Fig. 3.

Chromophore-binding pocket views of refined intermediate structures and mechanism for the isomerization and rotation of the pCA chromophore upon absorption of blue light. Five distinct structural intermediates (I_CP, pR_CW, pR_E46Q, pB₁, and pB₂) were identified from four chemical states (α, β, γ, and δ) shown in Fig. 2. I_CP is shown twice to demonstrate the biphasic pathways to pR_CW and pR_E46Q. Isomerization and rotation about single bonds are shown by arrows; hydrogen bonds are dotted. A bicycle pedal mechanism (44), which couples trans-cis isomerization of the C2─C3 double bond with rotation about a nonadjacent single bond, is used for the dark state to I_CP transition. Further rotations about single bonds result in the pB₁ conformation. pB₂ reverts thermally to the dark state with no further detectable intermediates.