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首页> 外文期刊>Journal of Molecular Biology >Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.
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Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

机译：蛋白质-DNA识别中的分子间和分子内读出机制。

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摘要

Protein-DNA recognition plays an essential role in the regulation of gene expression. Regulatory proteins are known to recognize specific DNA sequences directly through atomic contacts (intermolecular readout) and/or indirectly through the conformational properties of the DNA (intramolecular readout). However, little is known about the respective contributions made by these so-called direct and indirect readout mechanisms. We addressed this question by making use of information extracted from a structural database containing many protein-DNA complexes. We quantified the specificity of intermolecular (direct) readout by statistical analysis of base-amino acid interactions within protein-DNA complexes. The specificity of the intramolecular (indirect) readout due to DNA was quantified by statistical analysis of the sequence-dependent DNA conformation. Systematic comparison of these specificities in a large number of protein-DNA complexes revealed that both intermolecular and intramolecular readouts contribute to the specificity of protein-DNA recognition, and that their relative contributions vary depending upon the protein-DNA complexes. We demonstrated that combination of the intermolecular and intramolecular energies derived from the statistical analyses lead to enhanced specificity, and that the combined energy could explain experimental data on binding affinity changes caused by base mutations. These results provided new insight into the relationship between specificity and structure in the process of protein-DNA recognition, which would lead to prediction of specific protein-DNA binding sites.
机译：蛋白质-DNA识别在基因表达的调节中起着至关重要的作用。已知调节蛋白可直接通过原子接触（分子间读数）和/或通过DNA的构象特性（分子内读数）间接识别特定的DNA序列。但是，对于这些所谓的直接和间接读出机制所做出的各自贡献知之甚少。我们通过利用从包含许多蛋白质-DNA复合物的结构数据库中提取的信息来解决这个问题。我们通过统计分析蛋白质-DNA复合物中的碱基氨基酸相互作用来量化分子间（直接）读出的特异性。通过对序列依赖性DNA构象的统计分析来量化由于DNA引起的分子内（间接）读出的特异性。在大量蛋白质-DNA复合物中对这些特异性的系统比较显示，分子间和分子内的读数均有助于蛋白质-DNA识别的特异性，并且它们的相对贡献随蛋白质-DNA复合物而变化。我们证明了从统计分析得出的分子间和分子内能量的组合可导致增强的特异性，并且组合的能量可以解释由碱基突变引起的结合亲和力变化的实验数据。这些结果为蛋白质-DNA识别过程中特异性和结构之间的关系提供了新的见解，这将导致对特定蛋白质-DNA结合位点的预测。

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