Abstract
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 RMSDCα 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.
Highlights
FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies
Aiming at the FRET-assisted refinement of conformers or docked substructures, we developed two approaches that explicitly consider positional dye distributions and apply FRET restraints to the biomolecular system via the restrained mean position (RMP) approach: the command-line tool FRETrest for FRET-restrained molecular dynamics simulations; and a FRET-guided coarse-grained simulation approach based on the normal mode-based geometric simulations (NMSim) geometric conformational sampling software[26]
To optimize FRET experiments, our program suite FPS 2.0 uses a feature selection algorithm to determine automatically the smallest set of most informative FRET pairs (Supplementary Fig. 1 and Supplementary Table 1), which minimizes the expected uncertainty of the model for a given initial structural ensemble
Summary
FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. If biomolecular systems are complex, information from multiple experimental and computational methods is combined by integrative modeling (IM) for generating integrative structure models. In this context, FRET experiments with quantitative analysis are increasingly used to provide dynamic information on the studied system and to determine integrative structures[3]. For certain classes of systems, including multidomain proteins, biomacromolecular complexes, dynamic systems with unstructured regions, and systems with lowly populated conformational states, experimental structure determination is challenging. A generally available automated design of informative FRET experiments, previously suggested[16] and described here, will minimize the total experimental effort by maximizing the information content per measurement
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
