Impact of N‐Terminal Domain Conformation and Domain Interactions on <scp>RfaH</scp> Fold Switching
Bibliographic record
Abstract
ABSTRACT RfaH is a two‐domain metamorphic protein involved in transcription regulation and translation initiation. To carry out its 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 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 ( β 3– β 4) located on the NTD, helps trigger domain dissociation. To this end, we use homology modeling to construct a structure, H 1 , which is similar to free RfaH but with a remodeled β 3– β 4 hairpin. We then use an all‐atom physics‐based model enhanced with a dual basin structure‐based potential to simulate domain separation driven by the 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 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 β 3– β 4 orientation aids 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 tends 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 the proper functioning of RfaH.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".