以功能基團計分矩陣預測蛋白質與去氧核醣核酸交互作用之結合模式

Abstract

蛋白質與去氧核醣核酸(DNA)的交互作用出現在細胞的許多重要機制中，這些機制包括：基因的轉錄、複製、重組、以及轉譯等。探究基因轉錄調控機制中的蛋白質是以何種結合模式與DNA進行交互作用是重要的研究課題。然而，使用傳統的生物實驗方法通常較為昂貴且耗時；在現階段，不斷增加的蛋白質與去氧核醣核酸之共結晶結構即提供了一個研究胺基酸及核苷酸之間如何進行交互作用的豐富資料來源，根據這些資料，我們有機會針對此問題進行更深入的研究。 我們提出了一個計算方法，是以蛋白質與去氧核醣核酸其中所產生的空間位向以及各類化學鍵結，來建立這兩者之間交互作用的模型。此方法不但可以提供交互作用之模型，矩陣預測更可以呈現各類胺基酸及核苷酸之間鍵結的偏好程度。由ProNIT的70筆點突變資料來看，我們發現考慮氫鍵以及靜電吸引力之計分矩陣，較過去研究更能反映出胺基酸在點突變之後與核苷酸結合的自由能變化。 接著我們以環磷酸腺苷(cAMP)受質蛋白(cAMP receptor protein, CRP)做為建立模型的研究之實例，掃描其轉錄結合區(TFBS)的核酸序列。最後嘗試以提出的計分矩陣解釋環磷酸腺苷受質蛋白做為不同的調控轉錄因子與去氧核醣核酸結合之間的機制。我們發現位在轉錄結合區GTG motif上的鳥嘌呤胞嘧啶配對(GC pair)，其保留程度可能與環磷酸腺苷受質蛋白的正負向調控有關。

Protein–DNA interactions are involved in many important cellular processes, such as transcription, replication, recombination and translation. Understanding the binding model of protein–DNA complexes is essential to investigate many cellular regulations, including transcriptional regulation. However, it is usually expensive and time-consuming to clarify the binding model of proteins and DNA by using experimental approaches. Currently, because of the increasing number of solved protein–DNA complex structures, from which potentials of residue–nucleotide interaction could be derived, we have chance to address this issue. We proposed computational approach to modeling protein–DNA interactions by considering the contact information of the steric and specific energies. Such binding model and scoring matrices not only provided the binding model, but also indicated the preference of the pairs of interacting amino acids and nucleotides. By 70 mutated residues from ProNIT, we found that the scoring matrices considering hydrogen bonds and electrostatic interaction could reflect the change of free energy better than that without considering these interactions. We then started to scan on each transcription factor binding site (TFBS) sequences according to the template model of cAMP receptor protein (CRP). Finally, we tried to use our scoring matrices to explain the different regulation mechanisms while CRP served as activator, repressor, or dual. We found that the conservation of GC pairs in GTG motif have relations with gene regulations mediated by CRP.