蛋白質催化位置之結構特性

Abstract

大量的未知功能蛋白質結構已經被解出並存放於蛋白質資料銀行(Protein Data Bank-PDB)。因此，藉著蛋白質結構來臆測其功能也變得相當重要。為了達成這個目標，蛋白質結構-功能關係的知識將會成為非常有用。藉著一個有著887個已知酵素結構且有2368個催化殘基的資料集我們提出了一個非常廣泛的分析。我們發現(i) 多數的催化殘基不是有電性(charged)就是有極性(polar); (ii) 催化殘基通常座落於纏繞區(coil region); (iii) 催化位置通常較深層; (iv) 催化殘基具有較低的韌性(flexibility); (v) 催化位置似乎較喜歡座落於接近蛋白質領域(domain)的中心; (vi) 催化位置通常發生在蛋白質中較緊密的地方。我們的結果也提供了蛋白質催化殘基結構特性的資訊，這個資訊和序列保存度具有互補關係。總而言之，我們的結果在了解蛋白質結構-功能關係上也許會有幫助。更進一步而言，這樣的結果也許在未來預測蛋白質催化位置上能提供發展新方法的新視野。

An enormous number of structures of proteins with unknown function has been solved and deposited in PDB. Hence, it becomes increasingly important to infer function directly from protein structures. To do this, the knowledge of protein structure-function relationship will be valuable. We carried out a comprehensive analysis of the dataset consisting of 887 enzymes of known structure with a total of 2368 catalytic sites. We found that (i) most catalytic residues are either charged or polar; (ii) catalytic sites are usually located on coil region; (iii) catalytic sites are usually buried; (iv) catalytic residues appear to be less flexible; (v) catalytic sites seem to prefer to be in the proximity of the centroid of the domains; (vi) catalytic sites usually occur in the compact regions of proteins. Our results also provide information of structural characterization of catalytic residues in protein, which is complementary to that sequence conservation. In summary, our results may be helpful in understanding the protein structure-function relationship. Furthermore, they may give new insight into developing novel methods for the prediction of catalytic sites in protein.