title: Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups.
abstract: We study electrostatic charge complementarity along interfaces of DNA-protein complexes. We use the Protein Data Bank atomic coordinates of DNA-protein complexes for some DNA-binding proteins to study the distribution of positively charged protein residues in the close contact with DNA. We show that large structural proteins reveal a peculiar nonuniform distribution of Arg, Lys, and His amino acids in the frame of negatively charged DNA phosphate strands. We study the nucleosome core particles, DNA complexes with prokaryotic DNA-bending histone analogues, but also the basic binding motifs of small DNA-binding proteins. For large DNA-protein complexes, where extensive DNA wrapping around protein cores occurs, we show that positive amino acids on the proteins track sequence-specific positions of individual DNA phosphates. This specificity of electrostatic interactions can contribute to DNA recognition by DNA-binding proteins, which is governed for many DNA-protein complexes primarily by the hydrogen bond formation between protein residues and DNA bases.
authors.affiliation: Institut für Festkörperforschung, Theorie-II, Forschungszentrum Jülich, Germany. a.cherstvy@googlemail.com
authors.forename: A G
authors.initials: AG
authors.lastname: Cherstvy
mesh_terms: D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D010710:Phosphates / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013379:Substrate Specificity
chemical_list: D002412:Cations; D010710:Phosphates; D011506:Proteins; D004247:DNA