Recognition of DNA structure by 434 repressor
Recognition of DNA structure by 434 repressor
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DOI：
10.1093/nar/26.2.669
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发表时间：
1998-01-15
影响因子：
14.9
通讯作者：
Koudelka, GB
中科院分区：
文献类型：
--
作者：
Koudelka, GB
在噬菌体434结合位点与434阻遏物的复合物中，14 bp位点的中心4 bp不与蛋白质接触，尽管这些碱基的变化改变了结合位点对阻遏物的亲和力。我们以前的数据表明，在阻遏物-DNA复合物中，非接触的中心碱基被过度扭曲的能力决定了结合位点对434阻遏物的亲和力，通过检查两个中心序列变体434结合位点对434阻遏物的亲和力作为结合位点平均扭曲的函数来测试该想法。434阻遏物优选相对过度缠绕的结合位点而不是两个更欠缠绕的形式，最大的亲和力增强，从增加扭曲观察到的结合位点，是相对undervound和更耐扭曲变形。与434阻遏物在与DNA结合时过度扭曲其结合位点的想法一致，我们发现434阻遏物能够与在其中心具有单个碱基插入（15聚体）的位点结合，但与具有中心碱基缺失的结合位点结合较差（12聚体和13聚体），N-末端二聚体界面在决定434阻遏物中心碱基偏好方面起着重要作用，这种界面中的突变消除了中心碱基辨别和/或位点大小偏好。这些突变还导致与其结合特征一致的各种大小的DNA位点上的阻遏物足迹的大小变化。
In complexes of bacteriophage 434 binding sites with 434 repressor the central 4 bp of the 14 bp site are not contacted by the protein, although changes in these bases alter binding site affinity for the repressor, Our previous data suggested that the ability of the noncontacted central bases to be overtwisted in repressor-DNA complexes governs affinity of the binding site for 434 repressor, This idea was tested by examining the affinity of two central sequence variant 434 binding sites for 434 repressor as a function of binding site average twist, The 434 repressor preferred the relatively overwound binding site to the two more underwound forms, The greatest affinity enhancement resulting from increasing twist was observed with a binding site that is relatively underwound and more resistant to twisting deformation. Consistent with the idea that 434 repressor overtwists its binding site upon DNA binding, we show that 434 repressor is capable of binding to sites bearing a single base insertion in their center (a 15mer), but binds poorly to binding sites bearing central base deletions (12mer and 13mer), The N-terminal dimer interface plays a large role in determining 434 repressor central base preferences, Mutations in this interface eliminate central base discrimination and/or site size preferences, These mutations also lead to changes in the size of the repressor footprint on the various sized DNA sites that are consistent with their binding characteristics.