Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes

Biochem Mol Biol Educ. 2012 Nov-Dec;40(6):400-1. doi: 10.1002/bmb.20650. Epub 2012 Oct 13.

Abstract

3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biochemistry / education*
  • Biochemistry / methods
  • DNA / chemistry*
  • DNA / metabolism
  • Homeodomain Proteins / chemistry*
  • Homeodomain Proteins / metabolism
  • Humans
  • Imaging, Three-Dimensional*
  • Models, Molecular*
  • Molecular Sequence Annotation*
  • Tumor Suppressor Protein p53 / chemistry*
  • Tumor Suppressor Protein p53 / metabolism

Substances

  • Homeodomain Proteins
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • DNA