论文标题
建模与锚定的蛋白质簇相互作用的超螺旋DNA相互作用：定量估计染色体DNA超螺旋。
Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling
论文作者
论文摘要
我们使用蛋白质的DNA和DNA锚定簇之间的相互作用频率研究了沿染色体的DNA超螺旋密度（$σ$）的测量。具体而言，我们展示了DNA超螺旋的物理学如何导致细菌中PARB蛋白的结合特性的定量建模，其中心粒状位点{\ it pars}。使用此框架，我们在{\ it大肠杆菌}染色体中为$σ$提供了上限，与质粒值一致，并提供了概念证明，以进行高精度测量。为了得出这些结论，我们重新审视了PARB簇的形成问题。我们尤其预测它们是由于生产蛋白质的流入和多余蛋白质的流出之间的非平衡，固定平衡引起的，即它们的作用像液体样蛋白冷凝物，具有非常规的“漏水”边界。
We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $σ$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.
