Facilitated diffusion of proteins through crumpled fractal DNA globules.
Facilitated diffusion of proteins through crumpled fractal DNA globules.
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DOI：
10.1103/physreve.92.012702
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发表时间：
2015-07
期刊：
影响因子：
--
通讯作者：
J. Smrek;A. Grosberg
中科院分区：
文献类型：
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作者：
J. Smrek;A. Grosberg
我们探索了在高等真核生物和拓扑受限的致密聚合物的染色质纤维中发现的特定的分形球构象如何影响蛋白质在这种环境中的促进扩散。利用标度变元和支持的蒙特卡罗模拟，我们将DNA环概率分布、分维和蛋白质对DNA的非特异性亲和力与蛋白质的有效扩散参数联系起来。我们显式地考虑了蛋白质后续再吸附事件之间的相关性，我们发现，对于具有高节段间表面维度的皱缩球状构象，促进扩散比具有光滑表面的密集分形构象的促进扩散更快。作为副产品，我们得到了一种假设材料的宏观电导率的表达式，该材料由浸入弱导电介质中的导电分形纳米线组成。
We explore how the specific fractal globule conformation, found for the chromatin fiber of higher eukaryotes and topologically constrained dense polymers, affects the facilitated diffusion of proteins in this environment. Using scaling arguments and supporting Monte Carlo simulations, we relate DNA looping probability distribution, fractal dimension, and protein nonspecific affinity for the DNA to the effective diffusion parameters of the proteins. We explicitly consider correlations between subsequent readsorption events of the proteins, and we find that facilitated diffusion is faster for the crumpled globule conformation with high intersegmental surface dimension than in the case of dense fractal conformations with smooth surfaces. As a byproduct, we obtain an expression for the macroscopic conductivity of a hypothetic material consisting of conducting fractal nanowires immersed in a weakly conducting medium.