Photochemistry and transient intermediates in a bacteriophytochrome photocycle revealed by multiscale simulations

Phytochromes are photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of an embedded chromophore, which triggers a large conformational change in the structure of the entire protein. Although phytochromes have been subject of numerous studies, the photoisomerization mechanism and the following reaction path leading to the final active state remain elusive. Here, we use an integrated computational approach that combines non-adiabatic surface hopping and adiabatic ground-state molecular dynamics simulations to gain atomistic details on the photoactivation mechanism of Deinococcus radiodurans bacteriophytochrome. Our simulations show that the ps-scale photoisomerization of the chromophore proceeds through a hula-twist mechanism that forces a counterclockwise rotation of the D-ring. The initial photoproduct rapidly evolves in an early intermediate which we characterize through IR spectroscopy simulation. The early intermediate then evolves on the nanosecond-to-microsecond scale to a late intermediate, characterized by a more disordered binding pocket and a clear weakening of the aspartate-to-arginine salt bridge interaction, whose cleavage is essential to interconvert to the final active state.