ArticleCell reports2018
Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.
Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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Who cites it
25 citing papers in PubMed.
- Bioactive peptides fromFood chemistry: X · 2025Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Using the Conserved Hexapeptide in HOX Proteins as an Antagonist of HOX/PBX Interactions.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.Nucleic acids research · 2024Article
- Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.Nucleic acids research · 2024Article
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Phenotypic and molecular basis of SIX1 variants linked to non-syndromic deafness and atypical branchio-otic syndrome in South Korea.Scientific reports · 2023Article
- Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Transcriptional Regulation and Implications for ControllingJournal of developmental biology · 2022Review
- ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants.Nucleic acids research · 2022Article
- Mechanisms Underlying Hox-Mediated Transcriptional Outcomes.Frontiers in cell and developmental biology · 2021Review
- A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins.Genes & development · 2020Article
- Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns.Development (Cambridge, England) · 2020Article
- Article
- Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.International journal of molecular sciences · 2020Article
- Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.Nature communications · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to ∼20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.
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