"Multiscale characterization of the photocycle of photoactive yellow protein" - The postulated signaling state of the bacterial photoreceptor photoactive yellow protein (PYP) is found in experiments to be essentially indistinguishable from an on-pathway folding intermediate formed upon the isomerization of the chromophore embedded in the protein, suggesting a direct link between the folding and the photocycle of this protein. The wide range of time-scales covered during the photocycle/folding of PYP, together with the partially unfolded nature of the signaling state, make the structure determination of the signaling state challenging, either by simulation or by experiment. We have circumvented this problem by using a realistic coarse-grained protein model for PYP, that allows us to characterize the functional changes in the folding free energy landscape. While the folding landscape of the coarse-grained native protein indicates a two-state folding mechanism, the coarse-grained model of the photoactivated form of PYP populates an on-pathway intermediate ensemble, in line with experimental data. The folding intermediate detected in our coarse-grained study matches well all available experimental data on the putative signaling state of PYP, confirming the connection between the folding and function of this protein. These results allow us to use the coarse-grained model as a starting point to characterize the molecular structure of the signaling state at atomic level of detail.