Molecular and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy.
Molecular and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy
Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E2991-E2997. doi: 10.1073/pnas.1701321114. Epub 2017 Mar 28.
We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.
我们使用精确的粗粒化模型和随机分子动力学模拟来研究带有纽结的 10kbp 长 DNA 环的孔道转运。通过监测各种拓扑和物理可观测量，我们发现，与之前假设的不同，存在两种性质上不同的纽结转运模式。对于这两种模式，孔道阻塞由纽结通过引起，持续时间短暂，通常发生在转运的后期阶段。这两种效应都与实验结果非常吻合，可以用一个基于同时拉紧和滑动转运纽结链的透明模型来合理化。我们还观察到，孔道阻塞事件的持续时间更多地受到纽结转运速度的控制，而不是纽结大小的控制。这些特征应该会促进对生物聚合物自发纽结的未来实验的解释和设计。
