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首页> 外文期刊>The Journal of Chemical Physics >Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins
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Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins

机译：DNA在DNA弯曲核相关蛋白存在下的力 - 延伸行为

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Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAPDNA simulation model that incorporates both force-and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems. Published by AIP Publishing.
机译：核心相关蛋白质（抽头）和DNA之间的相互作用影响DNA聚合物构象，导致现象，例如浓度依赖性力延伸行为。这些效果又影响了蛋白质的局部结合行为，例如引起蛋白质的高力，或者在局部弯曲的DNA有利地结合蛋白质。我们开发了一种粗粒粒子的NAPDNA模拟模型，其包括依赖于浓度依赖性行为，以便研究NAP结合和DNA构象之间的相互作用。该模型系统包括多态蛋白质结合和未绑定，通过现有工作，但现在依赖于DNA的局部结构，其与作用在DNA链上的外力有关。我们观察到预期的定性结合行为，其中更多的蛋白质在较低力下束缚而不是较高力。我们的模型还包括NAP诱导的DNA弯曲，其影响DNA弹性。我们将模拟力延伸行为的半定量匹配与报告的实验数据看。通过使用粗粒粒度模拟，我们还能够查看非平衡行为，例如DNA股的动态延伸。我们以不同的速率和不同的午睡浓度延伸DNA链，观察系统的时间尺度（例如拉动时间和未绕线时间）在音乐会上工作。当这些时间尺度相似时，我们观察到系统中可测量的率依赖性变化，其包括蛋白质的数量和延伸DNA分子所需的力。这表明不同动态过程的相对时间尺度在NAP-DNA系统的行为中起重要作用。通过AIP发布发布。

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