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of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing
(Pfr) states triggers light adaptation of plants, bacteria and other organisms.
Using quantum chemistry, we elucidate the color-tuning mechanism of
phytochromes and identify the origin of the Pfr-state red-shifted spectrum.
Spectral variations are explained by resonance interactions of the protonated
linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole
ring D with the strictly conserved aspartate shifts the positive charge towards
ring D thereby inducing the red spectral shift. Our MD simulations demonstrate
that formation of the ring D–aspartate hydrogen bond depends on interactions
between the chromophore binding domain (CBD) and phytochrome specific domain
(PHY). Our study guides rational engineering of fluorescent phytochromes with a
far-red shifted spectrum.