分析鹼基對序列之形變能與階梯結構參數之關聯性

Abstract

生物資訊中關於去氧核醣核酸(以下簡稱DNA)和蛋白質鍵結方法的研究，大多著重於兩者的直接接觸，但其實蛋白質不只靠鹼基和胺基酸之間的直接接觸位置來辨識鍵結機制，也會透過間接的資訊來判別，例如DNA的結構就可以間接透露出其與蛋白質的互動關係，許多文獻指出，一個突變的鹼基雖然沒有和任何胺基酸接觸，但卻會影響到DNA和蛋白質間的鍵結親和力。在間接影響中，蛋白質可能會透過幾種方法辨識是否要與DNA鍵結，例如以水為媒介的接觸、以特定序列的DNA結構特徵或是以DNA在鍵結中被彎曲的程度來判別。此論文的目的是使用一組DNA結構參數，分析在Protein Data Bank資料庫(以下簡稱PDB)蒐集的DNA-蛋白質複合物檔案中DNA結構之形變能變化量。將所有檔案的DNA結構參數算出之後，分析大量結構參數的群聚關係，藉以找出DNA序列中可以互相替換的傾向，再以結構參數為基礎，利用彈力方程式算出DNA中鹼基對能量，由於能量較低一般來講結構較為穩定，透過能量變化量提供往後對DNA上鹼基做替換時之優先考量替換種類。

Studies of recognition between DNA and protein most focus on the direct contacts. In fact, amino acids recognize specific DNA sequences not only through direct contacts but also utilizing indirect interaction. Many studies have shown that mutations of base that are not in contact with any amino acids also affect binding affinities. Examples of indirect affection are proteins may recognize a DNA sequence via water-mediated contacts, sequence-dependent conformational features, or binding-induced distortion of the DNA. The purpose of this thesis is to analyze the DNA structure of protein-DNA complexes collected in Protein Data Bank. After calculation of DNA conformational parameters, base steps are clustered based on parameters and base steps with similar conformations are analyzed from the aspect of binding free energy. Statistical analysis concludes that some substitution of similar base step pairs can be the prior consideration when randomizing DNA sequences.