蛋白质定位与DNA弹性之间的协同作用：蛋白质修饰的DNA微环的能量最小化
The synergy between protein positioning and DNA elasticity: energy minimization of protein-decorated DNA minicircles
摘要：
蛋白质与DNA的结合有助于基因组的形成和包装以及特定遗传信息的表达。为了了解蛋白质的存在和DNA的变形之间的相互作用，在这样的过程中，我们开发了一种新的方法，以尽量减少弹性能量的DNA片段在介观水平。我们的方法使得有可能获得最佳途径的蛋白质修饰的DNA分子的末端碱基对的空间约束。在这项工作中，我们专注于选定的建筑蛋白质对环状DNA诱导的变形。我们报告的能量景观的DNA微环受到不同程度的扭转应力，并包含一个或两个蛋白质的功能的链长和蛋白质之间的间距。我们的研究结果揭示了双螺旋的弹性和结合蛋白引起的DNA结构扭曲之间的合作。我们发现，施加的机械应力会影响蛋白质在DNA上的位置，而蛋白质反过来又会调节机械应力，从而沿着DNA传播它们的存在。
英文摘要：
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation of DNA involved in such processes, we developed a new method to minimize the elastic energy of DNA fragments at the mesoscale level. Our method makes it possible to obtain the optimal pathways of protein-decorated DNA molecules for which the terminal base pairs are spatially constrained. We focus in this work on the deformations induced by selected architectural proteins on circular DNA. We report the energy landscapes of DNA minicircles subjected to different levels of torsional stress and containing one or two proteins as functions of the chain length and spacing between the proteins. Our results reveal cooperation between the elasticity of the double helix and the structural distortions of DNA induced by bound proteins. We find that the imposed mechanical stress influences the placement of proteins on DNA and that, the proteins, in turn, modulate the mechanical stress and thereby broadcast their presence along DNA.
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