Prof. Dr. rer. nat. Richard Börner
Hochschule Mittweida, Biophotonik am Laserinstitut
Abstract: The functional diversity of RNA is encoded in their innate conformational heterogeneity. The combination of single-molecule spectroscopy and computational modeling offers new opportunities to map structural transitions within ribonucleic acid ensembles to be used e.g. in computer-aided drug discovery. Here, we describe a framework to harmonize single-molecule FRET measurements with molecular dynamics simulations and de novo structure prediction. Using either all-atom or implicit fluorophore modeling we recreate FRET experiments in silico, visualize the underlying structural dynamics and quantify the simulated reaction coordinates. Using multiple accessible-contact volumes (multi-ACV) as a post-hoc scoring method for fragment-assembly in Rosetta FarFar2, we demonstrate that FRET effectively refines de novo RNA structure prediction without the need of explicit dye labeling in silico. We benchmark our FRET-assisted modeling approach on double-labeled DNA strands and validate it against an intrinsically dynamic Mn(II)-binding riboswitch and a Mg(II)-sensitive ribosomal RNA tertiary contact. We show that already one FRET coordinate, i. e., describing the assembly of a fourway junction and the GAAA binding to a kissing loop, allows to recapitulate the global fold of both, the riboswitch and the tertiary contact, and to significantly reduce the de novo generated structure ensemble.