节段间转移对蛋白质靶向定位的影响
Effects of intersegmental transfers on target location by proteins
摘要：
我们研究了一个模型的蛋白质搜索的目标，利用促进扩散，在一个DNA分子局限在一个有限的体积。该模型包括三种不同的易化扩散途径：（a）滑动-蛋白质沿着DNA的轮廓扩散;（b）跳跃-蛋白质通过三维扩散在DNA的两个位点之间移动;最后（c）片段间转移-蛋白质通过同时瞬时结合两个位点而从一个位点移动到另一个位点。典型的搜索时间计算使用的缩放参数，数值验证。我们的研究结果表明，包括intersegmental传输（i）大大减少了搜索时间（ii）使搜索时间更强大的模型参数的变化和（iii），最佳搜索时间发生在一个政权非常不同的模型，忽略intersegmental传输。我们发现的行为是丰富的，并显示出惊人的依赖性，例如，对DNA长度的依赖性。
英文摘要：
We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein diffuses along the contour of the DNA (b) jumping - where the protein travels between two sites along the DNA by three-dimensional diffusion, and finally (c) intersegmental transfer - which allows the protein to move from one site to another by transiently binding both at the same time. The typical search time is calculated using scaling arguments which are verified numerically. Our results suggest that the inclusion of intersegmental transfer (i) decreases the search time considerably (ii) makes the search time much more robust to variations in the parameters of the model and (iii) that the optimal search time occurs in a regime very different than that found for models which ignore intersegmental transfers. The behavior we find is rich and shows surprising dependencies, for example, on the DNA length.
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