FRET-Based Integrative Structural Models and Their Database Deposition

Abstract

Förster Resonance Energy Transfer (FRET) experiments provide information on the dynamics and the tertiary and super-tertiary structure of dynamic biomolecules. Combining FRET experiments with computational methods in integrative approaches allows to generate structural models of biomolecules with high accuracy and precision. We used single-molecule FRET measurements together with FRET-restrained structural modeling, molecular simulations and SAXS measurements in a hybrid approach to obtain structural models for a RNA four-way junction. This integrative approach allowed us to obtain structural models for three co-existing conformers with a precision between 1.3 and 3.0 Å. Software used in this workflow is available on our webpage (http://www.mpc.hhu.de/software.html). PDB-Dev is a prototype archiving system for deposition of integrative and hybrid structural models obtained from various experimental sources (https://pdb-dev.wwpdb.org/). In order to be able to deposit integrative structural models using data from FRET measurements, we worked with the PDB-Dev developers to extend the integrative/hybrid modeling (IHM) dictionary for fluorescence experiments. This extension (FLR dictionary: https://github.com/ihmwg/FLR-dictionary) includes the description of samples, fluorescent probes, analyses, structural modeling procedures and the resulting structural models. In addition to this, we developed a workflow to prepare fluorescence-based structural models and the respective metadata from fluorescence experiments to facilitate their deposition in PDB-Dev.