Energetics of Ionized Water Molecules in the H-Bond Network near the Ca2+ and Cl– Binding Sites in Photosystem II

Interplay of two low-barrier hydrogen bonds in long-distance proton-coupled electron transfer for water oxidation

D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O•), it accepts an electron from the oxygen-evolving Mn4CaO5 cluster, facilitating an increase in the oxidation state (Sn; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O• drives proton-coupled electron transfer during the S2 to S3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O• formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn4CaO5 together with an adjacent water molecule. The H-bond donation to the Mn4CaO5 cluster triggers the release of the proton from the lowest pKa site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn4CaO5]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O• formation and D1-Asp61 protonation.

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.

Substitution of Ca2+ and changes in the H-bond network near the oxygen-evolving complex of photosystem II

Ca²⁺, which provides binding sites for ligand water molecules W3 and W4 in the Mn₄CaO₅ cluster, is a prerequisite for O₂ evolution in photosystem II (PSII). We report structural changes in the H-bond network and the catalytic cluster itself upon the replacement of Ca²⁺ with other alkaline earth metals, using a quantum mechanical/molecular mechanical approach. The small radius of Mg²⁺ makes W3 donate an H-bond to D1-Glu189 in Mg²⁺-PSII. If an additional water molecule binds at the large surface of Ba²⁺, it donates H-bonds to D1-Glu189 and the ligand water molecule at the dangling Mn, altering the H-bond network. The potential energy profiles of the H-bond between D1-Tyr161 (TyrZ) and D1-His190 and the interconversion between the open- and closed-cubane S₂ conformations remain substantially unaltered upon the replacement of Ca²⁺. Remarkably, the O5⋯Ca²⁺ distance is shortest among all O5⋯metal distances irrespective of the radius being larger than that of Mg²⁺. Furthermore, Ca²⁺ is the only alkaline earth metal that equalizes the O5⋯metal and O2⋯metal distances and facilitates the formation of the symmetric cubane structure.

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.

The Role of Redox-Inactive Metals in Modulating the Redox Potential of the Mn4CaO4 Model Complex

Photosynthetic oxygen-evolving center (OEC), the "engine of life", is a unique Mn₄CaO₅ cluster catalyzing the water oxidation. The role of redox-inactive component Ca²⁺, which can only be functionally replaced by Sr²⁺ in a biological environment, has been under debate for a long time. Recently, its modulating effect on the redox potential of native OEC and artificial structural OEC model complex has received great attention, and linear relationship between the potential and the Lewis acidity of the redox-inactive metal has been proposed for the MMn₃O₄ model complex. In this work, the modulating effect has been studied in detail using the Mn₄CaO₄ model complex, which is the closest structural model to OEC to date and has a similar redox potential at the S₁-S₂ transition. We found the redox-inactive metal only has a weak modulating effect on the potential, which is comparable in strength to that of the ligand environments. Meanwhile, the net charge of the complex, which could be changed along with the redox-inactive metal, has a high impact on the potential and can be unified by protonation, deprotonation, or ligand modification. Although the modulating effect of the redox-inactive metal is not very strong, the linear relationship between the potential and the Lewis acidity is still valid for Mn₄MO₄ complexes. Our results of strong modulating effects for net charge and weak modulating effects for redox-inactive metal fit with the previous experimental observations on Mn₄MO₄ (M = Ca²⁺, Y³⁺, and Gd³⁺) model complexes, and suggest that Ca²⁺ can be structurally and electrochemically replaced with other metal cations, together with proper ligand modifications.

