1Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, CNRS and Université Pierre and Marie Curie, 75005 Paris, France.
2Department of Molecular Biosciences and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA.
Phys Rev Lett. 2014 Jun 13;112(23):238101. doi: 10.1103/PhysRevLett.112.238101. Epub 2014 Jun 11.
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multistep replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the dependence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive "rezipping" of the solution-phase protein onto DNA sites liberated by "unzipping" of the originally bound protein, (2) that a model in which solution-phase proteins bind nonspecifically to DNA can describe experiments on exchanges between the nonspecific DNA-binding proteins Fis-Fis and Fis-HU, and (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.
实验表明，蛋白质从 DNA 上的解链速率可能取决于附近溶液中蛋白质的浓度。在这里，我们提出了一种关于溶液相蛋白取代 DNA 结合蛋白的多步置换理论。对于四种不同的动力学情况，我们计算了蛋白质解链和置换速率对溶液蛋白浓度的依赖性。我们发现：（1）溶液相蛋白逐渐“重新包裹”在由原结合蛋白“解包裹”释放的 DNA 位点上，会产生强烈的影响；（2）一种模型表明，溶液相蛋白非特异性地与 DNA 结合，可以描述非特异性 DNA 结合蛋白 Fis-Fis 和 Fis-HU 之间的交换实验；（3）一种结合特异性模型描述了特定结合位点上 CueR 蛋白的交换实验。
