Cyanophyta‐phycocyanin (C‐PC) is the main constituent of the rod of phycobilisome (PBS), which is a highly ordered and large peripheral light‐harvesting protein complex present on the cytoplasmic side of the thylakoid membrane in cyanobacteria and red algae. The C‐PC monomer comprises two chains, α‐ and β‐subunits, and aggregates to form ring‐shaped trimers (αβ)sub3/sub with rotational symmetry. The ring‐shaped trimer (αβ)sub3/sub is a structural block unit (SBU) that forms the rod of PBS. Two (αβ)sub3/sub SBUs are arranged in a face‐to‐face manner to form an (αβ)sub6/sub‐hexamer. In this study, the electronic states of three phycocyanobilins, α84, β84, and β155 in C‐phycocyanin, constituting the rod of the PBS, were calculated for both the trimer and hexamer models by considering the effect of the electrostatic field of protein moieties and water molecules. For the hexamer, the absorption wavelengths of α84, β84, and β155 were similar to those obtained experimentally; however, for the trimer, only the absorption wavelength of β155 shifted toward a shorter‐wavelength. The nature of the hexamer structure as a hierarchical structure is revealed by considering the calculated absorption wavelength and energy transfer.
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