About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.

中文翻译：

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呼吸核小体的集合：一项计算研究

大约四分之三的人类 DNA 分子被包裹在核小体中，即带有 DNA 的蛋白质线轴。核小体是高度动态的，通过自发解开来瞬时暴露其 DNA。最近的实验允许通过 X 射线衍射与溶剂和蛋白质核心之间的对比度匹配来观察这种呼吸核小体的 DNA。在这项研究中，我们通过具有序列依赖 DNA 力学的粗粒核小体模型的蒙特卡罗模拟来计算这样的集合。我们的分析提供了对实验中观察到的核小体呼吸的序列依赖性的详细见解，并使我们能够确定与蛋白质核心结合的 DNA 的吸附能作为离子强度的函数。而且，