Analogies and differences in the photoactivation mechanism of bathy and canonical bacteriophytochromes revealed by multiscale modeling

Bacteriophytochromes are light-sensing biological machines that interconvert between two spectroscopically distinct states, Pr and Pfr. The relative stability of the two states is opposite in canonical and bathy bacteriophytochromes but in both cases the switch between them is triggered by a photoisomerization of an embedded bilin chromophore, the effects of which propagate throughout the protein with different timescales. Here, we applied an integrated multiscale strategy of (QM/)MM molecular dynamics simulations and excited-state QM/MM nonadiabatic dynamics with enhanced sampling techniques to the Agrobacterium fabrum bathy phytochrome and compared the results with those obtained for the canonical phytochrome Deinococcus radiodurans. Contrary to what recently suggested, we found that the photoactivation of both phytochromes is directly triggered by the same photoisomerization process involving an hula-twist motion. However, only in the bathy phytochrome the photoproduct evolves into a heterogeneous and dynamic intermediate, Lumi-F, in which the bilin has reached the final (Pr) configurational state. Moreover, the protein pocket of the bathy phytochrome responds in a microsecond timescale, by reorienting several aminoacidic residues and causing the spine to tilt.