RfaH is a compact two‐domain bacterial transcription factor that functions both as a regulator of transcription and an enhancer of translation. Underpinning the dual functional roles of RfaH is a partial but dramatic fold switch, which completely transforms the ~50‐amino acid C‐terminal domain (CTD) from an all‐α state to an all‐β state. The fold switch of the CTD occurs when RfaH binds to RNA polymerase (RNAP), however, the details of how this structural transformation is triggered is not well understood. Here we use all‐atom Monte Carlo simulations to characterize structural fluctuations and mechanical stability properties of the full‐length RfaH and the CTD as an isolated fragment. In agreement with experiments, we find that interdomain contacts are crucial for maintaining a stable, all‐α CTD in free RfaH. To probe mechanical properties, we use pulling simulations to measure the work required to inflict local deformations at different positions along the chain. The resulting mechanical stability profile reveals that free RfaH can be divided into a “rigid” part and a “soft” part, with a boundary that nearly coincides with the boundary between the two domains. We discuss the potential role of this feature for how fold switching may be triggered by interaction with RNAP.

中文翻译：

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变质蛋白RfaH的结构波动和机械稳定性

RfaH是一种紧凑的两结构域细菌转录因子，既可作为转录调节剂，又可作为翻译增强剂。RfaH双重功能的基础是部分但戏剧性的折叠开关，它将约50个氨基酸的C末端结构域（CTD）从全α状态完全转换为全β状态州。当RfaH与RNA聚合酶（RNAP）结合时，会发生CTD的倍数转换，但是，关于如何触发这种结构转化的细节尚不清楚。在这里，我们使用全原子蒙特卡罗模拟来表征全长RfaH和CTD的结构波动和机械稳定性，这些都是孤立的片段。与实验一致，我们发现域间联系对于维持稳定的全α至关重要。免费RfaH中的CTD。为了探究机械性能，我们使用拉力模拟来测量在链的不同位置造成局部变形所需的功。所得的机械稳定性概况表明，游离RfaH可以分为“刚性”部分和“软”部分，其边界几乎与两个域之间的边界重合。我们讨论此功能在与RNAP相互作用可能触发倍数转换方面的潜在作用。