Mutation of Lysine 317 in the D2 Subunit of Photosystem II Alters Chloride Binding and Proton Transport

Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels

Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.

Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O2-Evolving Mn4CaO5 Cluster in Photosystem II

The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.

Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations

At room temperature and neutral pH, the oxygen-evolving center (OEC) of photosystem II (PSII) catalyzes water oxidation. During this process, oxygen is released from the OEC, while substrate waters are delivered to the OEC and protons are passed from the OEC to the lumen through water channels known as the narrow or the O4 channel, broad or the Cl1 channel, and large or the O1 channel. Protein residues lining the surfaces of these channels play a critical role in stabilizing the hydrogen-bonding networks that assist in the process. We carried out an occupancy analysis to better understand the structural and possible substrate water dynamics in full PSII monomer molecular dynamics (MD) trajectories in both the S1 and S2 states. We find that the equilibrated positions of water molecules derived from MD-derived electron density maps largely match the experimentally observed positions in crystallography. Furthermore, the occupancy reduction in MD simulations of some water molecules inside the single-filed narrow channel also correlates well with the crystallographic data during a structural transition when the S1 state of the OEC advances to the S2 state. The overall reduced occupancies of water molecules are the source of their "vacancy-hopping" dynamic nature inside these channels, unlike water molecules inside an ice lattice where all water molecules have a fixed unit occupancy. We propose on the basis of findings in our structural and molecular dynamics analysis that the water molecule occupying a pocket formed by D1-D61, D1-S169, and O4 of the OEC could be the last steppingstone to enter into the OEC and that the broad channel may be favored for proton transfer.

Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation

In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.

Oxygen-evolving photosystem II structures during S1-S2-S3 transitions

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

How chloride functions to enable proton conduction in photosynthetic water oxidation: Time-resolved kinetics of intermediates (S-states) in vivo and bromide substitution

Chloride (Cl-) is essential for O2 evolution during photosynthetic water oxidation. Two chlorides near the water-oxidizing complex (WOC) in Photosystem II (PSII) structures from Thermosynechococcus elongatus (and T. vulcanus) have been postulated to transfer protons generated from water oxidation. We monitored four criteria: primary charge separation flash yield (P* → P+QA-), rates of water oxidation steps (S-states), rate of proton evolution, and flash O2 yield oscillations by measuring chlorophyll variable fluorescence (P* quenching), pH-sensitive dye changes, and oximetry. Br-substitution slows and destabilizes cellular growth, resulting from lower light-saturated O2 evolution rate (-20 %) and proton release (-36 % ΔpH gradient). The latter implies less ATP production. In Br- cultures, protonogenic S-state transitions (S2 → S3 → S0') slow with increasing light intensity and during O2/water exchange (S0' → S0 → S1), while the non-protonogenic S1 → S2 transition is kinetically unaffected. As flash rate increases in Cl- cultures, both rate and extent of acidification of the lumen increase, while charge recombination is suppressed relative to Br-. The Cl- advantage in rapid proton escape from the WOC to lumen is attributed to correlated ion-pair movement of H3O+Cl- in dry water channels vs. separated Br- and H+ ion movement through different regions (>200-fold difference in Bronsted acidities). By contrast, at low flash rates a previously unreported reversal occurs that favors Br- cultures for both proton evolution and less PSII charge recombination. In Br- cultures, slower proton transfer rate is attributed to stronger ion-pairing of Br- with AA residues lining the water channels. Both anions charge-neutralize protons and shepherd them to the lumen using dry aqueous channels.

