DNA looping plays a key role in the regulation of the lac operon in Escherichia coli. The presence of a tightly bent loop (between sequentially distant sites of Lac repressor protein binding) purportedly hinders the binding of RNA polymerase and subsequent transcription of the genetic message. The unexpectedly favorable binding interaction of this protein-DNA assembly with the catabolic activator protein (CAP), a protein that also bends DNA and paradoxically facilitates the binding of RNA polymerase, stimulated extension of our base-pair level theory of DNA elasticity to the treatment of DNA loops formed in the presence of several proteins. Here we describe in detail a procedure to determine the structures and free energies of multi-protein-DNA assemblies and illustrate the predicted effects of CAP binding on the configurations of the wild-type 92-bp Lac repressor-mediated O3-O1 DNA loop. We show that the DNA loop adopts an antiparallel orientation in the most likely structure and that this loop accounts for the published experimental observation that, when CAP is bound to the loop, one of the arms of LacR binds to an alternative site that is displaced from the original site by 5 bp.

中文翻译：

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多蛋白-DNA 组装体的中尺度建模：分解代谢激活蛋白在 Lac 阻遏物介导的循环中的作用。


DNA 环在大肠杆菌 lac 操纵子的调节中起着关键作用。据称，紧密弯曲环的存在（位于 Lac 阻遏蛋白结合的连续遥远位点之间）会阻碍 RNA 聚合酶的结合以及随后遗传信息的转录。这种蛋白质-DNA 组装体与分解代谢激活蛋白 (CAP) 之间出乎意料的有利结合相互作用，CAP 是一种能够弯曲 DNA 并相反地促进 RNA 聚合酶结合的蛋白质，刺激了我们的 DNA 弹性碱基对水平理论扩展到治疗在多种蛋白质存在下形成的 DNA 环。在这里，我们详细描述了确定多蛋白-DNA 组装体的结构和自由能的程序，并说明了 CAP 结合对野生型 92-bp Lac 阻遏物介导的 O3-O1 DNA 环构型的预测影响。我们证明 DNA 环在最可能的结构中采用反平行方向，并且该环解释了已发表的实验观察结果，即当 CAP 与环结合时，LacR 的一个臂与从与原始位点相比，减少了 5 bp。