified after functional evolution, and this type proteins play important roles in modulating diverse cellular pathways for most multicellular organisms. For example, ARDs were discovered as an important factor influencing hypoxia response through hydroxylation interaction with Factor Inhibiting HIF (FIH) enzymes which can repress HIF under normoxia environment, and it directly affects angiogenesis, tumor cell growth, and energy metabolism. In this study, we designed a sequence based method incorporated with secondary structural features to predict boundaries of all internal repeats within an ARD protein, and the binding positions for hydroxylation were also identified through pattern matching approaches. Performance of the proposed prediction system achieved a sensitivity of 94.9%, a specificity of 90.7%, and an accuracy of 92.8% for ARD recognition. Regarding internal repeat segmentation, the proposed system achieved a sensitivity of 94.6%, a specificity of 88.6%, and an accuracy of 92.7%. To perform function clustering analysis, we clustered all the detected human ARD proteins from PDB database into several groups based on sequence, structure, or GO term information. The results showed that GO term based and sequence based clustering results provided higher correlations, and several clustered groups indeed possess similar functions. We also performed comprehensive ARD prediction analysis on 69 model species collected in Ensembl database (version 82). The constructed database contains 17,157 ARD proteins through cross-species comparison, and all identified ARD sequences in conjunction with internal repeat locations and possible hydroxylated binding sites are all clearly annotated. We believe that the on-line ARD prediction system and constructed database can effectively facilitate biologists in further exploration on ARD related researches regarding protein-protein interaction mechanism and understanding its comprehensive function.

摘要 I
Abstract II
致謝 III
Table of Contents IV
List of Figures V
List of Tables VI
1 Introduction 1
2 Materials and Methods 8
2.1 Dataset 8
2.2 Methods 9
2.2.1 ARD Identification 9
2.2.2 Internal repeat identification for ARD proteins 10
2.2.3 FIH-ARD Hydroxylation site 12
2.3 ARD functional clustering 13
2.3.1 Methods of clustering 13
2.3.2 Consistency of clustering 15
3 Result and discussion 16
3.1 Statistical results 16
3.2 Internal repeat unit segmentation 17
3.3 Results of clustering 18
4 ARD database system 25
5 Conclusion 28
6 References 25

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