Structural and energetic insights into Mn-to-Fe substitution in the oxygen-evolving complex

Manganese (Mn) serves as the catalytic center for water splitting in photosystem II (PSII), despite the abundance of iron (Fe) on earth. As a first step toward why Mn and not Fe is employed by Nature in the water oxidation catalyst, we investigated the Fe₄CaO₅ cluster in the PSII protein environment using a quantum mechanical/molecular mechanical (QM/MM) approach, assuming an equivalence between Mn(III/IV) and Fe(II/III). Substituting Mn with Fe resulted in the protonation of μ-oxo bridges at sites O2 and O3 by Arg357 and D1-His337, respectively. While the Mn₄CaO₅ cluster exhibits distinct open- and closed-cubane S₂ conformations, the Fe₄CaO₅ cluster lacks this variability due to an equal spin distribution over sites Fe1 and Fe4. The absence of a low-barrier H-bond between a ligand water molecule (W1) and D1-Asp61 in the Fe₄CaO₅ cluster may underlie its incapability for ligand water deprotonation, highlighting the relevance of Mn in natural water splitting.

Does Serial Femtosecond Crystallography Depict State-Specific Catalytic Intermediates of the Oxygen-Evolving Complex?

Recent advances in serial femtosecond crystallography (SFX) of photosystem II (PSII), enabled by X-ray free electron lasers (XFEL), provided the first geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). These models are obtained by flash-advancing the OEC from the dark-stable state (S₁) to more oxidized intermediates (S₂ and S₃), eventually cycling back to the most reduced S₀. However, the interpretation of these models is controversial because geometric parameters within the Mn₄CaO₅ cluster of the OEC do not exactly match those expected from coordination chemistry for the spectroscopically verified manganese oxidation states of the distinct S-state intermediates. Here we focus on the first catalytic transition, S₁ → S₂, which represents a one-electron oxidation of the OEC. Combining geometric and electronic structure criteria, including a novel effective oxidation state approach, we analyze existing 1-flash (1F) SFX-XFEL crystallographic models that should depict the S₂ state of the OEC. We show that the 1F/S₂ equivalence is not obvious, because the Mn oxidation states and total unpaired electron counts encoded in these models are not fully consistent with those of a pure S₂ state and with the nature of the S₁ → S₂ transition. Furthermore, the oxidation state definition in two-flashed (2F) structural models is practically impossible to elucidate. Our results advise caution in the extraction of electronic structure information solely from the literal interpretation of crystallographic models and call for re-evaluation of structural and mechanistic interpretations that presume exact correspondence of such models to specific catalytic intermediates of the OEC.

Functional Water Networks in Fully Hydrated Photosystem II

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone Q_B. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.

Crystal structures of photosystem II from a cyanobacterium expressing psbA2 in comparison to psbA3 reveal differences in the D1 subunit

Three psbA genes (psbA₁, psbA₂, and psbA₃) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA₂ or psbA₃), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (Pheo_D1) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of Pheo_D1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in Pheo_D1 due to the change of D1-Y147F, which may explain the decrease in stability of Pheo_D1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S₂ in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near Q_B disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound Q_B with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high Q_B exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.

Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II

Photosynthetic water oxidation takes place at the Mn₄CaO₅ cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S₀-S₄). Although the PSII structures have shown the presence of several channels around the Mn₄CaO₅ cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S₂ → S₃ transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S₃ → S₀ transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S₂ → S₃ transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S₃ → S₀ transition.

Protonation structure of the closed-cubane conformation of the O2-evolving complex in photosystem II

In photosystem II (PSII), one-electron oxidation of the most stable state of the oxygen-evolving Mn₄CaO₅ cluster (S₁) leads to the S₂ state formation, Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (open-cubane S₂) or Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (closed-cubane S₂). In electron paramagnetic resonance (EPR) spectroscopy, the g = 4.1 signal is not observed in cyanobacterial PSII but in plant PSII, whereas the g = 4.8 signal is observed in cyanobacterial PSII and extrinsic-subunit-depleted plant PSII. Here, we investigated the closed-cubane S₂ conformation, a candidate for a higher spin configuration that accounts for g > 4.1 EPR signal, considering all pairwise exchange couplings in the PSII protein environment (i.e. instead of considering only a single exchange coupling between the [Mn₃(CaO₄)] cubane region and the dangling Mn4 site). Only when a ligand water molecule that forms an H-bond with D1-Asp61 (W1) is deprotonated at dangling Mn4(IV), the g = 4.1 EPR spectra can be reproduced using the cyanobacterial PSII crystal structure. The closed-cubane S₂ is less stable than the open-cubane S₂ in cyanobacterial PSII, which may explain why the g = 4.1 EPR signal is absent in cyanobacterial PSII.

