Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH

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 similar to 50-amino acid C-terminal domain (CTD) from an all-alpha state to an all-beta 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-alpha 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.

Automated summary

Research on RfaH reveals that interdomain contacts are vital for maintaining a stable, all-alpha CTD in free RfaH. Pulling simulations showed that free RfaH can be divided into a rigid part and a soft part, with the boundary roughly corresponding to the boundary between the two domains. This feature may play a role in how fold switching is triggered by interaction with RNAP.