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The Role of Water in Homeodomain-DNA Interaction

  • A. Karyagina
  • A. Ershova
  • S. Spirin
  • A. AlexeevskiEmail author
Chapter
  • 748 Downloads

Abstract

Interfacial water molecules in homeodomain-DNA complexes were analyzed involving all available 3D structures of homeodomains. The main results are as follows: (i) eight conserved water bridges between homeodomains and DNA phosphate groups were identified, as compared to ten ‘direct’ conserved hydrogen bonds with phosphates; (ii) conserved water molecules mediating contacts with DNA phosphate groups seem to be preorganized on an isolated homeodomain surface; (iii) water-mediated contacts of homeodomains with the DNA major groove could contribute to homeodomain specificity in addition to the direct hydrogen bonds and hydrophobic contacts; and (iv) almost all places for potential water bridges on the homeodomain-DNA interface are occupied by water molecules identified by X-ray crystallography.

Key words

homeodomain 3D structure water-mediated contact water bridge 

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • A. Karyagina
    • 1
  • A. Ershova
    • 1
  • S. Spirin
    • 2
  • A. Alexeevski
    • 2
    Email author
  1. 1.Institute of Agricultural BiotechnologyMoscowRussia
  2. 2.Belozersky InstituteMoscow State UniversityMoscowRussia

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