Binding and functions of the two chloride ions in the oxygen-evolving center of photosystem II

Light-driven water oxidation in photosynthesis occurs at the oxygen-evolving center (OEC) of photosystem II (PSII). Chloride ions (Cl^-) are essential for oxygen evolution by PSII, and two Cl^- ions have been found to specifically bind near the Mn₄CaO₅ cluster in the OEC. The retention of these Cl^- ions within the OEC is critically supported by some of the membrane-extrinsic subunits of PSII. The functions of these two Cl^- ions and the mechanisms of their retention both remain to be fully elucidated. However, intensive studies performed recently have advanced our understanding of the functions of these Cl^- ions, and PSII structures from various species have been reported, aiding the interpretation of previous findings regarding Cl^- retention by extrinsic subunits. In this review, we summarize the findings to date on the roles of the two Cl^- ions bound within the OEC. Additionally, together with a short summary of the functions of PSII membrane-extrinsic subunits, we discuss the mechanisms of Cl^- retention by these extrinsic subunits.

Energy Landscape for the Electrocatalytic Oxidation of Water by a Single-Site Oxomanganese(V) Porphyrin

A cationic manganese porphyrin, Mn^III-TDMImP, is an efficient, homogeneous, single-site water oxidation electrocatalyst at neutral pH. The measured turnover frequency for oxygen production is 32 s^-1. Mechanistic analyses indicate that Mn^V(O)(OH₂), the protonated form of the corresponding trans-Mn^V(O)₂ species, is generated from the Mn^III(OH₂)₂ precursor in a 2-e^- two-proton process and is responsible for O-O bond formation with a H₂O molecule. Chloride ion is a competitive substrate with H₂O for the Mn^V(O)(OH₂) oxidant, forming hypochlorous acid with a rate constant that is 3 orders of magnitude larger than that of water oxidation. The data allow the construction of an experimental energy landscape for this water oxidation catalysis process.

Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus

Photosystem II (PSII) has a number of hydrogen-bonding networks connecting the manganese cluster with the lumenal bulk solution. The structure of PSII from Thermosynechococcus vulcanus (T. vulcanus) showed that D1-R323, D1-N322, D1-D319 and D1-H304 are involved in one of these hydrogen-bonding networks located in the interfaces between the D1, CP43 and PsbV subunits. In order to investigate the functions of these residues in PSII, we generated seven site-directed mutants D1-R323A, D1-R323E, D1-N322R, D1-D319L, D1-D319R, D1-D319Y and D1-H304D of T. vulcanus and examined the effects of these mutations on the growth and functions of the oxygen-evolving complex. The photoautotrophic growth rates of these mutants were similar to that of the wild type, whereas the oxygen-evolving activities of the mutant cells were decreased differently to 63-91% of that of the wild type at pH 6.5. The mutant cells showed a higher relative activity at higher pH region than the wild type cells, suggesting that higher pH facilitated proton egress in the mutants. In addition, oxygen evolution of thylakoid membranes isolated from these mutants showed an apparent decrease compared to that of the cells. This is due to the loss of PsbU during purification of the thylakoid membranes. Moreover, PsbV was also lost in the PSII core complexes purified from the mutants. Taken together, D1-R323, D1-N322, D1-D319 and D1-H304 are vital for the optimal function of oxygen evolution and functional binding of extrinsic proteins to PSII core, and may be involved in the proton egress pathway mediated by Y_Z.

