title: An analysis of the relationship between hydration and protein-DNA interactions.
abstract: Eleven protein-DNA crystal structures were analyzed to test the hypothesis that hydration sites predicted in the first hydration shell of DNA mark the positions where protein residues hydrogen-bond to DNA. For nine of those structures, protein atoms, which form hydrogen bonds to DNA bases, were found within 1.5 A of the predicted hydration positions in 86% of the interactions. The correspondence of the predicted hydration sites with the hydrogen-bonded protein side chains was significantly higher for bases inside the conserved DNA recognition sequences than outside those regions. In two CAP-DNA complexes, predicted base hydration sites correctly marked 71% (within 1.5 A) of protein atoms, which form hydrogen bonds to DNA bases. Phosphate hydration was compared to actual protein binding sites in one CAP-DNA complex with 78% marked contacts within 2.0 A. These data suggest that hydration sites mark the binding sites at protein-DNA interfaces.
authors.affiliation: Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854-8087, USA.
authors.forename: J
authors.initials: J
authors.lastname: Woda
authors.forename: B
authors.initials: B
authors.lastname: Schneider
authors.forename: K
authors.initials: K
authors.lastname: Patel
authors.forename: K
authors.initials: K
authors.lastname: Mistry
authors.forename: H M
authors.initials: HM
authors.lastname: Berman
mesh_terms: D001665:Binding Sites / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D018398:Homeodomain Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D009698:Nucleoproteins / Q000737:chemistry*; D012097:Repressor Proteins / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009698:Nucleoproteins; D012097:Repressor Proteins; D014867:Water; D004247:DNA