Chapter 3 Results and Discussions
C- loop
3.2 在 T. thermophilus 30S rRNA 中辨識單股 α-loop 結構模體
α-loop 的名稱由來是它的三級結構外型就像「α」字母。α-loop 一共有八個鹼基，其中六個鹼基構成 loop 區域（Figure 3-17）。α-loop 在 23S 與 16S rRNA 中可以發現到，α-loop 可以被提供輔助大小次 單元核醣體組合的蛋白質所辨識，以幫助核醣體正確組合[4, 12]。本 實驗取 COMPADRES[28]所記載的兩個α-loop 其中之一當作 query
（PDB id 為 1JJ2，0 chain，位置 1100-1107）搜尋另一個在 T.
thermophilus 30S rRNA 中的α-loop。
Figure 3-17: α-loop 結構模體。(a) query 結構模體的鹼基對示意 圖。(b) query 結構模體的三級結構。
RNAMotifScan 一共找到兩個結果（Table 3-5）。在我們分析其 第一個結果的三級結構後，我們認為第一個是錯誤結果，因為三級
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結構並不相似（Figure 3-18b）。但是 RNAMotifScan 認為這一個結果 是最高分的原因是因為在目標結構模體裡的兩個鹼基對與 query 的 兩個鹼基對都是 match 的（Figure 3-18a）。比起第二個正確答案的目 標結構模體只有一個鹼基對與 query 是 match 的分數高很多（Figure 3-19a 與 3-19b）。因為我們的方法能夠反映出 loop 區域的相似性
（Figure 3-19a），所以能準確地辨認出正確答案，排除掉錯誤的答 案。經過這個實驗所示，我們的方法在辨識 loop 區域較長且鹼基對 數目相對較少的結構模體比 RNAMotifScan 能更精準。
Table 3-5: 我 們 的 方 法 與 RNAMotifScan 分 別 以 α -loop 在 T.
thermophilus 30S rRNA 中搜尋相似結構模體高分的結果比較。
符號註記：「-」代表未有結果。
Figure 3-18: RNAMotifScan 的第一個結果。(a)比對結果，兩組對在
RMSD FPR RMSD FPR
1 A 568-574 3.630 0.000
2 A 503-510 1.048 0.000 1.048 0.000
Our method RNAMotifScan No. Chain Location
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一起的鹼基對皆為 match。(b)比對結果的三級結構圖。
Figure 3-19: 我們的結果與 RNAMotifScan 的第二個結果。(a)我們的 比對結果，loop 區域的結構序列完全 match。(b) RNAMotifScan 的比 對結果。(c) 比對結果的三級結構圖。
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Chapter 4 Conclusions
在這個研究中，我們首先將 RNA 的二級與三級結構資訊編碼成弧線 註解的一維結構序列，接著再把 RNAMotifScan 的程式修改成利用 RNA 二級與三級結構資訊來辨識 RNA 的結構模體。最後，我們的實 驗結果也顯示出我們的方法確實可以進一步地提升 RNAMotifScan 在 辨識 RNA 結構模體的執行效能。然而，如本論文的 Introduction 中所 述，RNAMotifScan 在做弧線註解序列的比對時，對鹼基對（弧線）
而言，它只考慮了 match 與 mismatch 而已，事實上還有其它鹼基對比 對 方 式 （ 如 Figure 1-3 所 示 的 arc-breaking 、 arc-altering 與 arc-removing）。因此，如何在弧線註解一維結構序列兩兩比對方法中 將所有的鹼基對比對方式都納入考慮將會是一個有趣且值得研究的 問題。
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