Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
复制标题
DOI：
10.1107/s0021889807001707
复制
发表时间：
2007-04-01
影响因子：
6.1
通讯作者：
Doniach, Sebastian
中科院分区：
文献类型：
--
作者：
Lipfert, Jan;Chu, Vincent B.;Doniach, Sebastian
目前已有几种算法可用于从小角度溶液散射数据重建生物大分子的低分辨率电子密度图。这些算法已广泛应用于蛋白质和蛋白质复合物。在这里，我们通过重建一组已知的三维结构的RNA和DNA分子的小角度x射线散射剖面来证明它们对核酸的适用性。在所有的测试案例中，分子的总体大小和形状都得到了很好的再现。此外，我们表明所生成的头模型可以用作静电计算的输入。用粒子模型泊松-玻尔兹曼方程的数值解计算得到的不同溶液条件下的束缚离子数与晶体学中所有原子模型的计算结果吻合得很好。泊松-玻尔兹曼理论的预测也与实验确定的离子结合数大体一致。
Several algorithms are available to reconstruct low-resolution electron density maps of biological macromolecules from small-angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson-Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson-Boltzmann theory also agree generally well with experimentally determined ion binding numbers.