Cherstvy A G
Institut für Festkörperforschung, Theorie-II, Forschungszentrum Jülich, Germany.
J Phys Chem B. 2009 Apr 2;113(13):4242-7. doi: 10.1021/jp810009s.
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.
我们研究了DNA-蛋白质复合物界面上的静电荷互补性。我们使用一些DNA结合蛋白的DNA-蛋白质复合物的蛋白质数据库原子坐标，来研究与DNA紧密接触的带正电荷蛋白质残基的分布。我们发现，大型结构蛋白在带负电荷的DNA磷酸链框架内，呈现出精氨酸、赖氨酸和组氨酸氨基酸独特的非均匀分布。我们研究了核小体核心颗粒、与原核生物DNA弯曲组蛋白类似物的DNA复合物，以及小型DNA结合蛋白的基本结合基序。对于大型DNA-蛋白质复合物，其中DNA围绕蛋白质核心发生广泛缠绕，我们发现蛋白质上的正氨基酸追踪单个DNA磷酸的序列特异性位置。这种静电相互作用的特异性有助于DNA结合蛋白识别DNA，对于许多DNA-蛋白质复合物而言，这主要由蛋白质残基与DNA碱基之间形成的氢键所决定。
