The lifetimes of protein-DNA adducts are strictly related to the various protein functions. This feature must be encoded by the amino acids located at the protein-DNA interface. The large number of structurally characterized protein-DNA complexes now available from the Protein Data Bank (PDB) allows extensive structural bioinformatics investigations on protein-DNA interfaces. The modes of protein binding to DNA have been explored by dividing 629 non-redundant PDB files of protein-DNA complexes into separate classes for structural proteins, transcription factors and DNA-related enzymes. From the selected PDB structures, we could define 2953 protein-DNA contact regions. A systematic analysis of amino acid occurrences at these protein-DNA contact regions yielded composition profiles, which are typical for each of the three protein classes. The critical role of some amino acids to influence intermolecular contact lifetimes is discussed here. The occurrence of arginine at the protein-DNA interface, by far the most abundant amino acid in this protein moiety, is found to be the main feature that differentiates proteins from the three classes. Structural proteins and, to a lesser extent, transcription factors exhibit the highest Arg occurrence at protein-DNA contact regions. Reduced Arg/Lys ratios together with increased contents of Asp and Glu are observed in all the DNA-interacting enzymes. The amount of negatively charged side chains, highly conserved among homologous DNA-related enzymes at protein-DNA interfaces, is suggested as a tool to modulate protein mobility along DNA chains. Arg/Lys, Asp/Asn and Glu/Gln substitutions at protein-DNA interfaces may represent a very feasible way to control protein motion on DNA rails.

中文翻译：

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对蛋白质-DNA复合物的结构生物信息学研究描述了它们的相互作用方式。

蛋白质-DNA加合物的寿命与各种蛋白质功能严格相关。此功能必须由位于蛋白质-DNA界面的氨基酸编码。现在可以从蛋白质数据库（PDB）获得的大量具有结构特征的蛋白质-DNA复合物，可以对蛋白质-DNA界面进行广泛的结构生物信息学研究。通过将629个蛋白质-DNA复合物的非冗余PDB文件划分为结构蛋白质，转录因子和与DNA相关的酶的不同类别，已经探索了蛋白质与DNA结合的方式。从所选的PDB结构中，我们可以定义2953个蛋白质-DNA接触区域。对这些蛋白质-DNA接触区域发生的氨基酸的系统分析得出了组成概况，这对于三种蛋白质类别中的每一个都是典型的。本文讨论了某些氨基酸影响分子间接触寿命的关键作用。蛋白质-DNA界面上精氨酸的出现是该蛋白质部分中最丰富的氨基酸，被认为是将蛋白质与三类区别开的主要特征。结构蛋白和转录因子（在较小程度上）在蛋白质-DNA接触区域表现出最高的Arg发生率。在所有与DNA相互作用的酶中均观察到Arg / Lys比降低，Asp和Glu含量增加。建议在蛋白质-DNA界面上的同源DNA相关酶之间高度保守的带负电荷的侧链数量可作为调节蛋白质沿DN​​A链移动的工具。精氨酸/赖氨酸，