Integrative dynamic structural biology of biomolecular assemblies resolved by multi-scale super-resolution FRET spectroscopy and imaging

FRET spectroscopy and imaging can provide state-specific information on the structure and dynamics of complex dynamic biomolecular assemblies under ambient conditions with nanosecond time resolution and single-molecule sensitivity. To overcome the sparsity of FRET experiments, we developed procedures to combine these with computer simulations to map biomolecular dynamics and to resolve quantitative integrative structure models at a precision and accuracy better than 3 Å. The integrative structure models are deposited in the new protein data bank, PDB-dev [1-3]. Moreover, we combined super-resolution microscopy via stimulated emission depletion (STED) and Multi-parameter Fluorescence Image Spectroscopy (MFIS) [4] to reach molecular resolution with sub-nanometer precision in molecular imaging of biomolecules and their complexes. While STED-MFIS captures the spatial and temporal information of the cellular context with a resolution below 10 nm, the concurrent measurement of Förster resonance energy transfer (FRET) between an excited donor and acceptor provides a zoom with Ångström precision. Thus, integrative super-resolution FRET image spectroscopy exploits these synergies to reach molecular resolution.
I will introduce the concepts of our novel optical tools and demonstrate recent applications: (1) Detection of a so far hidden functionally important conformational state in the enzyme T4 Lysozyme [5], (2) Resolving the conformational transitions of Guanylate binding proteins (GBPs) during GTP-controlled phase transition to exert their function as part of the innate immune system of mammalian cells [6]. (3) Mapping the dynamic exchange network in chromatin fibers by studying a 12-mer nucleosome array [7].

[1] Kalinin et al.; Nat. Methods 9, 1218-1225 (2012).
[2] Dimura et al.; Curr. Opin. Struct. Biol. 40, 163–185 (2016).
[3] Dimura et. al. Nat Commun. 11, e5394 (2020).
[4] Weidtkamp-Peters et al.; Photochem. Photobiol. Sci. 8, 470-480 (2009).
[5] Sanabria et. al. Nat Commun. 11, e1231 (2020).
[6] Kravets et. al.; eLife 5, e11479 (2016).
[7] Kilic et al.; Nat. Commun. 9, 235 (2018).