D139N mutation of PsbP enhances the oxygen-evolving activity of photosystem II through stabilized binding of a chloride ion

Photosystem II (PSII) is a multisubunit membrane protein complex that catalyzes light-driven oxidation of water to molecular oxygen. The chloride ion (Cl-) has long been known as an essential cofactor for oxygen evolution by PSII, and two Cl- ions (Cl-1 and Cl-2) have been found to specifically bind near the Mn4CaO5 cluster within the oxygen-evolving center (OEC). However, despite intensive studies on these Cl- ions, little is known about the function of Cl-2, the Cl- ion that is associated with the backbone nitrogens of D1-Asn338, D1-Phe339, and CP43-Glu354. In green plant PSII, the membrane extrinsic subunits-PsbP and PsbQ-are responsible for Cl- retention within the OEC. The Loop 4 region of PsbP, consisting of highly conserved residues Thr135-Gly142, is inserted close to Cl-2, but its importance has not been examined to date. Here, we investigated the importance of PsbP-Loop 4 using spinach PSII membranes reconstituted with spinach PsbP proteins harboring mutations in this region. Mutations in PsbP-Loop 4 had remarkable effects on the rate of oxygen evolution by PSII. Moreover, we found that a specific mutation, PsbP-D139N, significantly enhances the oxygen-evolving activity in the absence of PsbQ, but not significantly in its presence. The D139N mutation increased the Cl- retention ability of PsbP and induced a unique structural change in the OEC, as indicated by light-induced Fourier transform infrared (FTIR) difference spectroscopy and theoretical calculations. Our findings provide insight into the functional significance of Cl-2 in the water-oxidizing reaction of PSII.

Release of a Proton and Formation of a Low-Barrier Hydrogen Bond between Tyrosine D and D2-His189 in Photosystem II

In photosystem II (PSII), the second-lowest oxidation state (S₁) of the oxygen-evolving Mn₄CaO₅ cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S₀) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential (E _m) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The E _m depends on the H⁺ position along the low-barrier H-bond, e.g., 680 mV when the H⁺ is at the D2-His189 moiety and 800 mV when the H⁺ is at the TyrD moiety, which can explain why TyrD mediates both the S₀ to S₁ oxidation and the S₂ to S₁ reduction.

Intriguing Chloride: Involvement of Chloride Ions in Proton Transfers

The proton transfer from carbon to a chloride ion and the proton transfer to a molecule of water promoted by chloride ions in the acid-catalyzed formation of hydroxamic acids from aldehydes and substituted nitrosobenzenes in mixed solvents have been proposed based on experimental and theoretical investigations. The formation of uncommon contact ion pairs consisting of the nitrosocarbinolic cation intermediate and a chloride anion, followed by the proton transfer from a C-H moiety of the cation intermediate, has been proposed. The influence of chloride on the proton transfer to a water molecule of the solvent-separated nitrosocarbinolic-cation–chloride ion pair was investigated too. The insights are based on the obtained kinetic and other evidence with regard to (1) influences of chloride anions on the observed reaction rates and primary kinetic isotope effects (PKIE) in the reaction; (2) the observed variation of the PKIE-s and rates of the reaction when perchlorate anions are present along with the chloride ions; and (3) the consideration of a model of the nitrosocarbinolic-cation-intermediate—chloride ion pair and transition structure for the proposed proton transfers based on the ab initio calculations.

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⁺.

Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter

Zinc homeostasis in mammals is constantly and precisely maintained by sophisticated regulatory proteins. Among them, the Zrt/Irt-like protein (ZIP) regulates the influx of zinc into the cytoplasm. In this work, we have employed all-atom molecular dynamics simulations to investigate the Zn²⁺ transport mechanism in prokaryotic ZIP obtained from Bordetella bronchiseptica (BbZIP) in a membrane bilayer. Additionally, the structural and dynamical transformations of BbZIP during this process have been analyzed. This study allowed us to develop a hypothesis for the zinc influx mechanism and formation of the metal-binding site. We have created a model for the outward-facing form of BbZIP (experimentally only the inward-facing form has been characterized) that has allowed us, for the first time, to observe the Zn²⁺ ion entering the channel and binding to the negatively charged M2 site. It is thought that the M2 site is less favored than the M1 site, which then leads to metal ion egress; however, we have not observed the M1 site being occupied in our simulations. Furthermore, removing both Zn²⁺ ions from this complex resulted in the collapse of the metal-binding site, illustrating the "structural role" of metal ions in maintaining the binding site and holding the proteins together. Finally, due to the long Cd²⁺-residue bond distances observed in the X-ray structures, we have proposed the existence of an H₃O⁺ ion at the M2 site that plays an important role in protein stability in the absence of the metal ion.

