ArticleThe journal of physical chemistry. B2008
p53-Induced DNA bending: the interplay between p53-DNA and p53-p53 interactions.
Article in The journal of physical chemistry. B, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites.Scientific reports · 2020Article
- Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting.Journal of molecular cell biology · 2019Review
- Bridge-Induced Translocation betweenFrontiers in oncology · 2017Article
- Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes.PloS one · 2016Article
- p53 dynamics upon response element recognition explored by molecular simulations.Scientific reports · 2015Article
- Time-Resolved Fluorescence Anisotropy Study of the Interaction Between DNA and a Peptide Truncated from the p53 Protein Core Domain.Journal of fluorescence · 2014Article
- Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.Nucleic acids research · 2014Article
- Lysine120 interactions with p53 response elements can allosterically direct p53 organization.PLoS computational biology · 2010Article
- Transcriptional regulation by p53.Cold Spring Harbor perspectives in biology · 2010Review
- Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer.Structure (London, England : 1993) · 2010Article
- Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations.Biophysical chemistry · 2009Article
- Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.Nucleic acids research · 2009Article
- Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.PLoS computational biology · 2009Article
- Nuance in the double-helix and its role in protein-DNA recognition.Current opinion in structural biology · 2009Review
- Crystal structure of a p53 core tetramer bound to DNA.Oncogene · 2009Article
- Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios.Journal of molecular recognition : JMRArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
Specific p53 binding-induced DNA bending and its underlying responsible forces are crucial for the understanding of selective transcription activation. Diverse p53-response elements exist in the genome; however, it is not known what determines the DNA bending and to what extent. In order to gain knowledge of the forces that govern the DNA bending, molecular dynamics simulations were performed on a series of p53 core domain tetramer-DNA complexes in which each p53 core domain was bound to a DNA quarter site specifically. By varying the sequence of the central 4-base pairs of each half-site, different DNA bending extents were observed. The analysis showed that the dimer-dimer interactions in p53 were similar for the complexes; on the other hand, the specific interactions between the p53 and DNA, including the interactions of Arg280, Lys120, and Arg248 with the DNA, varied more significantly. In particular, the Arg280 interactions were better maintained in the complex with the CATG-containing DNA sequence and were mostly lost in the complex with the CTAG-containing DNA sequence. Structural analysis shows that the base pairings for the CATG sequence were stable throughout the simulation trajectory, whereas those for the CTAG sequence were partially dissociated in part of the trajectory, which affected the stability of the nearby Arg280-Gua base interactions. Thus, DNA bending depends on the balance between the p53 dimer-dimer interactions and p53-DNA interactions, which is in turn related to the DNA sequence and DNA flexibility.
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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 OpenQuestion graph.