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Effects of conformational changes in the N-terminal domain of RfaH on domain dissociation and fold switching
  • Bahman Seifi,
  • Stefan Wallin
Bahman Seifi
Memorial University of Newfoundland

Corresponding Author:bahmansj@mun.ca

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Stefan Wallin
Memorial University of Newfoundland
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Abstract

RfaH is a two-domain metamorphic protein involved in transcription regulation and translation initiation. To carry out dual functions, RfaH relies on two coupled structural changes: domain dissociation and fold switching. In the free state, the C-terminal domain (CTD) of RfaH adopts an all- α fold and is tightly associated with the N-terminal domain (NTD). Upon binding to RNA polymerase (RNAP), the domains dissociate and the CTD completely transforms into an all- β fold, while the NTD remains largely, but not entirely, unchanged. We test the idea that a change in the conformation of an extended β-hairpin ( β3- β4) located on the NTD, helps trigger domain dissociation. To this end, we use homology modelling to construct a structure, H 1 , which is similar to free RfaH but with a remodeled β3- β4 hairpin. We then use an all-atom physics-based model enhanced with a dual-basin structure-based potential to simulate domain separation driven by thermal unfolding of the CTD with NTD in a fixed, folded conformation. We apply our model to both free RfaH and H 1 . For H 1 we find, in line with our hypothesis, that the CTD exhibits a lower stability and the domains dissociate at a lower temperature ( T), as compared to free RfaH. We do not, however, observe complete refolding to the all- β state in these simulations, suggesting that a change in β3- β4 orientation aid in, but is not sufficient for, domain dissociation. In addition, we study the reverse fold switch in which RfaH returns from a domain-open all- β state to its domain-closed all- α state. We observe a T-dependent transition rate; fold switching is slow at low T, where the CTD tend to be kinetically trapped in its all- β state, and at high- T, where the all- α state becomes unstable. Consequently, our simulations suggest an optimal T at which fold switching is most rapid. At this T, the stabilities of both folds are reduced. Overall, our study suggests that both inter-domain interactions and conformational changes within NTD may be important for proper functioning of RfaH.
12 Mar 2024Submitted to PROTEINS: Structure, Function, and Bioinformatics
14 Mar 2024Submission Checks Completed
14 Mar 2024Assigned to Editor
14 Mar 2024Review(s) Completed, Editorial Evaluation Pending
29 Apr 2024Editorial Decision: Revise Major
28 Aug 20241st Revision Received
02 Sep 2024Submission Checks Completed
02 Sep 2024Assigned to Editor
02 Sep 2024Review(s) Completed, Editorial Evaluation Pending
02 Sep 2024Reviewer(s) Assigned
26 Sep 2024Editorial Decision: Accept