O2 evolution and recovery of the water-oxidizing enzyme

In photosystem II, light-induced water oxidation occurs at the Mn4CaO5 cluster. Here we demonstrate proton releases, dioxygen formation, and substrate water incorporation in response to Mn4CaO5 oxidation in the protein environment, using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. In S2, H2O at the W1 site forms a low-barrier H-bond with D1-Asp61. In the S2-to-S3 transition, oxidation of OW1H– to OW1•–, concerted proton transfer from OW1H– to D1-Asp61, and binding of a water molecule Wn-W1 at OW1•– are observed. In S4, Wn-W1 facilitates oxo-oxyl radical coupling between OW1•– and corner μ-oxo O4. Deprotonation via D1-Asp61 leads to formation of OW1=O4. As OW1=O4 moves away from Mn, H2O at W539 is incorporated into the vacant O4 site of the O2-evolved Mn4CaO4 cluster, forming a μ-oxo bridge (Mn3–OW539–Mn4) in an exergonic process. Simultaneously, Wn-W1 is incorporated as W1, recovering the Mn4CaO5 cluster. Water splitting during photosynthesis results in the combination of two oxygen atoms to form O2. Here, based on computational simulations, the authors develop a possible mechanism for this reaction, which is different from the mechanisms previous studies have suggested.

D ioxygen can be produced by removing four electrons and four protons from two substrate water molecules: 2H 2 O → O 2 + 4 H + + 4e -. In a protein-pigment complex photosystem II (PSII), the water-oxidation reaction proceeds at the oxygen-evolving complex via the S n -state transitions (n represents the total number of oxidation steps) [1][2][3] . The oxygenevolving complex is linked with electron transfer pathways, proton transfer pathways, and substrate water intake pathways. Excitation of P680, which is composed of four chlorophyll a molecules, leads to electron transfer to the second plastoquinone, Q B , via pheophytin a and the first plastoquinone, Q A . The resulting P680 •+ state is stabilized by electron transfer from the Mn 4 CaO 5 cluster via redox active D1-Tyr161 (TyrZ) (Fig. 1).
Protons released from substrate water molecules are transferred via proton transfer pathways (e.g., O4-water chain 4 ), which proceeds from the Mn 4 CaO 5 cluster toward the protein bulk surface (Fig. 1). The releases of protons are observed with a typical stoichiometry of 1:0:1:2 for the S 0 → S 1 → S 2 → S 3 → S 0 transitions, respectively 5 . The O4-water chain is a chain of water molecules, which forms an H-bond with the O4 site of the Mn 4 CaO 5 cluster via a water molecule W539 4 . Since the rate constant is pH-independent in the S 0 -to-S 1 transition, the absence of ionizable groups in the O4-water chain fits with the suggestion that the O4-water chain is the relevant proton transfer pathway 5,6 . Although release of a proton is not observed in the S 1 -to-S 2 transition, it seems likely that migration of a proton or internal proton transfer can occur (e.g., ref. 7 ). On the other hand, the rate constant for the S 2 -to-S 3 transition is pH-dependent, which suggests that ionizable groups are involved in the proton-transfer pathway 5,8 . Ionizable groups that are not ligands near the Mn 4 CaO 5 cluster are D1-Asp61 and CP43-Arg357 9 . In the S 3 -to-S 0 transition, O-O bond formation and release of O=O occur. The rate constant of 1-2 ms involved in the S 3 -to-S 0 transition is pH-independent with a kinetic isotope effect (k D /k H ) of 1.4 6 , and may correspond to O 2 release and incorporation of a substrate water molecule 6,10 . k D /k H = 1.4 is also typical for alteration in the H-bond pattern along water chains before and after proton transfer (pre-PT and post-PT H-bond patterns, respectively) in the Grotthuss mechanism 11 . Once proton transfer occurs, the pre-PT pattern transforms to the post-PT pattern 4 .
