Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example

  • Álvaro Sebastián
  • Carlos P. Cantalapiedra
  • Bruno Contreras-Moreira
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6620)


The recently published 3D-footprint database contains an up-to-date repository of protein-DNA complexes of known structure that belong to different superfamilies and bind to DNA with distinct specificities. This repository can be scanned by means of sequence alignments in order to look for similar DNA-binding proteins, which might in turn recognize similar DNA motifs. Here we take the complete set of Homeobox proteins from Drosophila melanogaster and their preferred DNA motifs, which would fall in the largest 3D-footprint superfamily and were recently characterized by Noyes and collaborators, and annotate their interface residues. We then analyze the observed amino acid substitutions at equivalent interface positions and their effect on recognition. Finally we estimate to what extent interface similarity, computed over the set of residues which mediate DNA recognition, outperforms BLAST expectation values when deciding whether two aligned Homeobox proteins might bind to the same DNA motif.


protein-DNA interface DNA motif substitution matrices 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Álvaro Sebastián
    • 1
  • Carlos P. Cantalapiedra
    • 1
  • Bruno Contreras-Moreira
    • 1
    • 2
  1. 1.Laboratorio de Biología ComputacionalEstación Experimental de Aula Dei/CSICZaragozaEspaña
  2. 2.Fundación ARAIDZaragozaEspaña

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