辨別NAD依賴蛋白質上與NAD結合的胺基酸位置

Identification of NAD Binding Site on NAD-dependent Proteins

林督翔(Tu-Hsiang Lin)

指導教授 ： 趙雅婷

元智大學/資訊學院/生物與醫學資訊碩士學位學程/碩士(2011年)

摘要

輔因子(cofactors)或是配體(ligands)在細胞中會去辨識它們的目標蛋白，並且準確的結合上去以發生生物反應機制。煙醯胺腺嘌呤二核苷酸(Nicotinamide adenine dinucleotide, NAD+)是其中最為常見的輔因子，它在細胞中參與多種氧化還原反應。本研究利用生物資訊的方法預測NAD依賴蛋白質與NAD結合之殘基的位置，所使用的NAD蛋白質資料取自於PDB資料庫，並採用quickrbf作為分類工具。本研究使用的屬性有蛋白質二級結構特性、ASA、SPP、CPP、BPP、PSSM和AAindex等等。實驗結果顯示最佳的單一屬性為PSSM，它的正確性有85.37%；若使用多個屬性的結合，以PSSM+SPP屬性的結果較佳，正確性可達85.62%。

關鍵字

煙醯胺腺嘌呤二核苷 ； 酸

並列摘要

Some small molecular cofactors or ligands play crucial roles in cell metabolism. Nicotinamide adenine dinucleotide (NAD+) is one of the most important components of cellular redox reaction systems. In this study we identify NAD binding sites on NAD-dependent proteins using bioinformatic method. NAD binding protein sequences were collected from PDB database to train the quickrbf classifier and to evaluate the performance. Secondary structure data, ASA, SPP, CPP, PSSM, BPP and AA index were examined as features. We found that the PSSM were better than other features for prediction of NAD binding residues. The balance accuracy of 85.37% was obtained using PSSM features. The classifier achieved a balance accuracy of 85.62% using PSSM+SPP features.

並列關鍵字

(Nicotinamide adenine dinucleotide

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