打結蛋白質的分析

Abstract

蛋白質的結構與功能一直都是息息相關，然而特殊的蛋白質拓譜結構更令人遐想。自然界中打結的蛋白質不僅結構特殊，其摺疊的過程更是生物學家關心的課題。目前打結蛋白質只有四種，包含了31結（平結）、41結（八字結）、52結和61結（the Stevedore’s knot），然而得知打結蛋白的摺疊過程，卻是個具有挑戰的問題，因為我們無法去想像蛋白質摺疊過程中，是如何纏繞出有打結的結構。我們過去已經發表一篇有關於偵測打結蛋白質的網站pKNOT，以及一篇有關於綜合地分析蛋白質打結種類及特性的章節，在序列和基因分析的書刊上，現在我們首次利用序列比對以及結構預測的方法，在新版本的pKNOT v2的網站裡，提供使用者輸入或者上傳蛋白質序列，去分析是否為具有打結的特性，此外也同時更新了有關打結蛋白質的資料庫，以便使用者去做統計跟研究。我們深信利用生物資訊的方法，可以提供更多的便利及資訊，讓生物學家更容易去分析以及了解蛋白質的結構。

The relationship between the protein function and protein structure is close and important at all times. Knotted proteins, rarely seen in proteins, have recently received lots of attention due to their interesting topological novelty as well as its puzzling folding mechanisms. At present, there are only four types of knot identified in protein structures – the 31 knot (or the trefoil knot), the 41 knot (or the figure-eight knot), the 52 knot and the 61 knot (or the Stevedore’s knot). The folding mechanism of a knotted protein presents a very challenging problem, because it is hard to imagine a peptide chain will thread through loops several times form a knot. We previously published a pKNOT server to determine protein knot or not, which provides a structural database of knotted proteins, and comprehensive analysis of knotted protein in a book. However, there lacks a convenient platform performing similar tasks directly from protein sequence. In pKNOT v.2, we implement a homology modeling tool such that can now accept protein sequences in addition to 3D structures or PDB IDs and return knot analysis. In addition, we have updated the database of knotted proteins from the current PDB with a combination of automatic and manual procedure. We believe that the analytics and applications of protein structure will provide better convenience and information to biologists.