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In cyanobacteria, the thermal dissipation of excess excitation energy (=non-photochemical fluorescence quenching) at the level of phycobilisome (PBS)-antennae is triggered by absorption of blue-green light by the photoactive orange carotenoid protein (OCP) [1]. According to a current report this mechanism is evolutionarily rather old [2]. An in vitro reconstituted system with OCP and PBS’ isolated from the cyanobacterium Synechocystis sp. PCC 6803 provided direct evidence that the OCP is not only a photosensor in this process, but acts also as an effector [3,4]. To localize the primary site of quenching, we have analyzed the role of chromophorylated polypeptides of the PBS core using an in vitro system with isolated PBS components as well as PBS-deficient mutants [5]. The results have shown that neither bulk allophycocyanin trimers nor the ApcD or ApcF terminal emitters within the PBS are directly subjected to quenching. In contrast, the fluorescence emission of the core-membrane linker LCM is effectively quenched by photoactivated OCP in vitro. The conclusion is further supported by concentration dependence and fluorescence lifetime-measurements, 77 K fluorescence emission and fluorescence excitation spectra studies of quenched PBS as well as with ApcE-less Synechocystis cells. The data suggest that besides its central role in excitation energy transfer and as a key structural element in the PBS, LCM is the primary site of photoprotective excitation quenching in the PBS core. Changes in fluorescence lifetime of the fully assembled PBS and isolated LCM and linear dependences of fluorescence intensity on OCP concentration indicate that the quenching of LCM has a static character, while the corresponding secondary quenching of assembled PBS is of a dynamic type. A model for OCP-PBS interaction is proposed based on the 3D structures of the corresponding proteins. According to the model the OCP molecule is wedged between the chromophorylated PB domain of LCM inside the PBS core and the surface of the thylakoid membrane and there could be a direct contact between the phycocyanobilin chromophore of LCM and the ketocarotenoid chromophore of OCP. The distance between these chromophores is estimated as about 15 Å and two-fold longer in the unquenched state respectively.