ArticleNucleic acids research2007
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 34 citations in OpenAlex.
- The p53 R181C mutation accumulates through impaired deacetylation by Sirt1 and facilitates tumor development.Communications biology · 2026Article
- Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting.Journal of molecular cell biology · 2019Review
- Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family.Nucleic acids research · 2018Article
- Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly.Journal of virology · 2016Article
- Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics.Chemical reviews · 2015Review
- Dipeptide analysis of p53 mutations and evolution of p53 family proteins.Biochimica et biophysica acta · 2014Article
- Identification of new p53 target microRNAs by bioinformatics and functional analysis.BMC cancer · 2013Article
- Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.The journal of physical chemistry. B · 2012Article
- Cruciform structures are a common DNA feature important for regulating biological processes.BMC molecular biology · 2011Review
- Molecular dynamics simulations of protein dynamics and their relevance to drug discovery.Current opinion in pharmacology · 2010Review
- Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations.Biophysical chemistry · 2009Article
- Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences.Nucleic acids research · 2009Article
- Molecular dynamics simulations of nucleic acid-protein complexes.Current opinion in structural biology · 2008Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Symmetries in the p53 response-element (p53RE) encode binding modes for p53 tetramer to recognize DNA. We investigated the molecular mechanisms and biological implications of the possible binding modes. The probabilities evaluated with molecular dynamics simulations and DNA sequence analyses were found to be correlated, indicating that p53 tetramer models studied here are able to read DNA sequence information. The traditionally believed mode with four p53 monomers binding at all four DNA quarter-sites does not cause linear DNA to bend. Alternatively, p53 tetramer can use only two monomers to recognize DNA sequence and induce DNA bending. With an arrangement of dimer of AB dimer observed in p53 trimer-DNA complex crystal, p53 can recognize supercoiled DNA sequence-specifically by binding to quarter-sites one and four (H14 mode) and recognize Holliday junction geometry-specifically. Examining R273H mutation and p53-DNA interactions, we found that at least three R273H monomers are needed to disable the p53 tetramer, consistent with experiments. But just one R273H monomer may greatly shift the binding mode probabilities. Our work suggests that p53 needs balanced binding modes to maintain genome stability. Inverse repeat p53REs favor the H14 mode and direct repeat p53REs may have high possibilities of other modes.
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