Photosystem 2 and the oxygen evolving complex: a brief overview

These special issues of photosynthesis research present papers documenting progress in revealing the many aspects of photosystem 2, a unique, one-of-a-kind complex system that can reduce a plastoquinone to a plastoquinol on every second flash of light and oxidize 2 H₂O to an O₂ on every fourth flash. This overview is a brief personal assessment of the progress observed by the author over a four-decade research career, including a discussion of some remaining unsolved issues. It will come as no surprise to readers that there are remaining questions given the complexity of PS2, and the efforts that have been needed so far to uncover its secrets. In fact, most readers will have their own lists of outstanding questions.

High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.

Alteration of the O2-Producing Mn4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand

The O₂-evolving Mn₄Ca cluster in photosystem II (PSII) is arranged as a distorted Mn₃Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn₄Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn₄Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn₄Ca cluster in the dark-stable S₁ state so that a high-spin form of the S₂ state is produced during the S₁-to-S₂ transition instead of the low-spin form that gives rise to the S₂ state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn₄Ca cluster without substantially eliminating O₂ evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn₄Ca cluster in the mechanism of O₂ formation.

Requirement of Chloride for the Downhill Electron Transfer Pathway from the Water-Splitting Center in Natural Photosynthesis

In photosystem II (PSII), Cl^- is a prerequisite for the second flash-induced oxidation of the Mn₄CaO₅ cluster (the S₂ to S₃ transition). We report proton transfer from the substrate water molecule via D1-Asp61 and electron transfer via redox-active D1-Tyr161 (TyrZ) to the chlorophyll pair in Cl^--depleted PSII using a quantum mechanical/molecular mechanical approach. The low-barrier H-bond formation between the substrate water molecule and D1-Asp61 remained unaffected upon the depletion of Cl^-. However, the binding site, D2-Lys317, formed a salt bridge with D1-Asp61, leading to the inhibition of the subsequent proton transfer. Remarkably, the redox potential (E_m) of S₂/S₃ increased significantly, making electron transfer from S₂ to TyrZ energetically uphill, as observed in Ca²⁺-depleted PSII. The uphill electron transfer pathway was induced by the significant increase in E_m(S₂/S₃) caused by the loss of charge compensation for D2-Lys317 upon the depletion of Cl^-, whereas it was induced by the significant decrease in E_m(TyrZ) caused by the rearrangement of the water molecules at the Ca²⁺ binding moiety upon the depletion of Ca²⁺.

Proton and Water Transfer Pathways in the S2 → S3 Transition of the Water-Oxidizing Complex in Photosystem II: Time-Resolved Infrared Analysis of the Effects of D1-N298A Mutation and NO3- Substitution

Photosynthetic water oxidation is performed through a light-driven cycle of five intermediates (S₀-S₄ states) in photosystem II (PSII). The S₂ → S₃ transition, which involves concerted water and proton transfer, is a key process for understanding the water oxidation mechanism. Here, to identify the water and proton transfer pathways during the S₂ → S₃ transition, we examined the effects of D1-N298A mutation and NO₃^- substitution for Cl^-, which perturbed the O1 and Cl channels, respectively, on the S₂ → S₃ kinetics using time-resolved infrared spectroscopy. The S₂ → S₃ transition was retarded both upon NO₃^- substitution and upon D1-N298A mutation, whereas it was unaffected by further NO₃^- substitution in N298A PSII. The H/D kinetic isotope effect in N298A PSII was relatively small, revealing that water transfer is a rate-limiting step in this mutant. From these results, it was suggested that during the S₂ → S₃ transition, water delivery and proton release occur through the O1 and Cl channels, respectively.

Proton exit pathways surrounding the oxygen evolving complex of photosystem II

Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn₄CaO₅ inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.

