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Phycobilisomes are supramolecular protein complexes, which consist of phycobiliproteins and perform the function of light harvesting in the photosynthetic apparatus of cyanobacteria. During this work we show that phycobilisomes of the cyanobacteria Synechocystis are sensitive to ionizing radiation which simulates conditions of space flight. Modeling the behavior of biological objects in conditions of high radiation and attenuated geomagnetic field is important scientific problem. Because it is known that these conditions often affect vital activity of biological objects. However the mechanism is faintly studied and requires further investigation. In this study we compare the effects of “space flight” in vivo on the cells of Synechocystis and in vitro on isolated phycobilisomes. For modeling “space flight” conditions we used the cyclotron U-120 SINP MSU, which yields accelerated helium nuclei with energy of 30.3 MeV for irradiation of biological objects. Changes in the structural and functional state of the phycobilisomes of cyanobacteria was evaluated by using the optical methods - absorption spectroscopy, spectrofluorometry (Fluoromax-4, Horiba Jobin Yvon) and spectrofluorometry with picosecond time resolution (Simple-Tau 140, Becker & Hickl). It was found that the optical density of phycobilisomes and corresponding fluorescence intensities are decreased after irradiation and the effect is dose dependant. Probably, this effect can be explained by reducing concentration of the phycobilins and changing their states after irradiation. It was shown, that fluorescence lifetime of isolated phycobilisomes is reducing, at the same time in cyanobacteria cells the corresponding lifetime is increasing after irradiation with the same dose. We suppose that differences in dependencies of the lifetime can be explained by dissociation of phycobilisomes on to phycobiliproteins and interruption of the excitation energy transfer processes in vivo, while in vitro we observe denaturation of phycobiliproteins. Acknowledgements Thank the Russian Foundation for Basic Research (project 16-34-00394).