Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
Nat Commun. 2020 Oct 26;11(1):5394. doi: 10.1038/s41467-020-19023-1.
FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET experiments, they need to be combined with computer simulations. We introduce a program suite with (i) an automated design tool for FRET experiments, which determines how many and which FRET pairs should be used to minimize the uncertainty and maximize the accuracy of an integrative structure, (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (iii) a quantitative quality estimate for judging the accuracy of FRET-derived structures as opposed to precision. We benchmark our tools against simulated and experimental data of proteins with multiple conformational states and demonstrate an accuracy of ~3 Å RMSD against X-ray structures for sets of 15 to 23 FRET pairs. Free and open-source software for the introduced workflow is available at https://github.com/Fluorescence-Tools . A web server for FRET-assisted structural modeling of proteins is available at http://nmsim.de .
荧光能量转移（FRET）实验可以提供复杂动态生物分子组装体的特定状态结构信息。然而，为了克服 FRET 实验的稀疏性，它们需要与计算机模拟相结合。我们引入了一个程序套件，其中包括：（i）用于 FRET 实验的自动化设计工具，该工具确定应该使用多少个和哪些 FRET 对，以最小化不确定性并最大限度地提高综合结构的准确性；（ii）一种用于 FRET 辅助的粗粒度结构建模和基于全原子分子动力学模拟的细化的有效方法；（iii）一种定量质量估计方法，用于判断 FRET 衍生结构的准确性与精密度。我们使用具有多种构象状态的蛋白质的模拟和实验数据对我们的工具进行了基准测试，并针对 15 到 23 个 FRET 对的数据集，实现了与 X 射线结构相比约 3 Å RMSD 的准确性。所介绍工作流程的免费和开源软件可在 https://github.com/Fluorescence-Tools 上获得。一个用于蛋白质 FRET 辅助结构建模的网络服务器可在 http://nmsim.de 上获得。
