Taylor W R
Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK.
Nature. 2000 Aug 24;406(6798):916-9. doi: 10.1038/35022623.
The search for knots in protein has uncovered little that would cause Alexander the Great to reach for his sword. Excluding knots formed by post-translational crosslinking, the few proteins considered to be knotted form simple trefoil knots with one end of the chain extending through a loop by only a few residues, ten in the 'best' example. A knot in an open chain (as distinct from a closed circle) is not rigorously defined and many weak protein knots disappear if the structure is viewed from a different angle. Here I describe a computer algorithm to detect knots in open chains that is not sensitive to viewpoint and that can define the region of the chain giving rise to the knot. It characterizes knots in proteins by the number of residues that must be removed from each end to abolish the knot. I applied this algorithm to the protein structure database and discovered a deep, figure-of-eight knot in the plant protein acetohydroxy acid isomeroreductase. I propose a protein folding pathway that may explain how such a knot is formed.
在蛋白质中寻找纽结的研究，几乎没有发现什么会让亚历山大大帝拔剑相向的东西。除了翻译后交联形成的纽结外，少数被认为是纽结的蛋白质形成简单的三叶纽结，其中链的一端仅通过少数几个残基延伸穿过一个环，在“最佳”例子中是十个残基。开放链中的纽结（与封闭环不同）没有严格定义，如果从不同角度观察结构，许多弱蛋白质纽结就会消失。在这里，我描述了一种计算机算法，用于检测开放链中的纽结，该算法对视角不敏感，并且可以定义产生纽结的链区域。它通过从两端去除多少残基才能消除纽结来表征蛋白质中的纽结。我将此算法应用于蛋白质结构数据库，在植物蛋白乙酰羟酸异构还原酶中发现了一个深的八字形纽结。我提出了一种蛋白质折叠途径，可能解释这种纽结是如何形成的。
