蛋白質結構域交換現象之資料庫開發

Abstract

蛋白質結構域交換現象：three-dimensional (3D) domain swapping, 是種有趣且重要的蛋白質結構現象，不過相關研究資源卻不易取得，本研究旨在建立一個蛋白質結構域交換現象資料庫。在這份研究中，我們使用DS-SARST (Three-dimensional Domain Swapping Search Aided by Ramachandran Sequential Transformation) 做為偵測蛋白質結構域交換現象的搜尋引擎，選定具有寡聚體 (oligomer) 四級結構的蛋白質，將open-form polypeptide與closed-form polypeptide做疊合比對，再經人工篩選判定是否具有蛋白質結構域交換現象。篩選出具有DS現象之蛋白質後，進一步按蛋白質結構分類資料庫 SCOP (Structural Classification of Proteins) 做分類。最後，整合許多數據和文獻資料，建立了一個蛋白質結構域交換現象之資料庫，定名為3D Domain Swapping Protein Database (DSPDB）。研究過程中，我們對DS現象提出了與以往不同的分類方式，且發現了許多過去文獻中不曾討論過的「類DS現象」。 DSPDB 目前含有 4784 個95%序列相同度不重複(non-redundant)的蛋白質。網頁介面相當簡潔易用，可階層化地瀏覽或綜覽DS資料，並附有跨瀏覽器適用的結構展示功能。此資料庫對蛋白質結構域交換現象這研究領域的整體進展相信會有很大幫助，網址是: http://140.113.15.73/~wade/dspdb/srv/。

The purpose of the study was to create a database of domain swapping which was important but had lack of information. Another aim was to create a practical and convenient database. The study was conducted by the procedures below. At first, “DS-SARST” (three-dimensional Domain Swapping Search Aided by Ramachandran Sequential Transformation) was used as a search engine that for identifying quaternary structure of proteins which were oligomers. In order to examine domain swapping phenomenon, the open-form and the closed-form of the selected proteins were stacked up and were visually compared. Then, the results of comparison were sorted according to Structural Classification of Proteins (“SCOP”). Detecting DS relations between proteins in this step, we even added more details to the classification against some undefined structures. After we analyzed the data and integrated related studies, the Domain Swapping Protein Database (“DS-PDB”) was finally created. Therefore, it became accessible to any web browser and the user interface was easily operated. To conclude, the DS-PDB which we created was a feasible tool. It is used to find out the specific protein or analyze the relationship between protein structure and function. It takes less time to search for the information, and it helps people who are doing researches about domain swapping.