Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif

J Mol Biol. 2003 Jun 27;330(1):43-55. doi: 10.1016/s0022-2836(03)00532-1.

Abstract

A method for discerning protein structures containing the DNA-binding helix-turn-helix (HTH) motif has been developed. The method uses statistical models based on geometrical measurements of the motif. With a decision tree model, key structural features required for DNA binding were identified. These include a high average solvent-accessibility of residues within the recognition helix and a conserved hydrophobic interaction between the recognition helix and the second alpha helix preceding it. The Protein Data Bank was searched using a more accurate model of the motif created using the Adaboost algorithm to identify structures that have a high probability of containing the motif, including those that had not been reported previously.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Computational Biology / methods
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Databases, Protein
  • Decision Trees
  • Helix-Turn-Helix Motifs*
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular*
  • Models, Statistical*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*

Substances

  • DNA-Binding Proteins
  • Proteins
  • DNA