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Local and global effects of strong DNA bending induced during molecular dynamics simulations

机译：分子动力学模拟过程中引起的强烈DNA弯曲的局部和全局效应

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摘要

DNA bending plays an important role in many biological processes, but its molecular and energetic details as a function of base sequence remain to be fully understood. Using a recently developed restraint, we have studied the controlled bending of four different B-DNA oligomers using molecular dynamics simulations. Umbrella sampling with the AMBER program and the recent parmbsc0 force field yield free energy curves for bending. Bending 15-base pair oligomers by 90° requires roughly 5 kcal mol−1, while reaching 150° requires of the order of 12 kcal mol−1. Moderate bending occurs mainly through coupled base pair step rolls. Strong bending generally leads to local kinks. The kinks we observe all involve two consecutive base pair steps, with disruption of the central base pair (termed Type II kinks in earlier work). A detailed analysis of each oligomer shows that the free energy of bending only varies quadratically with the bending angle for moderate bending. Beyond this point, in agreement with recent experiments, the variation becomes linear. An harmonic analysis of each base step yields force constants that not only vary with sequence, but also with the degree of bending. Both these observations suggest that DNA is mechanically more complex than simple elastic rod models would imply.
机译：DNA弯曲在许多生物学过程中都起着重要作用，但是其分子和能量细节作为碱基序列的函数仍有待充分理解。使用最近开发的约束，我们已经使用分子动力学模拟研究了四种不同的B-DNA低聚物的受控弯曲。使用AMBER程序进行的雨伞采样以及最近的parmbsc0力场会产生弯曲的自由能曲线。将15个碱基对的低聚物弯曲90°大约需要5 kcal mol -1 ，而达到150°则需要12kkal mol -1 的数量级。适度的弯曲主要是通过耦合的基对步进辊产生的。强力弯曲通常会导致局部扭结。我们观察到的扭结都涉及两个连续的碱基对步骤，中间中央碱基对被破坏（在较早的工作中称为II型扭结）。对每种低聚物的详细分析表明，对于中等弯曲度，弯曲的自由能仅随弯曲角呈二次方变化。除此之外，与最近的实验一致，变化变为线性。对每个基本步骤进行谐波分析，得出的力常数不仅随顺序变化，而且随弯曲程度变化。这些观察结果都表明，DNA在机械上比简单的弹性杆模型所暗示的复杂。

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