The slow-exchanging and fast-exchanging water molecules are candidate substrates in the Mn 4 CaO 5 cluster 12 . In the S 0 -to-S 1 transition, the exchange rate of the slow-exchanging water molecule decreases 600 times 12 and deprotonation of the slowexchanging water molecule may occur, indicating that it may be a μ-OH bridge of the Mn 4 CaO 5 cluster in S 0 13 . In the S 1 -to-S 2 transition, the exchange rate of the slow-exchanging water molecule increases 100 times 12 . The exchange rate of the fastexchanging water molecule decreases three times in the S 2 -to-S 3 transition 14 . The fast-exchanging water molecule may be a terminal ligand to Mn [2] and possibly form an H-bond with D1-Asp61 13,15 . The corresponding water molecule is W1 in the crystal structure analyzed at 1.9 Å resolution 9 . These water molecules approach the catalytic site from the bulk region via water channels. The D1-Glu65/D2-Glu312 channel is a candidate substrate water intake channel. The D1-Glu65/D2-Glu312 channel provides water molecules near TyrZ and the Mn 4 CaO 5 cluster. It can also deliver water molecules to the W539 and W538 sites in the O4-water chain via D1-Asp61 16 .
Recently, the two-flash illuminated PSII structure analyzed at 2.35 Å resolution was reported, demonstrating several characteristic O sites in the Mn 4 CaO 6 moiety 17 (e.g., W538, W539, O4, and O6). W538 9 (i.e., W665 17 ) was unambiguously identified in both the 1.9 Å 9 and radiation-damage-free 18 19 . On the other hand, it is unclear whether the reaction model could also explain how the other characteristic O sites (e.g., W538, W539, and O4) are involved in the mechanism of water oxidation. It should be noted that the B-factor values of these O atoms are at the same level in the two-flash illuminated PSII structure.
Here we analyzed alterations in the Mn 4 CaO 5 structure and Hbond/water network in response to Mn 4 CaO 5 oxidation in the PSII protein environment, using a quantum mechanical/molecular mechanical (QM/MM) approach and molecular dynamics (MD) simulations based on the PSII crystal structure. In S 2 , the proton of H 2 O at W1 significantly migrates toward D1-Asp61 due to oxidation of Mn4, forming a low-barrier H-bond (HO W1 -…H + … -OOC D1-Asp61 ). In the S 2 -to-S 3 transition, oxidation of O W1 Hto O W1 •preferentially occurs with respect to oxidation of Mn1(III) to Mn1(IV), because D1-Asp61 accepts the proton from O W1 Hand facilitates oxidation to O W1 •via protoncoupled electron transfer (i.e., decreasing the redox potential of W1 for oxidation). In S 3 [20][21][22][23] . The pK a of H-bond donor and acceptor moieties in H-bonds can be analyzed from the potential-energy profiles of the H-bonds [24][25][26] . In H-bonds, a proton is more likely to populate the moiety with the higher pK a value between the two moieties 26 . The energy difference between the H-bond donor and acceptor moieties corresponds to the pK a difference and this feature also holds true for H-bonds in protein environments 27 (Fig. 2a). The potential-energy profile suggested that the O W1 …O D1-Asp61 H-bond is a low-barrier H-bond (LBHB, where the pK a difference for the donor and acceptor moieties is nearly zero 25,27 ) (Fig. 2b), and that the proton is significantly migrated toward D1-Asp61 and delocalized over the two moieties already in S 2 (Fig. 2a). This may correspond to the significant changes in the H-bond properties between D1-Asp61 and a water molecule in the S 1 -to-S 2 transition observed in Fourier transform infrared (FTIR) spectroscopy 7 . It should also be noted that the spin configurations (e.g., high, low, ferromagnetic, and antiferromagnetic) did not essentially affect the resulting optimized Mn 4 CaO 5 geometry and energies in the present case (Table 1). Potential-energy profiles also remained unaffected since proton transfer does not involve oxidation of Mn ions (Supplementary Figure 1).
Absence of Mn oxidation in the S 2 -to-S 3 transition. Unexpectedly, oxidation of S 2 to S 3 did not involve oxidation of Mn; however, oxidation of O W1 Hto O W1 •and concerted proton transfer from O W1 Hto D1-Asp61 did occur, resulting in Mn(III, IV,IV,IV)…O W1 •-…HOOC D1-Asp61 in the open-cubane conformation (Fig. 2a). Accordingly, the first proton of W1 (from H 2 O/OH -), which was delocalized over the low-barrier O W1 …H + …O D1-Asp61 bond in S 2 , seems likely to have been released toward    In the S 2 -to-S 3 transition, it remains unclear whether a Mncentered oxidation (e.g., ref. 31 ) or a ligand-centered oxidation (e.g., ref. 32 ) occurs (discussed in refs. 5,13,33,34 ). Some theoretical studies favor the Mn-centered oxidation model over the ligandcentered oxidation model (e.g., refs. [35][36][37][38][39]. Recent electrochemical analysis using the α-MnO 2 electrode shows that addition of carboxylic acid (benzoic acid) induced proton-coupled electron transfer, resulting in a decrease in the redox potential required for water oxidation and an increase in evolved O 2 at lower potentials 40 . Remarkably, FTIR spectra suggest that benzoic acids do not directly ligate to the Mn ion but form an H-bond with a ligand water molecule of the Mn ion, as identified in the Mn4… W1…D1-Asp61 moiety in PSII. The presence of benzoic acid as the proton acceptor facilitates proton-coupled electron transfer and can avoid accumulation of the positive charge in response to oxidation of Mn, leading to a decrease in the redox potential required for oxidation of water 40 . This may hold true for the present case, where proton-coupled electron transfer from W1 to D1-Asp61 occurs in response to the S 2 -to-S 3 transition, which can specifically decrease the redox potential of W1 for one-electron oxidation.
