Polymer compaction and bridging-induced clustering of protein-inspired patchy particles
Polymer compaction and bridging-induced clustering of protein-inspired patchy particles
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DOI：
10.1088/1361-648x/ab7f6c
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发表时间：
2020-07-22
影响因子：
2.7
通讯作者：
Brackley, C. A.
中科院分区：
文献类型：
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作者：
Brackley, C. A.
有许多蛋白质或蛋白质复合物具有多个DNA结合结构域。这使得它们能够同时结合到DNA分子（或染色质纤维）上的多个点。还发现许多蛋白质能够在体外压缩DNA，并且当在体内进行荧光标记和成像时，在病灶或斑点中观察到许多其他蛋白质。在这项工作中，我们研究，使用粗粒度的朗之万动力学模拟，由简单的模型蛋白质的聚合物的压实和一种现象被称为“桥接诱导吸引”。后者是在先前的模拟中观察到的机制[Brackley等人2013 Proc. Natl Acad. Sci. USA 110 E3605]，其中模拟为球体的蛋白质通过其与聚合物的多价相互作用形成簇，即使在没有任何明确的蛋白质-蛋白质吸引相互作用的情况下。在这里，我们扩展这一概念，考虑更详细的模型蛋白质，表示为简单的“补丁粒子”与半柔性珠和弹簧聚合物相互作用。我们发现，无论是压缩能力和桥接诱导的吸引力的效果依赖于模型蛋白质的价。这些效应还取决于蛋白质的形状，这决定了它形成桥梁的能力。
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to be able to compact DNA in vitro, and many others have been observed in foci or puncta when fluorescently labelled and imaged in vivo. In this work we study, using coarse-grained Langevin dynamics simulations, the compaction of polymers by simple model proteins and a phenomenon known as the 'bridging-induced attraction'. The latter is a mechanism observed in previous simulations [Brackley et al 2013 Proc. Natl Acad. Sci. USA 110 E3605], where proteins modelled as spheres form clusters via their multivalent interactions with a polymer, even in the absence of any explicit protein-protein attractive interactions. Here we extend this concept to consider more detailed model proteins, represented as simple 'patchy particles' interacting with a semi-flexible bead-and-spring polymer. We find that both the compacting ability and the effect of the bridging-induced attraction depend on the valence of the model proteins. These effects also depend on the shape of the protein, which determines its ability to form bridges.