Taylor William R
Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
Comput Biol Chem. 2007 Jun;31(3):151-62. doi: 10.1016/j.compbiolchem.2007.03.002. Epub 2007 Mar 24.
The current knowledge on topological knots in protein structure is reviewed, considering in turn, knots with three, four and five strand crossings. The latter is the most recent to be identified and has two distinct topological forms. The knot observed in the protein structure is the form that requires the least number of strand crossings to become un-knotted. The position of the chain termini must also correspond to a position that allows (un) knotting in one move. This is postulated as a general property of protein knots and other more complex knots with this property are proposed as the next most likely knots that might be found in a protein. It is also noted that the "Jelly-roll" fold found in some all-beta proteins would provide likely candidates. Alternative measures of knottedness and entanglement are reviewed, including the occurrence of slip-knots. These measures are related to the complexity of the protein fold and may provide useful filters for selecting predicted model structures.
本文综述了目前关于蛋白质结构中拓扑纽结的知识，依次考虑了具有三股、四股和五股交叉的纽结。五股交叉纽结是最近才被发现的，有两种不同的拓扑形式。在蛋白质结构中观察到的纽结是解开纽结所需股交叉数最少的形式。链端的位置也必须对应于一次移动就能实现（解）纽结的位置。这被假定为蛋白质纽结的一个普遍特性，具有此特性的其他更复杂的纽结被认为是下一个最有可能在蛋白质中发现的纽结。还指出，在一些全β蛋白中发现的“果冻卷”折叠可能是候选对象。本文还综述了纽结度和缠结的其他度量方法，包括活结的出现情况。这些度量方法与蛋白质折叠的复杂性有关，可能为选择预测的模型结构提供有用的筛选标准。