The absence of the Mn-centered oxidation in the S 2 -to-S 3 transition has been reported in spectroscopic studies by Messinger et al.; Mn was not oxidized, but a ligand substrate molecule was oxidized in the S 2 -to-S 3 transition and an O radical was present in S 3 (Mn(III)Mn(IV) 3 ) 32 , which is consistent with the present results. It should be noted that although TyrZ and the Hbond network were also considered quantum-chemically (i.e., in the QM region), we did not observe formation of TyrZ • .
According to the interpretation of FTIR difference spectroscopy, a water molecule was incorporated into the Mn 4 CaO 5 moiety in the S 2 to S 3 transition 41 . In S 3 , MD simulations showed that a water molecule existed near W1 (W n-W1 ) and could form an H-bond with O W1 •- (Fig. 3). The corresponding water molecule is absent in the PSII crystal structures 9,18 . The binding of W n-W1 seems to be made more pronounced by the negatively charged O W1 •in S 3 (Supplementary Table 1). Near W n-W1 there exists D1-Ser169, which has been proposed to provide access to water molecules for the substrate-binding site 42 . QM/MM calculations also showed that the H-bond between W1 and W n- . MD simulations suggested that water molecules at the W n-W1 binding moiety are exchangeable with bulk water via the D1-Glu65/D2-Glu312 water channel 16 , indicating that the D1-Glu65/D2-Glu312 water channel can serve as the intake channel for W n-W1 .
We did not observe any incorporation of water molecules (including W2 and W3) into the open-cubane O5 site, nor did we observe formation of O W2 •in QM/MM calculations, because of the absence of the proton acceptor groups (e.g., D1-Asp61). •nor a reactive Mn(V)=O species, we focused on O W1 •and O4. The potential-energy profile suggests that as oxo-oxyl radical coupling (e.g., ref. 43 Figure 3). Because W n-W1 lowers the energy barrier, it may serve as a catalyst for (O W1 -O4) 2formation in S 4 . As formation of (O W1 -O4) 2proceeded, the H atom of W n-W1 , which was initially oriented toward O W1 •-, became oriented away from (O W1 -O4) 2-. Simultaneously, the W n-W1 …Mn4 distance decreased from 3.60 to 3.24 Å, owing to displacement of W1 toward O4, allowing W n-W1 to approach Mn4 (Fig. 4). 45 , confirmed by O W1 -O4 = 1.29 Å and the spin density (2S) = 0.8 for O W1 and 0.4 for O4) and concerted electron transfer to Mn1 (Fig. 4).
Furthermore, the following events occurred concertedly:  Figure 4). The resulting oxidation state was Mn (III,IV,III,III), returning to an Mn oxidation state identical to that of S 0 [4].
