Determination of DNA structures by NMR and distance geometry techniques: a computer simulation.
Determination of DNA structures by NMR and distance geometry techniques: a computer simulation.
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通过 NMR 和距离几何技术测定 DNA 结构：计算机模拟。
DOI：
10.1073/pnas.85.23.8785
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发表时间：
1988
影响因子：
11.1
通讯作者：
Wang,C
中科院分区：
文献类型：
--
作者：
Pardi,A;Hare,DR;Wang,C
已经进行了计算机模拟，以确定如何准确和精确地从二维 NMR 实验获得的距离数据生成 DNA 寡聚物的结构。 Dickerson 十二聚体的六聚体片段 d(CGAATT) [Drew, H.R.、Wing, R.M.、Takano, T.、Broka, C.、Tanaha, S.、Itakura, K. & Dickerson, R.E. (1981) 程序。国家。阿卡德。科学。 USA 78, 2179-2183] 被用作这些模拟中的模型结构。将质子添加到原始 X 射线结构的坐标中，然后对其进行正则化程序，以尽量减少与标准键长和键角的偏差。核磁共振实验中通常观察到的质子-质子距离是根据这个正则化的目标结构测量的，并用作距离几何算法的输入。距离几何结构由两个距离组生成，一组具有基本精确的距离 (+/- 0.005 A)，一组具有模拟最佳 NMR 实验的精度 (+/- 0.2 A)。这些计算的结果用于判断从模拟的 NMR 距离数据中再现以下螺旋参数的准确度和精度：螺旋扭曲、螺旋上升、位错、滚动、倾斜、糖苷角、δ扭转角和假旋转角。这些数据为判断真实 NMR 实验产生的 DNA 结构的质量提供了基础。
Computer simulations have been performed to determine how accurately and precisely structures of DNA oligomers can be generated from distance data obtained from two-dimensional NMR experiments. A hexamer fragment d(CGAATT) of the Dickerson dodecamer [Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaha, S., Itakura, K. & Dickerson, R.E. (1981) Proc. Natl. Acad. Sci. USA 78, 2179-2183] was used as the model structure in these simulations. Protons were added to the coordinates of the original x-ray structure, which was then subjected to a regularization procedure to minimize deviations from standard bond lengths and bond angles. The proton-proton distances normally observed in NMR experiments were measured from this regularized target structure and used as input for a distance geometry algorithm. Distance geometry structures were generated from two distance sets, one with essentially exact distances (+/- 0.005 A) and one set with a precision (+/- 0.2 A) that simulates an optimal NMR experiment. The results of these calculations were used to judge how accurately and precisely the following helical parameters could be reproduced from this simulated NMR distance data: helical twist, helical rise, dislocation, roll, tilt, glycosidic angle, delta torsion angle, and pseudorotation angle. These data provide a basis from which to judge the quality of DNA structures produced from real NMR experiments.