Protein control of photochemistry and transient intermediates in phytochromes

Phytochromes are photoreceptors responsible for sensing light in plants, fungi and bacteria. Here the authors use computational simulations to reveal the molecular mechanism of photoactivation and characterize the involved reaction intermediates. Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.

Automated summary

The authors use computational simulations to uncover the molecular mechanism of photoactivation in phytochromes, the photoreceptors responsible for sensing light in plants, fungi, and bacteria. They find that chromophore-protein interactions play a crucial role in controlling the mechanism and timescale of the photoisomerization process.