Automated and optimally FRET-assisted structural modeling

• DOI: 10.1038/s41467-020-19023-1
• Publication Date: 2020-10-26T11:06:00Z
• Authors: Mykola Dimura; Thomas-Otavio Peulen; Hugo Sanabria; Dmitro Rodnin; Katherina Hemmen; Christian A. Hanke; Claus A. M. Seidel; Holger Gohlke
• Keywords: Single-molecule FRET; Benchmark (surveying)

Abstract FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity experiments, they need be combined with computer simulations. We introduce a program suite ( i ) an automated design tool for which determines how many and pairs should used minimize uncertainty maximize accuracy integrative structure, ii efficient approach FRET-assisted coarse-grained modeling, all-atom molecular dynamics simulations-based refinement, iii quantitative quality estimate judging FRET-derived structures as opposed precision. benchmark our tools against simulated experimental data proteins multiple conformational states demonstrate ~3 Å RMSD Cα X-ray sets 15 23 pairs. Free open-source software introduced workflow is available at https://github.com/Fluorescence-Tools . A web server modeling http://nmsim.de