Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase
Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase
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DOI：
10.1007/978-1-4939-9520-2_21
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发表时间：
2019-01-01
期刊：
影响因子：
--
通讯作者：
Bloom, Kerry
中科院分区：
文献类型：
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作者：
Lawrimore, Josh;He, Yunyan;Bloom, Kerry
染色质动力学和组织可以被凝缩蛋白复合物改变。反过来，缩合蛋白络合物的分子行为根据缩合蛋白所结合的底物的张力而改变。染色质组织和凝聚蛋白行为之间的这种相互作用表明需要工具，允许在各种染色质组织上观察凝聚蛋白复合物。我们提供了一种利用聚合物动力学模拟器ChromoShake和缩聚模拟器RotoStep在动态聚合物衬底上模拟缩聚络合物的方法。这些模拟可以转换成模拟荧光图像，能够直接与凝缩蛋白和荧光标记的染色质的实验图像进行比较。我们的管道使用户能够探索凝缩蛋白行为的变化如何改变染色质动力学，反之亦然，同时提供可以直接与实验观察相比较的模拟图像数据集。
Chromatin dynamics and organization can be altered by condensin complexes. In turn, the molecular behavior of a condensin complex changes based on the tension of the substrate to which condensin is bound. This interplay between chromatin organization and condensin behavior demonstrates the need for tools that allows condensin complexes to be observed on a variety of chromatin organizations. We provide a method for simulating condensin complexes on a dynamic polymer substrate using the polymer dynamics simulator ChromoShake and the condensin simulator RotoStep. These simulations can be converted into simulated fluorescent images that are able to be directly compared to experimental images of condensin and fluorescently labeled chromatin. Our pipeline enables users to explore how changes in condensin behavior alters chromatin dynamics and vice versa while providing simulated image datasets that can be directly compared to experimental observations.