Estimating Orientation Factors in the FRET Theory of Fluorescent Proteins: The TagRFP-KFP Pair and Beyond

The orientation factor kappa(2), one of the key parameters defining Forster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S-0,S-min -> S-1 excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S-1,S-min -> S-0 emission for TagRFP. These data allowed us to estimate kappa(2) values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.