Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
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DOI：
10.1021/ja805405a
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发表时间：
2009-02-11
影响因子：
15
通讯作者：
Berg, Mark A.
中科院分区：
文献类型：
--
作者：
Sen, Sobhan;Andreatta, Daniele;Ponomarev, Sergei Y.;Beveridge, David L.;Berg, Mark A.
时间分辨斯托克斯位移实验测量的动态生物分子和扰动溶剂附近的亚纳秒的时间尺度，但需要分子动力学模拟，以提供一个清晰的解释的结果。在这里，我们表明，模拟使用标准的方法定量再现TRSS实验在DNA中的主要特征，并提供了分子分配的动力学。模拟再现了在最近的实验中看到的斯托克斯位移的幅度和不寻常的幂律动力学[D。Andreatta等人，J. Am. 127，7270（2005）]。引入极化模型以消除对信号有贡献的不同分量之间的互相关。使用该模型，提取了DNA、水和反离子对实验信号的明确贡献。水被发现有最大的贡献，并负责幂律动力学。抗衡离子具有较小但不可忽略的贡献，时间常数为220 ps。DNA本身对信号的贡献很小，并且符合30 ps拉伸指数。计算了时间平均分布和动态分布。他们显示了一个小的离子子集与不同的耦合，但没有其他证据的substates或动态异质性。
Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [D. Andreatta, et al., J. Am. Chem. Soc. 127, 7270 (2005)]. A polarization model is introduced to eliminate cross correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling, but no other evidence of substates or dynamic heterogeneity.
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影响因子：
15
作者：
Andreatta, D;Lustres, JLP;Berg, MA
通讯作者：
Berg, MA
影响因子：
15
作者：
Andreatta, Daniele;Sen, Sobhan;Berg, Mark A.
通讯作者：
Berg, Mark A.
影响因子：
44.1
作者：
BERNARD, W;CALLEN, HB
通讯作者：
CALLEN, HB
影响因子：
2.9
作者：
Guha, S;Sahu, K;Bhattacharyya, K
通讯作者：
Bhattacharyya, K
影响因子：
56.9
作者：
Cohen, BE;McAnaney, TB;Jan, LY
通讯作者：
Jan, LY