Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.

中文翻译：

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调节环形蛋白动力学以促进配体结合后的功能机制

环形蛋白作为分子机器，在 DNA 复制和 RNA 转录等生物过程中发挥着至关重要的作用。尽管在几种环形蛋白的结构表征方面取得了进展，但我们仍然缺乏对其结构、寡聚化状态和分子间相互作用在定义其生物学功能方面的重要性的机械理解。在这项工作中，我们分析了具有不同寡聚化状态的环形蛋白的集体动力学，即二聚体和三聚体 DNA 滑动夹、核衣壳蛋白（4-、5-和 6-mers）和 Trp RNA 结合衰减蛋白（11-和 12 聚体）。我们观察到常见的全局模式，其中合作滚动是一种能够实现 DNA 合成的机制，和蛤壳式运动作为滑动夹具打开/关闭的基础。由于与 DNA 或夹具加载器的复合而导致的全局动态变化被证明有助于增强运动以实现强大的功能。该分析为亚基间和分子间相互作用的功能运动的分化和增强提供了新的见解。