Kwon Seulki, Sung Bong June
Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea.
Phys Rev E. 2020 Aug;102(2-1):022501. doi: 10.1103/PhysRevE.102.022501.
Chromatin undergoes condensation-decondensation processes repeatedly during its cell lifetime. The spatial organization of chromatin in nucleus resembles the fractal globule, of which structure significantly differs from an equilibrium polymer globule. There have been efforts to develop a polymer globule model to describe the fractal globulelike structure of tightly packed chromatin in nucleus. However, the transition pathway of a polymer toward a globular state has been often ignored. Because biological systems are intrinsically in nonequilibrium states, the transition pathway that the chromatin would take before reaching the densely packaged globule should be of importance. In this study, by employing a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from a swollen coil to a compact globule. We aim to elucidate the effect of transition pathways on the final globular structure. We show that a fast collapse induces a nonequilibrium structure even without a specific intramolecular interaction and that its relaxation toward an equilibrium globule is extremely slow. Due to a strong confinement, the fractal globule never relaxes into an equilibrium state during our simulations such that the globular structure becomes dependent on the transition pathway.
染色质在其细胞生命周期中反复经历凝聚-解凝聚过程。细胞核中染色质的空间组织类似于分形球，其结构与平衡聚合物球显著不同。人们一直在努力开发聚合物球模型来描述细胞核中紧密堆积的染色质的分形球状结构。然而，聚合物向球状状态的转变途径常常被忽视。由于生物系统本质上处于非平衡状态，染色质在达到紧密包装的球状体之前所采取的转变途径应该很重要。在本研究中，通过采用简单的聚合物模型和朗之万动力学模拟，我们研究了单个聚合物从膨胀线圈到紧密球状体的构象转变。我们旨在阐明转变途径对最终球状结构的影响。我们表明，即使没有特定的分子内相互作用，快速坍塌也会诱导出非平衡结构，并且其向平衡球状体的弛豫极其缓慢。由于强烈的限制，在我们的模拟过程中，分形球状体从未弛豫到平衡状态，因此球状结构取决于转变途径。
