ArticleJournal of molecular biology2007
Structure-based analysis of HU-DNA binding.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Pangenomics insights of enterococcus faecium human isolates and identification of novel therapeutic targets by in silico subtractive genomics.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Identification of the Integration/Excision Module and Regulatory Elements Involved in the Mobility of IME8, an Integrative and Mobilizable Element From Mosquitocidal Lysinibacillus sphaericus.Microbial biotechnology · 2026Article
- The nucleoid-associated protein subunit HupA positively regulates the Pqs system and pyocyanin production inApplied and environmental microbiology · 2026Article
- Molecular Kaleidoscope of Nucleoid-Associated Proteins Regulatory Network and Chromosome Architecture in Mycobacterium Tuberculosis.Current microbiology · 2026Review
- The nucleoid protein HU positively regulates the expression of type VI secretion systems inmSphere · 2024Article
- NFrontiers in microbiology · 2024Article
- Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin.Frontiers in microbiology · 2023Article
- Antimicrobial resistance and mechanisms of epigenetic regulation.Frontiers in cellular and infection microbiology · 2023Review
- Bacterial nucleoid-associated protein HU as an extracellular player in host-pathogen interaction.Frontiers in cellular and infection microbiology · 2022Review
- Article
- Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions.Scientific reports · 2021Article
- Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.The journal of physical chemistry. B · 2021Article
- Addressing the Possibility of a Histone-Like Code in Bacteria.Journal of proteome research · 2021Review
- Selection for ancient periodic motifs that do not impart DNA bending.PLoS genetics · 2020Article
- Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus.Nucleic acids research · 2020Article
- The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A bacteriophage mimic of the bacterial nucleoid-associated protein Fis.The Biochemical journal · 2020Article
- Chromosome organization in bacteria: mechanistic insights into genome structure and function.Nature reviews. Genetics · 2020Review
- Architecture of the Escherichia coli nucleoid.PLoS genetics · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.
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