A Universal Protein Ladder for Standardization of Diverse FRET Assays

ABSTRACT Fluorescence resonance energy transfer (FRET) is the highly distance dependent (3–10 nm) transfer of energy from a donor to an acceptor fluorophore, with transfer efficiency inversely proportional to the distance between the fluorophores. Consequently FRET serves as a powerful spectroscopic ruler for probing molecular interactions. Whilst cell based FRET assays report bulk relative changes in FRET efficiency in a population, single molecule FRET (smFRET) is capable of deconvoluting these population averages into distinct structural states. However, the lack of universal benchmarks prevents the direct translation of in vitro distance measurements to the intracellular environment and vice versa. Here, we present a modular protein ladder designed to harmonize FRET data across diverse platforms. Using an engineered repeating TPR motif and self‐labeling enzymes, we demonstrate that our standards yield consistent FRET efficiencies across expression systems (mammalian and bacterial) and labeling strategies (self labeling enzymes and click chemistry with non‐canonical amino acids). By providing a predictable calibration curve, the ladder enables interpolation between different experimental FRET modalities, including confocal smFRET, flow cytometry based‐FRET and Fluorescence Lifetime Imaging Microscopy FRET (FLIM‐FRET). This is the necessary infrastructure to relate molecular distances from the test tube to the cell.