Photosynthetic Parameters Show Specific Responses to Essential Mineral Deficiencies

In response to decreases in the assimilation efficiency of CO2, plants oxidize the reaction center chlorophyll (P700) of photosystem I (PSI) to suppress reactive oxygen species (ROS) production. In hydro-cultured sunflower leaves experiencing essential mineral deficiencies, we analyzed the following parameters that characterize PSI and PSII: (1) the reduction-oxidation states of P700 [Y(I), Y(NA), and Y(ND)]; (2) the relative electron flux in PSII [Y(II)]; (3) the reduction state of the primary electron acceptor in PSII, QA (1 - qL); and (4) the non-photochemical quenching of chlorophyll fluorescence (NPQ). Deficiency treatments for the minerals N, P, Mn, Mg, S, and Zn decreased Y(II) with an increase in the oxidized P700 [Y(ND)], while deficiencies for the minerals K, Fe, Ca, B, and Mo decreased Y(II) without an increase in Y(ND). During the induction of photosynthesis, the above parameters showed specific responses to each mineral. That is, we could diagnose the mineral deficiency and identify which mineral affected the photosynthesis parameters.

Role of redox-inactive metals in controlling the redox potential of heterometallic manganese-oxido clusters

Photosystem II (PSII) contains Ca2+, which is essential to the oxygen-evolving activity of the catalytic Mn4CaO5 complex. Replacement of Ca2+ with other redox-inactive metals results in a loss/decrease of oxygen-evolving activity. To investigate the role of Ca2+ in this catalytic reaction, we investigate artificial Mn3[M]O2 clusters redox-inactive metals  [M] ([M]  = Mg2+, Ca2+, Zn2+, Sr2+, and Y3+), which were synthesized by Tsui et al. (Nat Chem 5:293, 2013). The experimentally measured redox potentials (Em) of these clusters are best described by the energy of their highest occupied molecular orbitals. Quantum chemical calculations showed that the valence of metals predominantly affects Em(MnIII/IV), whereas the ionic radius of metals affects Em(MnIII/IV) only slightly.

Identification of intermediate conformations in the photocycle of the light-driven sodium-pumping rhodopsin KR2

The light-driven rhodopsin KR2 transports Na⁺via the M- and O-states. However, the mechanisms by which the retinal regulates Na⁺ pumping is unknown, in part because KR2 adopts both pentamer and monomer forms in crystal structures and in part because these structures show differences in the protein conformation near the Schiff base, even when they are of the same intermediate state within the photocycle. A particular open question is the nature of the H-bond networks and protonation state in the active site, including Asp116. Here, we analyze the protonation state and the absorption wavelength for each crystal structure, using a quantum mechanical/molecular mechanical approach. In the pentamer ground state, the calculated absorption wavelength reproduces the experimentally measured absorption wavelength (530 nm). The analysis also shows that ionized Asp116 is stabilized by the H-bond donations of both Ser70 and a cluster of water molecules. The absorption wavelength of 400 nm in the M-state can be best reproduced when the two O atoms of Asp116 interact strongly with the Schiff base, as reported in one of the previous monomer ground state structures. The absorption wavelengths calculated for the two Na⁺-incorporated O-state structures are consistent with the measured absorption wavelength (∼600 nm), which suggests that two conformations represent the O-state. These results may provide a key to designing enhanced tools in optogenetics.

