Fig. 4: Kinetic schemes of the photocycle of PYP in solution and in crystalline form.
From: Confinement in crystal lattice alters entire photocycle pathway of the Photoactive Yellow Protein
Top panel: PYP in solution, bottom panel: PYP in crystalline form. Upon absorption of light by pCa in the ground state (GS), the excited state is formed from which the system transitions through the reaction. The relevant states are indicated by the following abbreviations: ES1-3: excited states sharing the same spectrum, evolving sequentially from 1→2→3; GSI: ground state intermediate; I0, I1, I2 (pB1), I2’(pB2), pR0, pR1, pR2, pBcrystal: photocycle intermediates. Note that we use the symbol “IX” for notation of PYPS intermediate states, and “pC” (with C for color, i.e., red or blue) for those in PYPC, except for the final pB states. The transition rates indicated near the arrows are in ns−1, the lifetime of each state is indicated in italic. The rate constants involving the ES and GSI for PYPS have been fixed from ref. 24, all other parameters have been estimated. Note that in the crystal as evidenced from the UV–Vis data19 half of the pR2 states is converted to pB, whereas the other half branches directly to the ground state, with a rate of kR,VIS 2.4 × 10−6. Note that the longer time scales (after 100 ms) are based solely on the the UV–Vis data of ref. 19. Concentration profiles computed with these kinetic schemes for the photocycle intermediates states are shown in Supplementary Fig. 7.