After O 2 evolution, the O 2 -evolved Mn 4 Ca"O 4 " cluster formed, which resembled the O4-lacking Mn 4 CaO 4 cluster reported in the 3.5-Å PSII crystal structure 46 and the O4-lacking synthetic Mn 4 CaO 4 cluster reported by Zhang et al. 47 . The evolved O 2 molecule is present in the hydrophobic space between Mn4 and D1-Ile60 (next to D1-Asp61), which has been proposed to serve as an O 2 -exiting pathway 48 . Indeed, O 2 evolution was significantly lowered when D1-Ile60 was mutated to bulky phenylalanine 49 .    (Fig. 4) was quite similar to that of the original PSII crystal structure, demonstrating the ability to recover the initial state in the Kok cycle. D1-Asp61, the only acidic residue that is not a ligand near the Mn 4 CaO 5 cluster (i.e., a second sphere ligand), accepted an Hbond from W539, delocalizing the negative charge over [D1-Asp61…W539]and inducing O W539 δ-. Thus, D1-Asp61 provides a driving force for the incorporation (i.e., it facilitates interactions between O W539 δand Mn3(III)/Mn4(III)) (Fig. 5). Indeed, it has been reported that O 2 release was dramatically decelerated in the D1-D61N mutant [50][51][52] . As long as O 2 was present in the Mn3/Mn4 moiety, H 2 O at W539 did not incorporate into the O4-binding site (Supplementary Figure 4), i.e., the presence of O 2 at the Mn3/Mn4 moiety sterically inhibited incorporation of H 2 O at W539 into the O4 site. Therefore, the exergonic incorporation of W539, which was facilitated by D1-Asp61, could contribute to expulsion of O 2 (Supplementary Figure 4).
W539 forms an H-bond with D1-Ser169 (O W539 -O D1-Ser169 = 2.73 Å), which has been proposed to provide access to water molecules for the substrate-binding site 42 . Incorporation of W539 into the O4 site was also observed in QM/MM calculations using the original PSII crystal structure and depleting the O4 atom (Fig. 6a); the obtained geometry was consistent with the O4-incorporated geometry obtained through the S 2 , S 3 , and S 4 states (Fig. 4), which indicates the robustness of the present reaction scheme.
As H 2 O at W539 was incorporated into the Mn 4 CaO 4 cluster, the W539 site became vacant. When the W539 site was refilled by a water molecule, both Mn3-O W539 and Mn4-O W539 were further shortened to~2.2 Å (Fig. 6b). It seems likely that incorporation of a water molecule via D1-Asp61 into the W539 site 16 led to fixation of O4 as a component of the Mn 4 CaO 5 cluster.
Alteration of the H-bond pattern along the O4-water chain. QM/MM calculations indicated that O4 may exist as OHin S 0 , and release of the proton occurs in the S 0 -to-S 1 transition along the O4-water chain (Fig. 1), with transforming of the pre-PT to a post-PT H-bond pattern 4 . This implies that the pre-PT pattern must be recovered from the post-PT pattern before the next turnover.
As W539 approached Mn3 during O 2 evolution, the H-bond pattern along the O4-water chain (e.g., W538) transformed from the post-PT pattern to the pre-PT pattern, since W539 (i.e., new O4) needs to reorient to form a μ-oxo bridge (Mn3-O W539 -Mn4) (Fig. 7). Given that release of the first proton from H 2 O at O4 occurs via D1-Asp61 in the pre-S 0 -to-S 0 transition (i.e., the O4water chain is not used), the O4-water chain remains in the pre-PT pattern, ready for release of the proton in the S 0 -to-S 1 transition.
The rate-limiting step in O=O formation has been reported to exhibit a k D /k H of 1.4 6 , which is consistent with the k D /k H value for transformation between pre-and post-PT patterns 11 . This may correspond to H-bond transformation along the O4-water chain (Fig. 7), since the corresponding water chain or H-bond network is absent at the O5/O6 moiety 9,17,18 .
Characteristic O sites in the two-flash structure. The two-flash illuminated PSII structure shows the extremely short averaged O4…O W539 distance of 2.32 Å (2.47 and 2.17 Å) 17 Fig. 6b). The absence of W538 (i.e., disordered W538) in the twoflash illuminated PSII structure 17 can be explained by the present reaction scheme, as O4 is consumed and thus incorporation of W539 and displacement of W538 occur (Fig. 6). The vacant W539-binding site (Fig. 6a) can be refilled by H 2 O, as MD simulations indicated that bulk water could enter the W539 and W538 sites via D1-Asp61 16 . Even in the Mn-depleted PSII crystal structure, both W539 and W538 exist and are well-ordered (Bfactor values are 33.9 and 43.4, respectively) 53 , highlighting the originally large binding affinity due to D1-Asp61. This, in turn, suggests that the absence of well-ordered W538 in the two-flash illuminated PSII structure 17 is exceptional (Table 2), and can be understood only when reorganization of W539 and W538 occurs.

