Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

Significance Proteins adopt disordered ensembles prior to folding and sometimes as a part of their function. Simulations and FRET studies often described disordered conformations as more compact than the random coil states observed at high denaturant, whereas small-angle X-ray scattering (SAXS) indicates that these conformations remain expanded. Resolving this discrepancy improves our understanding of the properties of proteins, such as whether water is a sufficiently poor solvent to drive nonspecific collapse. We achieve reconciliation by showing the addition of FRET fluorophores reduces the disordered protein’s dimensions. Detailed analysis of FRET and SAXS, along with accounting for fluorophore-induced contraction, demonstrates that disordered and unfolded proteins often remain solvated and expanded without denaturant, properties that minimize misfolding and aggregation.