Spectroscopic study of the light-harvesting protein c-phycocyanin associated with colorless linker peptides

The phycobilisome (PBS) light-harvesting antenna is composed of chromophore-containing biliproteins and 'colorless' linker peptides and is structurally designed to support unidirectional transfer of excitation energy from the periphery of the PBS to its core. The linker peptides have a unique role in this transfer process by modulating the spectral properties of the associated biliprotein. There is only one three-dimensional structure of a biliprotein/linker complex available to date (APC/LC7.8), and the details of the spectral modulation induced by the linker remain unknown. This study brings together a detailed spectroscopic characterization of C-phycocyanin (PC)-linker complexes (isolated from Synechococcus sp. PCC 7002) with proteomic analysis of the linker amino acid sequences to produce a model for biliprotein/linker interaction.;The amino acid sequences of the rod linkers [LR8.9 , LR32.3 and LRC28.5] were examined to identify evolutionarily conserved regions important to either the structure or function of this protein family. Although there is not one common homologous site among all the linkers, there are strong trends across each separate subset (LC, LR and LRC), and the N-terminal segments of both LR32.3 and L RC28.5 display multiple regions of similarity with other linkers. Predictions of the secondary structure of LR32.3 and LRC28.5, and comparison to the crystal structure of LC7.8, further narrowed the candidates for interaction sites with the PC chromophores.;Measurements of the absorption, fluorescence, CD and excitation anisotropy of PC trimer, PC/LR32.3, and PC/LRC 28.5 document the spectroscopic effect of each linker peptide on the PC chromophores at a series of temperatures (298 to 77 K). Because L R32.3 and LRC28.5 modulate the PC trimer spectral properties in distinct manners, it suggests different chromophore-interaction mechanisms for each linker. The low-temperature absorbance spectrum of the PC trimer is consistent with an excitonic coupling interaction between neighboring alpha84 and beta84 chromophores. Association with LR32.3 does not greatly alter this band shape, but the absorbance of the PC/LRC28.5 complex is dramatically different. This indicates that LRC28.5 is disrupting the alpha84 - beta84 relation established in the PC trimer. From these and other polarized spectroscopy measurements, we conclude that both L R32.3 and LRC28.5 affect the spectral properties of the terminally emitting PC trimer chromophore (beta84), and that LRC28.5 is additionally perturbing the relationship between the alpha84 and beta84 chromophores to either disrupt or enhance their coupling interaction. The linker can perturb the PC chromophores through either specific aromatic residues or a concentration of electrostatically charged residues. Structurally, the linker disrupts the C3 symmetry of the associated biliprotein, and this asymmetric interaction can serve to guide the transfer of excitation energy in one direction.