The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (≈80%), RNA (≈10%), and a number of different proteins (≈10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrapping the DNA. These so-called architectural properties of nucleoid proteins are still poorly understood. For example, the reason why certain proteins compact the DNA coil in certain environments but make instead the DNA more rigid in other environments is the matter of ongoing debates. Here, we address the question of the impact of the self-association of nucleoid proteins on their architectural properties and try to determine whether differences in self-association are sufficient to induce large changes in the organization of the DNA coil. More specifically, we developed two coarse-grained models of proteins, which interact identically with the DNA but self-associate differently by forming either clusters or filaments in the absence of the DNA. We showed through Brownian dynamics simulations that self-association of the proteins increases dramatically their ability to shape the DNA coil. Moreover, we observed that cluster-forming proteins compact significantly the DNA coil (similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming proteins increase instead significantly the stiffness of the DNA chain (similar to the DNA-stiffening mode of H-NS proteins). This work consequently suggests that the knowledge of the DNA-binding properties of the proteins is in itself not sufficient to understand their architectural properties. Rather, their self-association properties must also be investigated in detail, because they might actually drive the formation of different DNA/protein complexes.

中文翻译：

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自缔合对细菌类核蛋白结构特性的影响

细菌的染色体 DNA 折叠成一个致密体，称为类核，它基本上由 DNA (≈80%)、RNA (≈10%) 和许多不同的蛋白质 (≈10%) 组成。这些类核蛋白充当基因表达的调节剂，并通过桥接、弯曲或包裹 DNA 来影响类核的组织。类核蛋白的这些所谓的结构特性仍然知之甚少。例如，为什么某些蛋白质在某些环境中压缩 DNA 线圈，但在其他环境中使 DNA 更加坚硬，这是一个持续争论的问题。这里，我们解决了类核蛋白的自缔合对其结构特性的影响的问题，并试图确定自缔合的差异是否足以引起 DNA 线圈组织的巨大变化。更具体地说，我们开发了两种粗粒度的蛋白质模型，它们与 DNA 相互作用相同，但通过在没有 DNA 的情况下形成簇或细丝来不同地自我关联。我们通过布朗动力学模拟表明，蛋白质的自结合显着提高了它们塑造 DNA 线圈的能力。此外，我们观察到成簇蛋白显着压缩 DNA 线圈（类似于 H-NS 蛋白的 DNA 桥接模式），而丝状蛋白则显着增加了 DNA 链的刚度（类似于 H-NS 蛋白的 DNA 硬化模式）。因此，这项工作表明，蛋白质的 DNA 结合特性的知识本身不足以理解它们的结构特性。相反，还必须详细研究它们的自关联特性，因为它们实际上可能驱动不同 DNA/蛋白质复合物的形成。