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.