Molecular dynamics simulations of alpha-synuclein ensemble FRET measurements from different force fields.

Alpha-Synuclein is a 140 residue disordered peptide which is key to the onset of Parkinson's disease. Knowledge about the dynamics of alpha-synuclein's structural ensemble is essential for the understanding of pathological alpha-synuclein aggregation. Due to the disordered nature of alpha-synuclein, the challenge to experimentally characterize its structural ensemble and its dynamics renders molecular dynamics simulations particularly relevant. Here, we present the simulation and analysis of ensemble Forster Resonance Energy Transfer (FRET) measurements with a tryptophan / coumarin FRET dye pair at eight different labeling positions. Each labeled peptide was sampled for >80 μs from eight different starting structures, using different AMBER and CHARMM force field / water model combinations. Taking the three competing decay channels of tryptophan as well as their environment dependence into account, FRET fluorescence decay curves were calculated and compared to experiment. The CHARMM22∗//TIP4P-D ensembles agreed slightly better with the measurements than the AMBER99sb//TIP3P and TIP4P ones. Further, a small population of transient ordered states with predominant beta-sheet content (AMBER99sb) and equal beta-sheet/alpha-helical content (CHARMM22∗) was observed, accompanied by an increased radius of gyration, 1.6 vs 1.8 nm, respectively. Overall, the beta-sheet content presumed to be essential for amyloid aggregation was found to be higher in the AMBER ensembles. The radius of gyration for both force field families was lower than that expected from experiment, suggesting an over-stabilization of the transiently ordered states.