Structural exploration and Förster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-β peptides

Abstract

The distance-dependence of excitation energy transfer, e.g., being described by Förster theory (Förster resonance energy transfer (FRET)), allows the use of optical techniques for the direct observation of structural properties. Recently, this technique has been successfully applied in the gas phase. The detailed interpretation of the experimental FRET results, however, relies on the comparison with structural modeling. We therefore present a complete first-principles modeling approach that explores the gas-phase structure of chromophore-grafted peptides and achieves accurate predictions of FRET efficiencies. We apply the approach to amyloid-β 12-28 fragments, known to be involved in amyloid plaque formation connected to Alzheimer's disease. We sample structures of the peptides that are grafted with 5-carboxyrhodamine 575 (Rh575) and QSY-7 chromophores by means of replica-exchange molecular dynamics simulations upon an Amber-type forcefield parametrization as a function of the charge state. The generated ensembles provide chromophore-distance and -orientation distributions which are used with the spectral parameters of the Rh575/QSY-7 chromophores to model FRET-efficiencies for the systems. The theoretical values agree with the experimental average "action"-FRET efficiencies and motivate to use the herein reported parametrization, sampling, and FRET-modeling technique in future studies on the structural properties and aggregation-behavior of related systems.

Action-FRET of a Gaseous Protein

“…A detailed description of the theoretical determination of FRET efficiencies can be found elsewhere, and here they are estimated for these final structures using Förster theory and assuming isotropic chromophore orientations [15]. The predicted range of FRET efficiencies for the 6+ N-state model is 0.66 and 0.91 (the range is due to existence of a protruding chromophore configuration with 3.6 nm separation and a tight-fitted chromophore configuration with 2.7 nm separation, see Supplementary Figure S5).…”

“…The structure of chromophore-tagged ubiquitin was studied by molecular dynamics (MD) simulations in the frame of an Amber99/GAFF force field parametrization [33, 34], which has been successfully applied to determine structural properties of chromophore-tagged amyloid-β monomers and dimer in the gas phase [14, 15]. The same parameter set is used both for gas-phase and preparative solution-phase simulations.…”

“…The chromophores (rhodamine 575 C 5 -maleimide and QSY7 C 5 -maleimide functionalized cysteine residues) have been treated within a GAFF parametrization as described previously and the details of the FRET-efficiency calculations used herein are also described in detail elsewhere [15]. In brief, the FRET efficiencies are calculated from chromophore separations and orientation factors of the ensemble of structures found in the molecular dynamics runs and using spectral parameters of the chromophores from experiments and TDDFT calculations (see Ref.…”

“…In brief, the FRET efficiencies are calculated from chromophore separations and orientation factors of the ensemble of structures found in the molecular dynamics runs and using spectral parameters of the chromophores from experiments and TDDFT calculations (see Ref. [15], R 0 = 40.3 Å with chromophores being isotopically oriented). Gas-phase MD simulations were performed after removing all solvent and ions in the box, using a 1 fs time step and neither cut-offs for the evaluation of non-bonded interactions nor bond-constraints.…”

“…The transposition of FRET to the gas phase has been demonstrated by several groups via the detection of fluorescence or fragmentation, with a concurrent development of computational methods for obtaining theoretical FRET efficiencies from chromophore-tagged structural ensembles [8–15]. This emerging technique has been recently applied to biologically relevant systems to elucidate differences in the structural landscape of mutants of the 12–28 fragment of amyloid-β in order to probe differences in aggregation phenomena, and has also been applied to probe the structure of dimers of the same system, showing the coexistence of two distinct binding motifs [14, 16].…”