The Nature of the Short Oxygen-Oxygen Distance in the Mn4CaO6 Complex of Photosystem II Crystals

The O···O distance for a typical H-bond is ∼2.8 Å, whereas the radiation-damage-free structures of photosystem II (PSII), obtained using the X-ray free electron laser (XFEL), shows remarkably short O···O distances of ∼2 Å in the oxygen-evolving Mn₄CaO_5/6 complex. Herein, we report the protonation/oxidation states of the short O···O atoms in the XFEL structures using a quantum mechanical/molecular mechanical approach. The O5···O6 distance of 1.9 Å is reproduced only when O6 is an unprotonated O radical (O^•-) with Mn(IV)₃Mn(III), i.e., the S₃ state. The potential energy profile shows a barrier-less energy minimum region when O5···O6 = 1.90-2.05 Å (O^•- ↓) or 2.05-2.20 Å (O^•- ↑). Formation of such a short O5···O6 distance is not possible when O6 is OH^- with Mn(IV)₄. In the case in which the O5···O6 distance is 1.9 Å, it seems likely that the O radical species exists in the oxygen-evolving complex of the XFEL-S₃ crystals.

Proton transfer pathway from the oxygen-evolving complex in photosystem II substantiated by extensive mutagenesis

We report a structure-based biological approach to identify the proton-transfer pathway in photosystem II. First, molecular dynamics (MD) simulations were conducted to analyze the H-bond network that may serve as a Grotthuss-like proton conduit. MD simulations show that D1-Asp61, the H-bond acceptor of H₂O at the Mn₄CaO₅ cluster (W1), forms an H-bond via one water molecule with D1-Glu65 but not with D2-Glu312. Then, D1-Asp61, D1-Glu65, D2-Glu312, and the adjacent residues, D1-Arg334, D2-Glu302, and D2-Glu323, were thoroughly mutated to the other 19 residues, i.e., 114 Chlamydomonas chloroplast mutant cells were generated. Mutation of D1-Asp61 was most crucial. Only the D61E and D61C cells grew photoautotrophically and exhibit O₂-evolving activity. Mutations of D2-Glu312 were less crucial to photosynthetic growth than mutations of D1-Glu65. Quantum mechanical/molecular mechanical calculations indicated that in the PSII crystal structure, the proton is predominantly localized at D1-Glu65 along the H-bond with D2-Glu312, i.e., pK_a(D1-Glu65) > pK_a(D2-Glu312). The potential-energy profile shows that the release of the proton from D1-Glu65 leads to the formation of the two short H-bonds between D1-Asp61 and D1-Glu65, which facilitates downhill proton transfer along the Grotthuss-like proton conduit in the S₂ to S₃ transition. It seems possible that D1-Glu65 is involved in the dominant pathway that proceeds from W1 via D1-Asp61 toward the thylakoid lumen, whereas D2-Glu312 and D1-Arg334 may be involved in alternative pathways in some mutants.

pKa of the ligand water molecules in the oxygen-evolving Mn4CaO5 cluster in photosystem II

Release of the protons from the substrate water molecules is prerequisite for O₂ evolution in photosystem II (PSII). Proton-releasing water molecules with low pK_a values at the catalytic moiety can be the substrate water molecules. In some studies, one of the ligand water molecules, W2, is regarded as OH^-. However, the PSII crystal structure shows neither proton acceptor nor proton-transfer pathway for W2, which is not consistent with the assumption of W2 = OH^-. Here we report the pK_a values of the four ligand water molecules, W1 and W2 at Mn4 and W3 and W4 at Ca²⁺, of the Mn₄CaO₅ cluster. pK_a(W1) ≈ pK_a(W2) << pK_a(W3) ≈ pK_a(W4) in the Mn₄CaO₅ cluster in water. However, pK_a(W1) ≈ pK_a(D1-Asp61) << pK_a(W2) in the PSII protein environment. These results suggest that in PSII, deprotonation of W2 is energetically disfavored as far as W1 exists.

Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H⁺ position in low-barrier H-bonds.

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.