ArticleThe journal of physical chemistry. B2021
The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
- Biofilm-mediated antibiotic tolerance in bacterial pathogens: Integrated molecular networks and novel therapeutic avenues.Virulence · 2026Review
- A tailored CoA ligase-Nature catalysis · 2026Article
- A Twist of Fate: The Helix-Turn-Helix Motif inJournal of chemical information and modeling · 2025Article
- Discovery of synthetic small molecules targeting the central regulator ofScience advances · 2025Article
- Targeting MarA N-terminal domain dynamics to prevent DNA binding.Protein science : a publication of the Protein Society · 2025Article
- Role of Natural Binding Proteins in Therapy and Diagnostics.Life (Basel, Switzerland) · 2024Article
- Genome-wide analysis of the soybeanFrontiers in plant science · 2024Article
- Evolutionary Conserved Short Linear Motifs Provide Insights into the Cellular Response to Stress.Antioxidants (Basel, Switzerland) · 2022Article
- Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.Nucleic acids research · 2022Article
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-dependent changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step toward the efficient design of antivirulence agents that target these proteins.
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Registered trials
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 Socratic graph.