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The functioning of light-sensitive proteins is closely connected to the ways by which the protein environment tunes the intrinsic photo-response of their chromophores and guides their excited-state evolution. By using the excited-state XMCQDPT2 electronic structure calculations of the isolated Tyr-based Green Fluorescent Protein (GFP) chromophore anion, we have been able to disclose a striking interplay between the electronic and nuclear dynamics that are coupled with a remarkable efficiency in the ultrafast excited-state decay channels of this chromophore. The energy exchange is found to be ultrafast and, importantly, mode-specific. This results in vibrationally mediated photo-detachment out of the first electronically bound excited state of the anion or in internal conversion back to the hot ground state, where the latter is shown to proceed through the two distinct types of the conical intersections. We consider this non-adiabatic coupling in the excited states dynamics of biological chromophores as a key for understanding various mechanisms, by which the proteins efficiently tune their response to the absorption of light. A direct disclosure of the relevance of our findings to the functioning of the proteins is revealed by performing state-of-the-art, large-scale calculations of the GFP photo-response. By simulating the photo-initiated early-time nuclear dynamics of GFP, its absorption spectral profile has been retrieved, which appears to be remarkably similar to that of the isolated chromophore. Here, the high-frequency stretching modes play an important role, defining the spectral widths. Remarkably, these modes also serve as reaction coordinates for possible photo-induced electron transfer, which may compete with internal conversion. The non-adiabatic mechanism of hidden photo-induced proton transfer has been disclosed in the case of the Tyr-based Blue Fluorescent Protein. The complete photocycle of this protein has been proposed, including the intra-protein proton transfer coupled to the photo-induced isomerization as well as the radical formation induced by multi-photon ionization.