Mazur Alexey K
CNRS UPR9080, Institut de Biologie Physico-Chimique 13, rue Pierre et Marie Curie, Paris 75005, France.
J Phys Chem B. 2009 Feb 19;113(7):2077-89. doi: 10.1021/jp8098945.
Recent theoretical and experimental studies have suggested that the elastic behavior of the small-length double-helical DNA does not correspond to the simple harmonic model. This article presents a thorough comparison of classical atom-level molecular dynamics (MD) and coarse-grained harmonic approximations. It is shown that the previously predicted duration of MD trajectories necessary for accurate assessment of DNA elasticity was significantly overestimated and that reliable estimates of elastic parameters can be obtained after a few tens of nanoseconds. The all-atom and coarse-grained ensembles were compared head-to-head, including the amplitudes and relaxation rates of internal fluctuations as well as translational diffusion. The computed diffusion rates were found to be similar, with good correspondence to experimental data. The torsional persistence length (PL) in MD agrees reasonably well with experiment, with the relaxation rate of twisting fluctuations corresponding well to the harmonic model. The bending PL also agrees reasonably well with experiment, but the corresponding relaxation rate is much higher than the harmonic approximation. For a tetradecamer DNA, the difference reaches 1 order of magnitude, with the bending dynamics faster than the twisting dynamics, in qualitative contrast to the coarse-grained model. The possible mechanisms of this anomalous behavior are discussed.
最近的理论和实验研究表明，短长度双螺旋DNA的弹性行为并不符合简谐模型。本文对经典的原子级分子动力学（MD）和粗粒度谐近似进行了全面比较。结果表明，先前预测的准确评估DNA弹性所需的MD轨迹持续时间被显著高估，并且在几十纳秒后即可获得弹性参数的可靠估计值。对全原子和粗粒度系综进行了直接比较，包括内部涨落的幅度和弛豫率以及平动扩散。计算得到的扩散率相似，与实验数据吻合良好。MD中的扭转持久长度（PL）与实验结果相当吻合，扭转涨落的弛豫率与谐模型相符。弯曲PL也与实验结果相当吻合，但相应的弛豫率远高于谐近似。对于一个十四聚体DNA，差异达到1个数量级，弯曲动力学比扭转动力学快，这与粗粒度模型在性质上形成对比。本文讨论了这种异常行为的可能机制。
