Langevin dynamics simulation of DNA ejection from a phage.
Langevin dynamics simulation of DNA ejection from a phage.
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噬菌体 DNA 喷射的 Langevin 动力学模拟。
DOI：
10.1007/s10867-013-9316-x
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发表时间：
2013
影响因子：
1.8
通讯作者：
Muthukumar,M
中科院分区：
文献类型：
--
作者：
Mahalik,JP;Hildebrandt,B;Muthukumar,M
我们已经进行了Langevin动力学模拟的一个粗粒度的模型的喷射dsDNA从Φ29噬菌体。我们的模拟结果表明，在局部喷射速度的显着变化，在体内和体外系统的文献中报道的实验观察结果一致。在努力了解这种变化的起源，在当地的喷射速度，我们已经调查了当地的喷射动力学和包装结构在各种电机的力量和链的灵活性之间的相关性。在较低的马达力下，包装的DNA长度较短，具有较好的组织。另一方面，在更高的电机力典型的现实情况下，衣壳内的DNA组织遭受显着的方向紊乱，但还具有长的方向相关时间。这反过来又会导致DNA片段的方向和退出方向之间缺乏登记。因此，成功退出需要大量的本地动量转移。因此，DNA喷射暂时减慢，表现出停顿。这种减速在弹射过程中随机发生，完全由规定的马达力产生的特定起始构型决定。为了增加我们的推论，我们还研究了故意改变持久长度的链的弹射。对于不太灵活的链，成功弹射的大动量转移发生的需求较弱，导致更均匀的弹射动力学。虽然与实验观察相一致，我们的研究结果表明，喷射动力学的非遍历性，并呼吁更好的理论模型来描绘基因组喷射的动力学。
We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.