綜合分析蛋白質的打結

Abstract

近年來，隨著在Protein Data Bank (PDB)已知的結構越來越多，蛋白質打結的結構也被不斷的發現出來。研究指出打結的區域有助於配體的結合以及酵素的活性，蛋白質中植物光敏色素的色基結合的範圍以及酮醇酸還原異位酶或SPOU甲基轉移酶。此外，在文獻中有著很多被定義錯誤的打結，因此，我們做出了protein Knot 的database 以及可提供使用者更容易去觀察protein 是否打結，在pKNOT 上面使用者可以輸入pdb id 或者上傳pdb structure 的座標。pKNOT將會使用Taylor’s smoothing algorithm 去判斷是否有打結。所有偵測protein的knot 都會以Java 的圖形介面方式呈現，讓使用者更容易去得知其位置跟結構。我們深信pKNOT 對於生物結構以及生物領域，會有著很大的幫助。

Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank(PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol–acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the general biologists. Here, we present the first web server to detect the knots in proteins as well as provide information on knotted proteins in PDB—the protein KNOT (pKNOT) web server. In pKNOT, users can either input PDB ID or upload protein coordinates in the PDB format. The pKNOT web server will detect the knots in the protein using the Taylor’s smoothing algorithm. All the detected knots can be visually inspected using a Java-based 3D graphics viewer. We believe that the pKNOT web server will be useful to both biologists in general and structural biologists in particular.