ArticleComputational and structural biotechnology journal2022
Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states.Nucleic acids research · 2026Article
- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.Nucleic acids research · 2025Article
- Future Directions of the Prokaryotic Chromosome Field.Molecular microbiology · 2025Article
- Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production.Nucleic acids research · 2025Article
- DNA supercoiling enhances DNA condensation by ParB proteins.Nucleic acids research · 2024Article
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA.Nature communications · 2024Article
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- Read-through transcription of tRNA underlies the cell cycle-dependent dissociation of IHF from the DnaA-inactivating sequenceFrontiers in microbiology · 2024Article
- IHF and Fis asInternational journal of molecular sciences · 2023Review
- Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome.TranscriptionReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The integration host factor (IHF) is a prominent example of indirect readout as it imposes one of the strongest bends on relaxed linear DNA. However, the relation between IHF and torsionally constrained DNA, as occurs physiologically, remains unclear. By using atomistic molecular dynamics simulations on DNA minicircles, we reveal, for the first time, the reciprocal influence between a DNA-bending protein and supercoiling. On one hand, the increased curvature of supercoiled DNA enhances wrapping around IHF making the final complex topologically dependent. On the other hand, IHF acts as a 'supercoiling relief' factor by compacting relaxed DNA loops and, when supercoiled, it pins the position of plectonemes in a unique and specific manner. In addition, IHF restrains under- or overtwisted DNA depending on whether the complex is formed in negatively or positively supercoiled DNA, becoming effectively a 'supercoiling buffer'. We finally provide evidence of DNA bridging by IHF and reveal that these bridges divide DNA into independent topological domains. We anticipate that the crosstalk detected here between the 'active' DNA and the multifaceted IHF could be common to other DNA-protein complexes relying on the deformation of DNA.
Indexed as
Identifiers
What OpenQuestion holds
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 OpenQuestion graph.