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J Phys Chem B. 2009 Apr 2;113(13):4242-7. doi: 10.1021/jp810009s.

Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups.

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Institut für Festkörperforschung, Theorie-II, Forschungszentrum Jülich, Germany.


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.

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