The Role of Water in Homeodomain-DNA Interaction
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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 wordshomeodomain 3D structure water-mediated contact water bridge
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