结合剂和单体的价决定了染色质坍塌和溶胀的程度。

IF 3.1 2区 化学 Q3 CHEMISTRY, PHYSICAL
Sougata Guha
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引用次数: 0

摘要

多价dna桥接蛋白介导的染色质聚合物塌缩是细胞内染色质组织的驱动因素之一。这些多价蛋白可以结合到染色质主干上的远端结合位点,并使它们在空间上接近,导致构象崩溃。最近,有人提出,这些蛋白质不仅驱动染色质聚合物的崩溃,而且在较高浓度下也会溶胀。在这项研究中,我们研究了这种意想不到的肿胀行为背后的物理机制。我们使用了一种粗粒均聚物的朗之万动力学模拟来研究结合剂和单体的价对聚合物构象的影响。我们发现,虽然聚合物的坍塌程度强烈依赖于粘结剂的价,但溶胀的程度在很大程度上取决于单体的价。此外,我们还发现了两种不同的物理机制,驱动聚合物排除体积效应的重新膨胀和远程环的损失。最后,我们获得了一个分类图,以确定每种机制是导致聚合物重新膨胀的主要因素的机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Binder and monomer valencies determine the extent of collapse and reswelling of chromatin.

Multivalent DNA-bridging protein-mediated collapse of chromatin polymers have long been established as one of the driving factors in chromatin organization inside cells. These multivalent proteins can bind to distant binding sites along the chromatin backbone and bring them together in spatial proximity, leading to collapsed conformations. Recently, it has been suggested that these proteins not only drive the collapse of the chromatin polymer but also reswelling at higher concentrations. In this study, we investigate the physical mechanisms underlying this unexpected reswelling behavior. We use the Langevin dynamics simulation of a coarse-grained homopolymer to investigate the effects of the valencies of both the binders and the monomers on the polymer conformations. We find that while the extent of collapse of the polymer is strongly dependent on the binder valency, the extent of reswelling is largely determined by the monomer valency. Furthermore, we also discovered two different physical mechanisms that drive the reswelling of the polymer-excluded volume effects and loss of long-range loops. Finally, we obtain a classification map to determine the regimes in which each of these mechanisms is the dominant factor leading to polymer reswelling.

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来源期刊
Journal of Chemical Physics
Journal of Chemical Physics 物理-物理:原子、分子和化学物理
CiteScore
7.40
自引率
15.90%
发文量
1615
审稿时长
2 months
期刊介绍: The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance. Topical coverage includes: Theoretical Methods and Algorithms Advanced Experimental Techniques Atoms, Molecules, and Clusters Liquids, Glasses, and Crystals Surfaces, Interfaces, and Materials Polymers and Soft Matter Biological Molecules and Networks.
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