Flexible protein regions, often enriched in glycine- and serine-rich segments, play a central role in biomolecular dynamics and function. The combination of time-resolved fluorescence resonance energy transfer (FRET) spectroscopy and molecular dynamics simulations provides a powerful framework to characterize these motions at atomic resolution. In this work, we investigate the conformational and kinetic properties of Trp-(GS)n-Dbo and Trp-(PP)n-Dbo peptides (n = 0, 1, 2, 3) in aqueous solution using microsecond-scale MD simulations, informed by an improved description of the Dbo-labeled aspartic residue compatible with the G54A7 force field. The simulations quantitatively reproduce experimental end-to-end distances derived from FRET measurements, with deviations below 5% for all (GS)n peptides, and correctly capture the systematic relationship between chain flexibility and fluorophore separation. Analysis of looping kinetics further shows quantitative agreement with experimentally measured contact formation rates after viscosity correction, supporting a diffusion-controlled mechanism for intrachain contact formation. Together, these results establish a consistent, quantitative link between structural ensembles, dynamical observables, and FRET experiments, and provide benchmark data for modeling fluorophore-labeled peptides and intrinsically disordered protein segments.
Danilo Roccatano (Fri,) studied this question.