Photo active yellow fluorescent protein absorbs blue light. It contains a photoactive center called a chromophore that changes its conformation when it absorbs a blue photon, thereby enabling the protein to sense blue light.
Given the importance of the chromophore’s motion in enabling the protein’s function, naturally I want to emphasize how the its motion changes the protein’s color. The system reminds me of a light bulb, with the chromophore being the switch. The reasoning being that the movement of the chromophore causes a photochemical change in the protein. An alternative representation could be with two side-by-side representations, where one shows the protein before the chromophore absorbs light, and one after, highlighting the change in color.
Source: PDB website
