pH dependence of the photoactive yellow protein photocycle recovery reaction reveals a new late photocycle intermediate with a deprotonated chromophore

The recovery reaction of the signaling state of photoactive yellow protein includes the following: (i) deprotonation of the p-coumaryl chromophore, (ii) refolding of the protein, and (iii) chromophore re-isomerization from the cis to the trans configuration. Through analysis of the pH dependence of this recovery reaction, we were able to provide proof for the existence of an additional photocycle intermediate. The spectral similarity between this new intermediate and the dark state indicates that the new intermediate has a deprotonated chromophore, which may facilitate chromophore re-isomerization. This spectral similarity also explains why this new intermediate has not been noticed in earlier studies. For our data analysis we introduce a photocycle model that takes into account the effect of the specific light regime selected, a model that was also used for simulations