Paillard Guillaume, Deremble Cyril, Lavery Richard
Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France.
Nucleic Acids Res. 2004 Dec 21;32(22):6673-82. doi: 10.1093/nar/gkh1003. Print 2004.
We present a quantitative, theoretical analysis of the recognition mechanisms used by two zinc finger proteins: Zif268, which selectively binds to GC-rich sequences, and a Zif268 mutant, which binds to a TATA box site. This analysis is based on a recently developed method (ADAPT), which allows binding specificity to be analyzed via the calculation of complexation energies for all possible DNA target sequences. The results obtained with the zinc finger proteins show that, although both mainly select their targets using direct, pairwise protein-DNA interactions, they also use sequence-dependent DNA deformation to enhance their selectivity. A new extension of our methodology enables us to determine the quantitative contribution of these two components and also to measure the contributions of individual residues to overall specificity. The results show that indirect recognition is particularly important in the case of the TATA box binding mutant, accounting for 30% of the total selectivity. The residue-by-residue analysis of the protein-DNA interaction energy indicates that the existence of amino acid-base contacts does not necessarily imply sequence selectivity, and that side chains without contacts can nevertheless contribute to defining the protein's target sequence.
一种是选择性结合富含GC序列的Zif268，另一种是与TATA盒位点结合的Zif268突变体。该分析基于一种最近开发的方法（ADAPT），该方法可通过计算所有可能的DNA靶序列的络合能来分析结合特异性。锌指蛋白的研究结果表明，尽管两者主要通过直接的蛋白质-DNA成对相互作用来选择其靶标，但它们也利用序列依赖性的DNA变形来提高其选择性。我们方法的一个新扩展使我们能够确定这两个组成部分的定量贡献，并测量单个残基对整体特异性的贡献。结果表明，在TATA盒结合突变体的情况下，间接识别尤为重要，占总选择性的30%。蛋白质-DNA相互作用能的逐个残基分析表明，氨基酸-碱基接触的存在不一定意味着序列选择性，而没有接触的侧链仍可有助于确定蛋白质的靶序列。