Probing the role of arginine 323 of the D1 protein in photosystem II function

The Mn₄ CaO₅ cluster of photosystem II (PSII) advances sequentially through five oxidation states (S₀ to S₄ ). Under the enzyme cycle, two water molecules are oxidized, O₂ is generated and four protons are released into the lumen. Umena et al. (2011) have proposed that, with other charged amino acids, the R323 residue of the D1 protein could contribute to regulate a proton egress pathway from the Mn₄ CaO₅ cluster and Tyr_Z via a proton channel identified from the 3D structure. To test this suggestion, a PsbA3/R323E site-directed mutant has been constructed and the properties of its PSII have been compared to those of the PsbA3-PSII by using EPR spectroscopy, polarography, thermoluminescence and time-resolved UV-visible absorption spectroscopy. Neither the oscillations with a period four nor the kinetics and S-state-dependent stoichiometry of the proton release were affected. However, several differences have been found: (1) the P₆₈₀ ⁺ decay in the hundreds of ns time domain was much slower in the mutant, (2) the S₂ Q_A ^- /DCMU and S₃ Q_A ^- /DCMU radiative charge recombination occurred at higher temperatures and (3) the S₀ Tyr_Z ^• , S₁ Tyr_Z ^• , S₂ Tyr_Z ^• split EPR signals induced at 4.2 K by visible light from the S₀ Tyr_Z , S₁ Tyr_Z , S₂ Tyr_Z , respectively, and the (S₂ Tyr_Z ^• )' induced by NIR illumination at 4.2 K of the S₃ Tyr_Z state differed. It is proposed that the R323 residue of the D1 protein interacts with Tyr_Z likely via the H-bond network previously proposed to be a proton channel. Therefore, rather than participating in the egress of protons to the lumen, this channel could be involved in the relaxations of the H-bonds around Tyr_Z by interacting with the bulk, thus tuning the driving force required for Tyr_Z oxidation.

Acquirement of water-splitting ability and alteration of the charge-separation mechanism in photosynthetic reaction centers

In photosynthetic reaction centers from purple bacteria (PbRC) and the water-oxidizing enzyme, photosystem II (PSII), charge separation occurs along one of the two symmetrical electron-transfer branches. Here we report the microscopic origin of the unidirectional charge separation, fully considering electron-hole interaction, electronic coupling of the pigments, and electrostatic interaction with the polarizable entire protein environments. The electronic coupling between the pair of bacteriochlorophylls is large in PbRC, forming a delocalized excited state with the lowest excitation energy (i.e., the special pair). The charge-separated state in the active branch is stabilized by uncharged polar residues in the transmembrane region and charged residues on the cytochrome c ₂ binding surface. In contrast, the accessory chlorophyll in the D1 protein (Chl_D1) has the lowest excitation energy in PSII. The charge-separated state involves Chl_D1 ^•+ and is stabilized predominantly by charged residues near the Mn₄CaO₅ cluster and the proceeding proton-transfer pathway. It seems likely that the acquirement of water-splitting ability makes Chl_D1 the initial electron donor in PSII.

Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

Early Binding of Substrate Oxygen Is Responsible for a Spectroscopically Distinct S2 State in Photosystem II

The biological generation of oxygen by the oxygen-evolving complex (OEC) in photosystem II (PS II) is one of nature's most important reactions. The OEC is a Mn₄Ca cluster that has multiple Mn-O-Mn and Mn-O-Ca bridges and binds four water molecules. Previously, binding of an additional oxygen was detected in the S₂ to S₃ transition. Here we demonstrate that early binding of the substrate oxygen to the five-coordinate Mn₁ center in the S₂ state is likely responsible for the S₂ high-spin EPR signal. Substrate binding in the Mn₁-OH form explains the prevalence of the high-spin S₂ state at higher pH and its low-temperature conversion into the S₃ state. The given interpretation was confirmed by X-ray absorption spectroscopic measurements, DFT, and broken symmetry DFT calculations of structures and magnetic properties. Structural, electronic, and spectroscopic properties of the high-spin S₂ state model are provided and compared with the available S₃ state models. New interpretation of the high-spin S₂ state opens opportunity for analysis of factors controlling the oxygen substrate binding in PS II.