Discussion
Based on the findings reported here, we are able to propose the following reaction scheme (Fig. 8)  •is also pronounced (Fig. 3). S 4 is initially Mn(IV,IV,IV,IV) with O W1 •-. Oxo-oxyl radical coupling between O4 and O W1 •leads to formation of (O W1 -O4) 2and reduction to Mn(IV,IV,III,IV) (Fig. 4); W n-W1 decreases the energy barrier for the (O W1 -O4) 2formation, serving as a catalyst. As O W1 =O4 moves away from the Mn3/Mn4 moiety toward D1-Ile60 in the proposed O 2 -exiting pathway 48 , H 2 O at W539 is incorporated into the vacant O4 site, forming a μ-oxo bridge with Mn3-O W539 and Mn4-O W539 in a concerted exergonic process. W n-W1 is also incorporated into the Mn 4 CaO 5 cluster as the new W1 ligand. The two Mn3-O W539 and Mn4-O W539 bonds are further shortened when the vacant W539 site is refilled by a water molecule, which approaches via D1-Asp61 16 , recovering the original Mn 4 CaO 5 structure. Incorporation of W539 into the O4 site also seems to lead to transformation of the H-bond pattern along the O4-water chain to the pre-PT pattern (Fig. 7), in readiness for proton transfer in the S 0 -to-S 1 transition 4 .
The proton releasing sites are identified as W1 in the S 2 -to-S 3 and the S 3 -to-S 0 transitions and O4 in the pre-S 0 -to-S 0 and S 0 -to-S 1 4 transitions. Based on these observations, W1 and O4 are deprotonatable substrate water molecules on the current turnover, and W n-W1 and W539 serve as "holding sites 7 " and become W1 and O4, respectively, on the next turnover. Then, the D1-Glu65/D2-Glu312 channel serves as a water intake channel for both substrate water molecules 16 . The location of O4/W539 at the dead end of the narrow region of the D1-Glu65/D2-Glu312 channel 16 may also make the exchange rate slow.
If the fast-exchanging and slow-exchanging water molecules represent two substrate water molecules, they might be W1 and O4, respectively. Then, the decrease in the exchange rate for the fast-exchanging water molecule in the S 2 -to-S 3 transition 12 might be explained by the pronounced binding of W1 at Mn4 (O W1 •in S 3 ) (Supplementary Figure 5). However, as suggested by Noguchi and coworkers based on FTIR difference spectroscopy, it seems also possible that the exchanging water molecule is not necessarily a substrate water molecules on the current turnover (W1 and O4 in the present reaction scheme) but rather a substrate water molecule on the next turnover (W n-W1 as next W1 and W539 as next O4) 41 . In this case, the increase in the exchange rate of the slow-exchanging water molecule (i.e., W539) in the S 1 -to-S 2 transition 12 is due to the relaxed H-bond network of the O4water chain (including O4 and W539) in the S 1 -to-S 2 transition (i.e., after proton transfer) with respect to the strongly coupled Hbond network in the S 0 -to-S 1 transition 4 . The decrease in the exchange rate for the fast-exchanging water molecule (i.e., W n-W1 ) in the S 2 -to-S 3 transition 12 can be explained by the pronounced binding of W n-W1 at O W1 •-. W n-W1 , a substrate on the next turnover, decreases the energy barrier for (O W1 -O4) 2formation in S 4 , serving as a catalyst. W539, another substrate on the next turnover, is the direct proton acceptor      for the current turnover substrate H 2 O at O4. The remarkable cooperativity of the next substrate water molecules to catalyze the current substrate water molecule (Fig. 4b), as well as the selfrecovery of the Mn 4 CaO 5 cluster from the O 2 -evolved Mn 4 CaO 4 cluster in a concerted exergonic process (Fig. 4a), suggest that W1/ W n-W1 and O4/W539 are substrate water molecules.

Methods
Coordinates and atomic partial charges. The atomic coordinates of PSII were taken from the X-ray structure of PSII monomer unit "A" of the PSII complexes from Thermosynechococcus vulcanus at a resolution of 1.9 Å (PDB code, 3ARC) 9 . During optimization of hydrogen atom positions with CHARMM 54 , the positions of all heavy atoms were fixed and all titratable groups (e.g., acidic and basic groups) were ionized. In QM/MM calculations, additional counter ions were added to neutralize the entire system. Atomic partial charges of the amino acids and cofactors were obtained from the CHARMM22 55 parameter set and our previous studies on PSII 4 , respectively. D1-His337 was considered to be protonated 56 .
