Unraveling multi-state molecular dynamics in single-molecule FRET experiments- Part I: Theory of FRET-Lines

Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule F\"orster Resonance Energy Transfer (smFRET) is a powerful approach to inform on the structure and the dynamics of labeled molecules. If the dynamics occur on the sub-millisecond timescale, capturing and quantifying conformational dynamics can be challenging by intensity-based smFRET. Multiparameter fluorescence detection (MFD) addresses this challenge by simultaneously registering intensities and fluorescence lifetimes. Together, the mean donor fluorescence lifetime and the fluorescence intensities inform on the variance, and the mean FRET efficiency tells the conformational dynamics. Here, we present a general framework that relates average fluorescence lifetimes and intensities in smFRET counting histograms. Using this framework, we show how to compute parametric relations (FRET-lines) of these observables that facilitate a graphical interpretation of experimental data, can be used to test models, identify conformational states, resolve the connectivity of states, and can be applied to unstructured systems to infer properties of polymer chains or study fast protein folding. To simplify the graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data and show how to decouple the motion of the fluorescence labels from the conformational dynamics of the biomolecule.
Comment: Main Text (47 pages, 14 figures, 3 tables) with Supporting Information (22 pages, 2 figures)