Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration.
Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration.
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溶液中DNA十二聚体d(CGCGAATTCGCG)的分子动力学模拟研究：构象和水合。
DOI：
10.1006/jmbi.1997.1247
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发表时间：
1997
期刊：
影响因子：
--
通讯作者：
Rosenberg,JM
中科院分区：
文献类型：
--
作者：
Duan,Y;Wilkosz,P;Crowley,M;Rosenberg,JM
利用粒子网格埃瓦尔德和对十二聚体双相d（CGCGAATTCGCG）进行分子动力学模拟，假设其B -构象与观察到的x射线结构非常接近。埃瓦尔德求和法有效地消除了通常的远距离相互作用的“截止”，使我们能够评估静电力的全部作用。该模拟结果在平均结构和b因子上与Dickerson x射线结构具有显著的一致性；在EcoRI站点内，平均理论和观测结构之间的均方根偏差为1.1 Å。小凹槽的宽度在宽和窄之间波动，后者与x射线结构密切相关。模拟还表明，在宽和窄的构象中，小凹槽宽度都有很强的序列依赖特征。在主要沟槽和次要沟槽中均观察到水化壳。小沟内“水化脊”明显。在主槽中，第一个水化壳呈带状结构，再现了观察到的x射线结构的主要特征；这种水合模式的微妙变化表明了序列依赖性。序列相关的特征也检查了螺旋和其他几何参数。许多实验观察到的精细结构特征的成功再现表明，埃瓦尔德求和显着提高了计算的保真度。
A molecular dynamics simulation of the dodecamer duplex d(CGCGAATTCGCG) using the particle mesh Ewald sum assumed a B -conformation remarkably close to the observed X-ray structure. The Ewald summation method effectively eliminates the usual “cut-off” of long-range interactions and allowed us to evaluate the full effect of the electrostatic forces. This simulation showed remarkable agreement with the Dickerson X-ray structure in both average structure and B-factors; within the EcoRI site itself, the rms deviation between the average theoretical and observed structures was 1.1 Å. The width of the minor groove fluctuated between a wide and narrow configuration with the latter corresponding closely to the X-ray structure. The simulation also suggested a strong sequence-dependent signature on the minor groove width in both wide and narrow conformers. Hydration shells in both the major and minor grooves were observed. The “spine of hydration” in the minor groove was clear. In the major groove the first hydration shell appears to be a ribbon-like structure that reproduces the principal features of observed X-ray structures; subtle variations of this hydration pattern suggest sequence dependencies. Sequence-dependent features were also examined for helical and other geometric parameters. The successful reproduction of many experimentally observed fine structural features shows that the Ewald summation significantly improves the fidelity of the calculations.