Köfinger Jürgen, Hummer Gerhard
Laboratory of Chemical Physics, Bldg. 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 May;87(5):052712. doi: 10.1103/PhysRevE.87.052712. Epub 2013 May 20.
The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions. However, in small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) experiments only their Fourier transform is measured over a restricted range of scattering angles. We therefore developed a mathematically simple and computationally efficient method to calculate the PDDFs as well as accurate scattering intensities from molecular dynamics simulations. The calculated solution scattering intensities are in excellent agreement with SAXS and wide-angle x-ray scattering (WAXS) experiments for a series of proteins. The corresponding PDDFs are remarkably rich in features reporting on the detailed protein structure. Using an inverse Fourier transform method, most of these features can be recovered if scattering intensities are measured up to a momentum transfer of q≈2-3Å(-1). Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold.
对距分布函数（PDDF）包含了在大分子溶液的弹性散射实验中探测到的所有结构信息。然而，在小角X射线散射（SAXS）或小角中子散射（SANS）实验中，仅在有限的散射角范围内测量其傅里叶变换。因此，我们开发了一种数学上简单且计算效率高的方法，用于从分子动力学模拟中计算PDDF以及精确的散射强度。对于一系列蛋白质，计算得到的溶液散射强度与SAXS和广角X射线散射（WAXS）实验结果高度吻合。相应的PDDF具有丰富的特征，能够反映蛋白质的详细结构。使用逆傅里叶变换方法，如果在动量转移q≈2 - 3Å⁻¹范围内测量散射强度，这些特征中的大部分都可以恢复。我们的结果表明，利用X射线自由电子激光和第三代同步辐射源进行的高精度溶液散射实验能够解析亚纳米级别的结构细节，远远超出了尺寸、形状和折叠信息。
