Flammini Alessandro, Maritan Amos, Stasiak Andrzej
International School for Advanced Studies, Trieste, Italy.
Biophys J. 2004 Nov;87(5):2968-75. doi: 10.1529/biophysj.104.045864. Epub 2004 Aug 23.
The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases.
随机环化聚合物可用的构型空间被划分为各个纽结类型可及的子空间。聚合物数值模拟中使用的理想链可以探索所有子空间,而例如形成8字结的真实闭合链则仅局限于对应于该纽结类型的子空间。人们可以从概念上将各种纽结类型的构型空间组装与一种复杂泡沫进行比较,其中各个单元界定了给定纽结类型可用的构型空间。泡沫中的相邻单元包含仅通过一次链段间通道就能相互转化的纽结。在纽结构型层面发生的这种链段 - 链段通道对应于在泡沫状纽结空间中相邻单元之间的界面处的通道。我们在此使用受DNA拓扑异构酶启发的模拟方法来表征相邻纽结空间之间的有效界面面积以及各个纽结空间的表面积与体积之比。这些结果提供了一个更好理解各种DNA拓扑异构酶作用机制所需的参考系统。