We report on single-molecule fluorescence measurements performed on the phycobiliprotein allophycocyanin (APC). Our data support the presence of a unidirectional Förster-type energy transfer process involving spectrally different chromophores, α84 (donor) and β84 (acceptor), as well as of energy hopping amongst β84 chromophores. Single-molecule fluorescence spectra recorded from individual immobilized APC proteins indicate the presence of a red-emitting chromophore with emission peaking at 660 nm, which we connect with β84, and a species with the emission peak blue shifted at 630 nm, which we attribute to α84. Polarization data from single APC trimers point to the presence of three consecutive red emitters, suggesting energy hopping amongst β84 chromophores. Based on the single-molecule fluorescence spectra and assuming that emission at the ensemble level in solution comes mainly from the acceptor chromophore, we were able to resolve the individual absorption and emission spectra of the α84 and β84 chromophores in APC.
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