模拟粗粒染色体的熵塌缩
Simulating the Entropic Collapse of Coarse-Grained Chromosomes
摘要：
消耗力在简单细胞中染色体物质的压实和去压实中起作用，但它们是否足以解释染色体塌陷仍有争议。我们提出了粗粒度的分子动力学模拟，这表明，耗尽诱导的吸引力是足以导致一个大的结构单体的柔性链的崩溃沉浸在一个浴较小的depletants。这些模拟使用了一个显式的粗粒度计算模型，将超螺旋DNA结构单体和较小的蛋白质拥挤剂视为组合的截断Lennard-Jones球体。通过提出一个简单的理论模型，我们定量地铸造作为一种有效的溶剂质量的expletants超螺旋细菌DNA的行动。模拟柔性染色体在预测的耗尽体体积分数下的快速崩溃是一个连续的相变。这种简单的染色体模型的额外的物理效应，如结构单体或链刚性之间的相互作用，需要如果崩溃是一个一级相变。
英文摘要：
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.
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