Mechanism of proton-coupled quinone reduction in Photosystem II

Abstract

Photosystem II uses light to drive water oxidation and plastoquinone (PQ) reduction. PQ reduction involves two PQ cofactors, Q(A) and Q(B), working in series. Q(A) is a one-electron carrier, whereas Q(B) undergoes sequential reduction and protonation to form Q(B)H(2). Q(B)H(2) exchanges with PQ from the pool in the membrane. Based on the atomic coordinates of the Photosystem II crystal structure, we analyzed the proton transfer (PT) energetics adopting a quantum mechanical/molecular mechanical approach. The potential-energy profile suggests that the initial PT to Q(B)(•-) occurs from the protonated, D1-His252 to Q(B)(•)(-) via D1-Ser264. The second PT is likely to occur from D1-His215 to Q(B)H(-) via an H-bond with an energy profile with a single well, resulting in the formation of Q(B)H(2) and the D1-His215 anion. The pathway for reprotonation of D1-His215(-) may involve bicarbonate, D1-Tyr246 and water in the Q(B) site. Formate ligation to Fe(2+) did not significantly affect the protonation of reduced Q(B), suggesting that formate inhibits Q(B)H(2) release rather than its formation. The presence of carbonate rather than bicarbonate seems unlikely because the calculations showed that this greatly perturbed the potential of the nonheme iron, stabilizing the Fe(3+) state in the presence of Q(B)(•-), a situation not encountered experimentally. H-bonding from D1-Tyr246 and D2-Tyr244 to the bicarbonate ligand of the nonheme iron contributes to the stability of the semiquinones. A detailed mechanistic model for Q(B) reduction is presented.

Fig. 1.

Changes in the H-bond network geometry of Q_B in response to changes in the protonation/redox state. O and N atoms are depicted as red and blue spheres, respectively. Only the H atoms involved in H-bonds or protonation sites are depicted as cyan spheres.

Fig. 2.

Potential-energy profiles of the H-bond donor–acceptor pairs: (Right) H-bond between D1-Ser264 and the distal Q_B carbonyl (purple, in the neutral Q_A state, and blue, in the reduced Q_A state, curves); (Left) H-bond between D1-His215 and the proximal Q_B carbonyl (red curves). At each point, all of the atomic coordinates in the QM region were fully relaxed (i.e., not fixed). Arrows indicate the directions of PT.

Fig. 3.

H-bond arrangements of D1-Tyr246, D2-Tyr244, and the bicarbonate ligand of the nonheme Fe complex upon formation of Q_A^•– (H atoms in cyan and C atoms in blue) or Q_B^•– (H atoms in pink and C atoms in yellow). For clarity, D1-His272 and D2-His268, which were also included in the QM region, are not shown in the figure. Atomic coordinates are provided in Dataset S1.

Fig. 4.

(Upper) The electron density map in the neighborhood of D1-Tyr246. QM/MM optimized geometry of D1-Tyr246 is shown as (Left) Tyr-OOH or (Right) Tyr-OH and H₂O in the presence of Q_B. (Lower) H-bond network (red dotted lines) linking bicarbonate to D1-His215. D1-Tyr246 was modeled as Tyr-OH. (Left) A single water molecule (red cross) is required to establish the H-bond network with His215 in the presence of Q_BH₂, (Right) whereas two water molecules are required in the absence of Q_BH₂.