Forrey Christopher, Muthukumar M
Department of Polymer Science and Engineering, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA.
Biophys J. 2006 Jul 1;91(1):25-41. doi: 10.1529/biophysj.105.073429. Epub 2006 Apr 14.
We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general.
我们使用朗之万动力学模拟来研究粗粒度DNA链在二十面体容器内的包装过程。我们将研究重点放在病毒包装中三个感兴趣的领域：包装好的DNA凝聚物不断演变的结构；包装速度；以及能量的内部积累和合力。这些领域中的每一个都已通过实验进行了研究，我们发现我们能够定性地重现实验结果。然而，我们的研究结果还表明，噬菌体基因组包装过程与反向卷轴模型所暗示的过程有根本不同。我们认为，一般来说，包装并非以反向卷轴模型的确定性方式进行，而是具有随机性。随着链构型在衣壳内被压缩，结构、能量和包装速度都变得依赖于聚合物动力学。包装过程中许多观察到的特征都源于凝聚相聚合物动力学，这表明统计力学而非力学应作为基因组包装的适当理论基础。最后我们认为，由于噬菌体T7特有的一种内部蛋白质，T7基因组可能比一般噬菌体的基因组具有明显更高的有序性。
