A large number of novel phytochromes named cyanobacteriochromes (CBCRs) have been recently identified. CBCRs appear to be attractive for further in-depth studies as paradigms for phytochromes because of their related photochemistry, but simpler domain architecture. Elucidating the mechanisms of spectral tuning for the bilin chromophore down to the molecular/atomic level is a prerequisite to design fine-tuned photoswitches for optogenetics. Several explanations for the blue shift during photoproduct formation associated with the red/green CBCRs represented by Slr1393g3 have been developed. There are, however, only sparse mechanistic data concerning the factors controlling stepwise absorbance changes along the reaction pathways from the dark state to the photoproduct and vice versa in this subfamily. Conventional cryotrapping of photocycle intermediates of phytochromes has proven experimentally intractable for solid-state NMR spectroscopy within the probe. Here, we have developed a simple method to circumvent this hindrance by incorporating proteins into trehalose glasses which allows four photocycle intermediates of Slr1393g3 to be isolated for NMR use. In addition to identifying the chemical shifts and chemical shift anisotropy principal values of selective chromophore carbons in various photocycle states, we generated QM/MM models of the dark state and photoproduct as well as of the primary intermediate of the backward-reaction. We find the motion of all three methine bridges in both reaction directions but in different orders. These molecular events channel light excitation to drive distinguishable transformation processes. Our work also suggests that polaronic self-trapping of a conjugation defect by displacement of the counterion during the photocycle would play a role in tuning the spectral properties of both the dark state and photoproduct.
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