Photosystem II oxygen-evolving complex photoassembly displays an inverse H/D solvent isotope effect under chloride-limiting conditions

Metal clusters play important roles in a wide variety of proteins. In cyanobacteria, algae, and plants, photosystem II uses light energy to oxidize water and release O₂ at an active site that contains 1 calcium and 4 manganese atoms. This cluster must be built within the protein environment through a process known as photoassembly. Through experiments and simulations, we found that the efficiency of photoassembly was highly dependent on protons and chloride. Surprisingly, when the solvent was switched from H₂O to deuterated water, D₂O, the yield of photoassembly was higher. These results provide insights into the stepwise mechanism of photoassembly that can inform synthesis and repair strategies being developed for artificial photosynthesis technologies.

Photosystem II (PSII) performs the solar-driven oxidation of water used to fuel oxygenic photosynthesis. The active site of water oxidation is the oxygen-evolving complex (OEC), a Mn₄CaO₅ cluster. PSII requires degradation of key subunits and reassembly of the OEC as frequently as every 20 to 40 min. The metals for the OEC are assembled within the PSII protein environment via a series of binding events and photochemically induced oxidation events, but the full mechanism is unknown. A role of proton release in this mechanism is suggested here by the observation that the yield of in vitro OEC photoassembly is higher in deuterated water, D₂O, compared with H₂O when chloride is limiting. In kinetic studies, OEC photoassembly shows a significant lag phase in H₂O at limiting chloride concentrations with an apparent H/D solvent isotope effect of 0.14 ± 0.05. The growth phase of OEC photoassembly shows an H/D solvent isotope effect of 1.5 ± 0.2. We analyzed the protonation states of the OEC protein environment using classical Multiconformer Continuum Electrostatics. Combining experiments and simulations leads to a model in which protons are lost from amino acid that will serve as OEC ligands as metals are bound. Chloride and D₂O increase the proton affinities of key amino acid residues. These residues tune the binding affinity of Mn^2+/3+ and facilitate the deprotonation of water to form a proposed μ-hydroxo bridged Mn²⁺Mn³⁺ intermediate.

Relative stability of the S2 isomers of the oxygen evolving complex of photosystem II

The oxidation of water to O₂ is catalyzed by the Oxygen Evolving Complex (OEC), a Mn₄CaO₅ complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S₀ to S₄. The S₂ state, (Mn^III)(Mn^IV)₃, coexists in two redox isomers: S_2,g=2, where Mn4 is Mn^IV and S_2,g=4.1, where Mn1 is Mn^IV. Mn4 has two terminal water ligands, whose proton affinity is affected by the Mn oxidation state. The relative energy of the two S₂ redox isomers and the protonation state of the terminal water ligands are analyzed using classical multi-conformer continuum electrostatics (MCCE). The Monte Carlo simulations are done on QM/MM optimized S₁ and S₂ structures docked back into the complete PSII, keeping the protonation state of the protein at equilibrium with the OEC redox and protonation states. Wild-type PSII, chloride-depleted PSII, PSII in the presence of oxidized Y_Z/protonated D1-H190, and the PSII mutants D2-K317A, D1-D61A, and D1-S169A are studied at pH 6. The wild-type PSII at pH 8 is also described. In qualitative agreement with experiment, in wild-type PSII, the S_2,g=2 redox isomer is the lower energy state; while chloride depletion or pH 8 stabilizes the S_2,g=4.1 state and the mutants D2-K317A, D1-D61A, and D1-S169A favor the S_2,g=2 state. The protonation states of D1-E329, D1-E65, D1-H337, D1-D61, and the terminal waters on Mn4 (W1 and W2) are affected by the OEC oxidation state. The terminal W2 on Mn4 is a mixture of water and hydroxyl in the S_2,g=2 state, indicating the two water protonation states have similar energy, while it remains neutral in the S₁ and S_2,g=4.1 states. In wild-type PSII, advancement to S₂ leads to negligible proton loss and so there is an accumulation of positive charge. In the analyzed mutations and Cl^- depleted PSII, additional deprotonation is found upon formation of S₂ state.

Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II

The influence of the environment on the functionality of the oxygen-evolving complex (OEC) of photosystem II has long been a subject of great interest. In particular, various water channels, which could serve as pathways for substrate water diffusion, or proton translocation, are thought to be critical to catalytic performance of the OEC. Here, we address the dynamical nature of hydrogen bonding along the water channels by performing molecular dynamics (MD) simulations of the OEC and its surrounding protein environment in the S1 and S2 states. Through the eigenvector centrality (EC) analysis, we are able to determine the characteristics of the water network and assign potential functions to the major channels, namely that the narrow and broad channels are likely candidates for proton/water transport, while the large channel may serve as a path for larger ions such as chloride and manganese thought to be essential during PSII assembly.

Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase

Photosystem II (PSII) uses water as the terminal electron donor, producing oxygen in the Mn4CaO5 oxygen evolving complex (OEC), while cytochrome c oxidase (CcO) reduces O2 to water in its heme–Cu binuclear center (BNC). Each protein is oriented in the membrane to add to the proton gradient. The OEC, which releases protons, is located near the P-side (positive, at low-pH) of the membrane. In contrast, the BNC is in the middle of CcO, so the protons needed for O2 reduction must be transferred from the N-side (negative, at high pH). In addition, CcO pumps protons from N- to P-side, coupled to the O2 reduction chemistry, to store additional energy. Thus, proton transfers are directly coupled to the OEC and BNC redox chemistry, as well as needed for CcO proton pumping. The simulations that study the changes in proton affinity of the redox active sites and the surrounding protein at different states of the reaction cycle, as well as the changes in hydration that modulate proton transfer paths, are described.

Substitution of the D1-Asn87 site in photosystem II of cyanobacteria mimics the chloride-binding characteristics of spinach photosystem II

Photoinduced water oxidation at the O₂-evolving complex (OEC) of photosystem II (PSII) is a complex process involving a tetramanganese-calcium cluster that is surrounded by a hydrogen-bonded network of water molecules, chloride ions, and amino acid residues. Although the structure of the OEC has remained conserved over eons of evolution, significant differences in the chloride-binding characteristics exist between cyanobacteria and higher plants. An analysis of amino acid residues in and around the OEC has identified residue 87 in the D1 subunit as the only significant difference between PSII in cyanobacteria and higher plants. We substituted the D1-Asn⁸⁷ residue in the cyanobacterium Synechocystis sp. PCC 6803 (wildtype) with alanine, present in higher plants, or with aspartic acid. We studied PSII core complexes purified from D1-N87A and D1-N87D variant strains to probe the function of the D1-Asn⁸⁷ residue in the water-oxidation mechanism. EPR spectra of the S₂ state and flash-induced FTIR spectra of both D1-N87A and D1-N87D PSII core complexes exhibited characteristics similar to those of wildtype Synechocystis PSII core complexes. However, flash-induced O₂-evolution studies revealed a decreased cycling efficiency of the D1-N87D variant, whereas the cycling efficiency of the D1-N87A PSII variant was similar to that of wildtype PSII. Steady-state O₂-evolution activity assays revealed that substitution of the D1 residue at position 87 with alanine perturbs the chloride-binding site in the proton-exit channel. These findings provide new insight into the role of the D1-Asn⁸⁷ site in the water-oxidation mechanism and explain the difference in the chloride-binding properties of cyanobacterial and higher-plant PSII.

