ArticlePLoS computational biology2015
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 57 citations in OpenAlex.
- Exploration of the structural and functional diversity in the metamorphic RfaH subfamily.bioRxiv : the preprint server for biology · 2026Article
- Article
- Mapping the energy landscape of a fold-switching protein MAD2.Protein science : a publication of the Protein Society · 2025Article
- Computational and experimental assessment of key interdomain residues controlling the fold-switch of RfaH.Protein science : a publication of the Protein Society · 2025Article
- A contact-based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold-switch.Protein science : a publication of the Protein Society · 2024Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.PLoS computational biology · 2024Article
- Metamorphic proteins and how to find them.Current opinion in structural biology · 2024Review
- Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.Nature communications · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.bioRxiv : the preprint server for biology · 2024Article
- Local energetic frustration conservation in protein families and superfamilies.Nature communications · 2023Article
- Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions.Communications chemistry · 2023Article
- Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models.Biophysical reviews · 2023Review
- Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1.The Journal of chemical physics · 2023Article
- Article
- Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors.Protein science : a publication of the Protein Society · 2022Article
- Dimer dissociation is a key energetic event in the fold-switch pathway of KaiB.Biophysical journal · 2022Article
- The role of C-terminal helix in the conformational transition of an arginine binding protein.Journal of structural biology: X · 2022Article
- Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein.Computational and structural biotechnology journal · 2022Review
- The N-terminal domain of RfaH plays an active role in protein fold-switching.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD) undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD), masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.