A toolkit and benchmark study for FRET-restrained high-precision structural modeling
A toolkit and benchmark study for FRET-restrained high-precision structural modeling
复制标题
DOI：
10.1038/nmeth.2222
复制
发表时间：
2012-12-01
期刊：
影响因子：
48
通讯作者：
Seidel, Claus A. M.
中科院分区：
文献类型：
--
作者：
Kalinin, Stanislav;Peulen, Thomas;Seidel, Claus A. M.
我们提出了一个全面的工具包福斯特共振能量转移（FRET）限制建模的生物分子及其复合物的定量应用结构生物学。通过明确考虑染料位置的空间分布，这大大降低了由于灵活的染料接头的不确定性，FRET衍生的结构的精度的显着改善。通过严格的误差估计计算模型的精度和置信水平。通过将DNA引物模板对接到HIV-1逆转录酶来证明这种方法的准确性。导出的模型与已知的X射线结构一致，具有r.m.s. 0.5埃的偏差。此外，我们介绍FRET引导的“筛选”的一个大的结构合奏分子动力学模拟。我们使用这种混合的方法来确定以前未知的配置灵活的单链模板突出。
We present a comprehensive toolkit for Forster resonance energy transfer (FRET)-restrained modeling of biomolecules and their complexes for quantitative applications in structural biology. A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers. The precision and confidence levels of the models are calculated by rigorous error estimation. The accuracy of this approach is demonstrated by docking a DNA primer-template to HIV-1 reverse transcriptase. The derived model agrees with the known X-ray structure with an r.m.s. deviation of 0.5 angstrom. Furthermore, we introduce FRET-guided 'screening' of a large structural ensemble created by molecular dynamics simulations. We used this hybrid approach to determine the formerly unknown configuration of the flexible single-strand template overhang.