Inhibitory and Non-Inhibitory NH3 Binding at the Water-Oxidizing Manganese Complex of Photosystem II Suggests Possible Sites and a Rearrangement Mode of Substrate Water Molecules

The identity and rearrangements of substrate water molecules in photosystem II (PSII) water oxidation are of great mechanistic interest and addressed herein by comprehensive analysis of NH₄⁺/NH₃ binding. Time-resolved detection of O₂ formation and recombination fluorescence as well as Fourier transform infrared (FTIR) difference spectroscopy on plant PSII membrane particles reveals the following. (1) Partial inhibition in NH₄Cl buffer occurs with a pH-independent binding constant of ∼25 mM, which does not result from decelerated O₂ formation, but from complete blockage of a major PSII fraction (∼60%) after reaching the Mn(IV)₄ (S₃) state. (2) The non-inhibited PSII fraction advances through the reaction cycle, but modified nuclear rearrangements are suggested by FTIR difference spectroscopy. (3) Partial inhibition can be explained by anticooperative (mutually exclusive) NH₃ binding to one inhibitory and one non-inhibitory site; these two sites may correspond to two water molecules terminally bound to the "dangling" Mn ion. (4) Unexpectedly strong modifications of the FTIR difference spectra suggest that in the non-inhibited PSII, ammonia binding obliterates the need for some of the nuclear rearrangements occurring in the S₂-S₃ transition as well as their reversal in the O₂ formation transition, in line with the carousel mechanism [Askerka, M., et al. (2015) Biochemistry 54, 5783]. (5) We observe the same partial inhibition of PSII by NH₄Cl also for thylakoid membranes prepared from mesophilic and thermophilic cyanobacteria, suggesting that the results described above are valid for plant and cyanobacterial PSII.

D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine YZ for proton exit during water oxidation

In photosynthetic water oxidation, two water molecules are converted into one oxygen molecule and four protons at the Mn₄CaO₅ cluster in photosystem II (PSII) via the S-state cycle. Efficient proton exit from the catalytic site to the lumen is essential for this process. However, the exit pathways of individual protons through the PSII proteins remain to be identified. In this study, we examined the involvement of a hydrogen-bond network near the redox-active tyrosine Y_Z in proton transfer during the S-state cycle. We focused on spectroscopic analyses of a site-directed variant of D1-Asn-298, a residue involved in a hydrogen-bond network near Y_Z We found that the D1-N298A mutant of Synechocystis sp. PCC 6803 exhibits an O₂ evolution activity of ∼10% of the wild-type. D1-N298A and the wild-type D1 had very similar features of thermoluminescence glow curves and of an FTIR difference spectrum upon Y_Z oxidation, suggesting that the hydrogen-bonded structure of Y_Z and electron transfer from the Mn₄CaO₅ cluster to Y_Z were little affected by substitution. In the D1-N298A mutant, however, the flash-number dependence of delayed luminescence showed a monotonic increase without oscillation, and FTIR difference spectra of the S-state cycle indicated partial and significant inhibition of the S₂ → S₃ and S₃ → S₀ transitions, respectively. These results suggest that the D1-N298A substitution inhibits the proton transfer processes in the S₂ → S₃ and S₃ → S₀ transitions. This in turn indicates that the hydrogen-bond network near Y_Z can be functional as a proton transfer pathway during photosynthetic water oxidation.

Differences in the Active Site of Water Oxidation among Photosynthetic Organisms

The site of biological water oxidation is highly conserved across photosynthetic organisms, but differences of unidentified structural and electronic origin exist between taxonomically discrete clades, revealed by distinct spectroscopic signatures of the oxygen-evolving Mn₄CaO₅ cluster and variations in active-site accessibility. Comparison of atomistic models of a native cyanobacterial form (Thermosynechococcus vulcanus) and a chimeric spinach-like form of photosystem II allows us to identify the precise atomic-level differences between organisms in the vicinity of the manganese cluster. Substitution of cyanobacterial D1-Asn87 by higher-plant D1-Ala87 is the principal discriminating feature: it drastically rearranges a network of proximal hydrogen bonds, modifying the local architecture of a water channel and the interaction of second coordination shell residues with the manganese cluster. The two variants explain species-dependent differences in spectroscopic properties and in the interaction of substrate analogues with the oxygen-evolving complex, enabling assignment of a substrate delivery channel to the active site.