QM/MM calculations. The unrestricted density functional theory (DFT) method was employed with the B3LYP functional and LACVP* basis sets, using the QSite 57 program. In the QM region, all the atomic coordinates were fully relaxed. In the MM region, the positions of H atoms were optimized using the OPLS2005 force field, while the positions of heavy atoms were fixed. The cluster was considered to be in the S 2 , S 3 , S 4 , and S 0 states with antiferromagnetically coupled Mn ions; the resulting Mn oxidation states (Mn1, Mn2, Mn3, Mn4) and the total spin S were as follows: (III, IV Table 1, Supplementary Figures 1 and 3 for other spin configurations). The Mn 4 CaO 5 geometry in S n was obtained as follows: first we prepared the QM/MM-optimized S n geometry with ferromagnetically coupled Mn ions, using the QM/MM-optimized S n-1 geometry. The resulting S n geometry was then optimized as antiferromagnetically coupled Mn ions. The initial-guess wave functions were obtained by using the ligand-field theory 58 implemented in the QSite program. See Supplementary Data 1 for the atomic coordinates.
To obtain the potential-energy profiles of H-bonds ( Fig. 2b and Supplementary  Fig. 1), the QM/MM optimized geometry was used as the initial geometry. The H atom under investigation was moved from the H-bond donor atom (O donor ) toward the acceptor atom (O acceptor ) by 0.05 Å, after which the geometry was optimized by constraining the O donor -H and H-O acceptor distances and the energy was calculated. This procedure was repeated until the H atom reached the O acceptor atom. To obtain the potential-energy profiles of (O W1 -O4) 2formation ( Fig. 4b and Supplementary Fig. 3) and O 2 release ( Fig. 7 and Supplementary Fig.  4), the QM/MM optimized geometry was used as the initial geometry; e.g., the O W1 …O4 distance was then decreased by 0.05 Å, after which the geometry was In the S 0 -to-S 1 transition, a low-barrier H-bond between OHat O4 and W539 (as indicated in the crystal structure 9 ) releases the proton via the O4-water chain 4 . In the O4-water chain, the pre-PT pattern transforms into the post PT pattern as a result of proton transfer. In the S 1 -to-S 2 transition, oxidation of Mn4(III) to Mn4(IV) occurs, resulting in a decrease in pK a of W1 and formation of a low-barrier H-bond between W1 and D1-Asp61. In the S 2 -to-S 3 transition, D1-Asp61 decreases the redox potential of W1 and facilitates proton-coupled oxidation of O W1 Hto O W1 •-. O W1 •attracts W n-W1 . In S 4 , oxo-oxyl radical coupling occurs between O W1 •and corner μ-oxo O4, leading to formation of (O W1 -O4) 2-, reduction of Mn, incorporation of W n-W1 as new W1, and approach of W539. In the S 4 -to-pre-S 0 transition, as O W1 =O4 moves away from the Mn 4 CaO 5 moiety, water incorporation occurs near two second sphere ligands, D1-Asp61 and CP43-Arg357: D1-Asp61 accepts an H-bond from W539 and incorporation of W539 into the vacant O4 site near CP43-Arg357 leads to reorientation of W539 and formation of a μ-oxo bridge with Mn3-O W539 and Mn4-O W539 . Reorientation of W539 (i.e., new O4) at the O4 site propagates along the O4-water chain, transforming the post-PT pattern to the pre-PT pattern. The vacant W539 site can be filled by a water molecule from the D1-Glu65/D2-Glu312 channel via D1-Asp61 16 . Pre-S 0 , where H 2 O is present at O4, can be stabilized by release of a proton from the newly incorporated O4 site and proceeds to S 0 optimized by constraining the O W1 …O4 distance and the energy was calculated. This procedure was repeated until formation of (O W1 -O4) 2-.
MD simulations. The PSII structure was embedded in a lipid bilayer, which is composed of 546 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC), and soaked in 78889 flexible water molecules (SPC-Fw) 60 , using the CHARMM-GUI program 61 . After geometry optimization with position restraints on heavy atoms, the system was heated from 0.001 K to 300 K during 5.0 ps. The position restraints on heavy atoms were gradually released over 16.5 ns. An equilibrating MD run was conducted for 45 ns using the MD engine AMBER 14 62 with the SHAKE algorithm for hydrogen constraint 63 . The production run was conducted with an MD time step of 0.5 fs without hydrogen constraint, using AMBER 14. To control temperature and pressure, the Berendsen thermostat and barostat were employed 65 . See ref. 16 for force field parameters.
Data availability. All the data supporting the findings of this study are available within the article and its Supplementary Information files or from the corresponding author upon reasonable request.