Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements (Q36360657)

13 August 2017

Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements (English)

1 reference

13 August 2017

1

1 reference

13 August 2017

Arnold J Levine

2

1 reference

PMCID

2190717

13 August 2017

language of work or name

English

0 references

publication date

5 November 2007

1 reference

13 August 2017

Nucleic Acids Research

1 reference

13 August 2017

35

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13 August 2017

22

1 reference

13 August 2017

7733-7747

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

p53 alterations in human cancer: more questions than answers.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Structure of the p53 core domain dimer bound to DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Gene-specific mechanisms of p53 transcriptional control and prospects for cancer therapy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

The stacked-X DNA Holliday junction and protein recognition.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

The versatile interactions of p53 with DNA: when flexibility serves specificity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

The biological impact of the human master regulator p53 can be altered by mutations that change the spectrum and expression of its target genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Core domain interactions in full-length p53 in solution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Scalable molecular dynamics with NAMD

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Mutant p53 proteins bind DNA in a DNA structure-selective mode

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Interactions between BRCT repeats and phosphoproteins: tangled up in two

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

How many mutant p53 molecules are needed to inactivate a tetramer?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

The structure of DNA in the nucleosome core

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Structural plasticity of the Flp-Holliday junction complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

The p53MH algorithm and its application in detecting p53-responsive genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

p53 and recombination intermediates: role of tetramerization at DNA junctions in complex formation and exonucleolytic degradation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Crystal structure of the mouse p53 core DNA-binding domain at 2.7 A resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

30 September 2017

Surfing the p53 network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

DNA bending: the prevalence of kinkiness and the virtues of normality

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Definition of a consensus binding site for p53

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

p53 DNA binding can be modulated by factors that alter the conformational equilibrium

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Structural basis for p53 binding-induced DNA bending

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Cooperative fluctuations point to the dimerization interface of p53 core domain

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Structural basis of DNA recognition by p53 tetramers.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Comparative binding of p53 to its promoter and DNA recognition elements.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Structures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Binding of Rad51 and other peptide sequences to a promiscuous, highly electrostatic binding site in p53.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Determinants of T box protein specificity.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Reactivity of zinc finger cores: analysis of protein packing and electrostatic screening.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Binding of p53 and its core domain to supercoiled DNA.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2190717

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKM890

Cooperative binding of p53 to DNA: regulation by protein-protein interactions through a double salt bridge

21 January 2018

1 reference

12 December 2020

DNA binding and 3′–5′ exonuclease activity in the murine alternatively-spliced p53 protein

1 reference

12 December 2020

Human p53 binds Holliday junctions strongly and facilitates their cleavage

1 reference

12 December 2020

DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKM890

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

PMCID

2190717