Figure 2: smFRET time averaging impacts proteins across the ordered.

A) FRET efficiencies for T4 Lysozyme labeled at 44 (para-acetylphenylalanine ) and 150 (cysteine) with Alexa 488 and Alexa 647 or B) Aβ40 labeled at positions 1 (para-acetylphenylalanine) and 40 (cysteine) with Alexa 488 and Alexa 647. In black is the experimental distribution, red the result when not accounting for protein dynamics, and purple accounting for protein dynamics via time-averaging. Protein structures are the 15 most probable states in the MSM with labeling positions indicated in orange spheres. Experimental donor only counts (E < 0.25) have been removed for ease of comparison.