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Structural basis for p53 binding-induced DNA bending.

Yongping Pan1, Ruth Nussinov

  • 1Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA.

The Journal of Biological Chemistry
|November 7, 2006
PubMed
Summary
This summary is machine-generated.

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Specific p53 binding induces DNA bending, crucial for transcription activation. Molecular dynamics simulations reveal how p53 dimers cause DNA bending, providing atomic models for p53-DNA complexes.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • Specific p53 binding to DNA induces DNA bending, which is vital for biological processes like transcription activation.
  • The precise structural mechanisms of p53-induced DNA bending and p53-DNA complexes remain incompletely understood.

Purpose of the Study:

  • To elucidate the atomic-level details of DNA bending induced by p53 binding.
  • To understand the mechanism of p53-induced DNA bending and its biological significance.

Main Methods:

  • Molecular dynamics simulations were employed.
  • Simulations were performed on DNA segments with consensus p53-binding sequences, including half-site and full-site DNA-p53 complexes.

Main Results:

Related Experiment Videos

  • Each DNA-bound p53 core domain induced local DNA conformational changes.
  • p53 dimer binding resulted in DNA bending at the half-site center.
  • Two p53 dimers bound to full-site DNA induced bending of 20 and 35 degrees, depending on the DNA sequence.
  • Simulations revealed a preferred staggered conformation for the two p53 dimers, necessitating DNA conformational changes and sequence-dependent bending.

    • Conclusions:

    • The study provides a detailed atomic model of the DNA-p53 tetramer complex.
    • The findings delineate the roles of DNA-p53 interactions, p53 dimer-dimer interfaces, and DNA sequence in p53-induced DNA bending.