Structural Effects of Ammonia Binding to the Mn4CaO5 Cluster of Photosystem II

Comprehensive Evaluation of Models for Ammonia Binding to the Oxygen Evolving Complex of Photosystem II

The identity and insertion pathway of the substrate oxygen atoms that are coupled to dioxygen by the oxygen-evolving complex (OEC) remains a central question toward understanding Nature's water oxidation mechanism. In several studies, ammonia has been used as a small "water analogue" to elucidate the pathway of substrate access to the OEC and to aid in determining which of the oxygen ligands of the tetramanganese cluster are substrates for O-O bond formation. On the basis of structural and spectroscopic investigations, five first-sphere binding modes of ammonia have been suggested, involving either substitution of an existing H2O/OH-/O2- group or addition as an extra ligand to a metal ion of the Mn4CaO5 cluster. Some of these modes, specifically the ones involving substitution, have already been subject to spectroscopy-oriented quantum chemical investigations, whereas more recent suggestions that postulate the addition of ammonia have not been examined so far with quantum chemistry for their agreement with spectroscopic data. Herein, we use a common structural framework and theoretical methodology to evaluate structural models of the OEC that represent all proposed modes of first-sphere ammonia interaction with the OEC in its S2 state. Criteria include energetic, magnetic, kinetic, and spectroscopic properties compared against available experimental EPR, ENDOR, ESEEM, and EDNMR data. Our results show that models featuring ammonia replacing one of the two terminal water ligands on Mn4 align best with experimental data, while they definitively exclude substitution of a bridging μ-oxo ligand as well as incorporation of ammonia as a sixth ligand on Mn1 or Mn4.

Coordination Number in High-Spin-Low-Spin Equilibrium in Cluster Models of the S2 State of the Oxygen Evolving Complex

The S2 state of the Oxygen Evolving Complex (OEC) of Photosystem II (PSII) shows high-spin (HS) and low-spin (LS) EPR signals attributed to distinct structures based on computation. Five-coordinate MnIII centers are proposed in these species but are absent in available spectroscopic model complexes. Herein, we report the synthesis, crystal structure, electrochemistry, SQUID magnetometry, and EPR spectroscopy of a MnIIIMnIV3O4 cuboidal complex featuring five-coordinate MnIII. This cluster displays a spin ground state of S = 5/2, while conversion to a six-coordinate Mn upon treatment with water results in a spin state change to S = 1/2. These results demonstrate that coordination number, without dramatic changes within the Mn4O4 core, has a substantial effect on spectroscopy.

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.

Water oxidation in oxygenic photosynthesis studied by magnetic resonance techniques

The understanding of light-induced biological water oxidation in oxygenic photosynthesis is of great importance both for biology and (bio)technological applications. The chemically difficult multistep reaction takes place at a unique protein-bound tetra-manganese/calcium cluster in photosystem II whose structure has been elucidated by X-ray crystallography (Umena et al. Nature 2011, 473, 55). The cluster moves through several intermediate states in the catalytic cycle. A detailed understanding of these intermediates requires information about the spatial and electronic structure of the Mn₄ Ca complex; the latter is only available from spectroscopic techniques. Here, the important role of Electron Paramagnetic Resonance (EPR) and related double resonance techniques (ENDOR, EDNMR), complemented by quantum chemical calculations, is described. This has led to the elucidation of the cluster's redox and protonation states, the valence and spin states of the manganese ions and the interactions between them, and contributed substantially to the understanding of the role of the protein surrounding, as well as the binding and processing of the substrate water molecules, the O-O bond formation and dioxygen release. Based on these data, models for the water oxidation cycle are developed.

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.

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.

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn₄Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S₀-S₄). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this study, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S₂ state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the "narrow" channel is altered in D1-N87A PSII, allowing for the binding of deprotonated ¹³C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S₂ state. This has important implications on the mechanistic models for water oxidation in PSII.

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.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.

Pulse EPR Spectroscopic Characterization of the S3 State of the Oxygen-Evolving Complex of Photosystem II Isolated from Synechocystis

The S₃ state is the last semi-stable state in the water splitting reaction that is catalyzed by the Mn₄O₅Ca cluster that makes up the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent high-field/frequency (95 GHz) electron paramagnetic resonance (EPR) studies of PSII isolated from the thermophilic cyanobacterium Thermosynechococcus elongatus have found broadened signals induced by chemical modification of the S₃ state. These signals are ascribed to an S₃ form that contains a five-coordinate Mn^IV center bridged to a cuboidal Mn^IV₃O₄Ca unit. High-resolution X-ray free-electron laser studies of the S₃ state have observed the OEC with all-octahedrally coordinated Mn^IV in what is described as an open cuboid-like cluster. No five-coordinate Mn^IV centers have been reported in these S₃ state structures. Here, we report high-field/frequency (130 GHz) pulse EPR of the S₃ state in Synechocystis sp. PCC 6803 PSII as isolated in the presence of glycerol. The S₃ state of PSII from Synechocystis exhibits multiple broadened forms (≈69% of the total signal) similar to those seen in the chemically modified S₃ centers from T. elongatus. Field-dependent ELDOR-detected nuclear magnetic resonance resolves two classes of ⁵⁵Mn nuclear spin transitions: one class with small hyperfine couplings (|A| ≈ 1-7 MHz) and another with larger hyperfine couplings (|A| ≈ 100 MHz). These results are consistent with an all-Mn^IV₄ open cubane structure of the S₃ state and suggest that the broadened S₃ signals arise from a perturbation of Mn4A and/or Mn3B, possibly induced by the presence of glycerol in the as-isolated Synechocystis PSII.

D1-S169A substitution of photosystem II reveals a novel S2-state structure

In photosystem II (PSII), photosynthetic water oxidation occurs at the O₂-evolving complex (OEC), a tetramanganese-calcium cluster that cycles through light-induced redox intermediates (S₀-S₄) to produce oxygen from two substrate water molecules. The OEC is surrounded by a hydrogen-bonded network of amino-acid residues that plays a crucial role in proton transfer and substrate water delivery. Previously, we found that D1-S169 was crucial for water oxidation and its mutation to alanine perturbed the hydrogen-bonding network. In this study, we demonstrate that the activation energy for the S₂ to S₁ transition of D1-S169A PSII is higher than wild-type PSII with a ~1.7-2.7× slower rate of charge recombination with Q_A^- relative to wild-type PSII. Arrhenius analysis of the decay kinetics shows an E_a of 5.87 ± 1.15 kcal mol^-1 for decay back to the S₁ state, compared to 0.80 ± 0.13 kcal mol^-1 for the wild-type S₂ state. In addition, we find that ammonia does not affect the S₂-state EPR signal, indicating that ammonia does not bind to the Mn cluster in D1-S169A PSII. Finally, a QM/MM analysis indicates that an additional water molecule binds to the Mn4 ion in place of an oxo ligand O5 in the S₂ state of D1-S169A PSII. The altered S₂ state of D1-S169A PSII provides insight into the S₂➔S₃ state transition.

EPR Spectroscopy of Iron- and Nickel-Doped [ZnAl]-Layered Double Hydroxides: Modeling Active Sites in Heterogeneous Water Oxidation Catalysts

Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to interspin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into nonmagnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (S = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites was solvent-exposed (i.e., at an edge, corner, or defect site). These solvent-exposed sites featured an axial ZFS of 0.21 cm^-1 when hydrated. The ZFS increased dramatically upon dehydration (to -1.5 cm^-1), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other ("inert") Fe(III) site maintained an axial ZFS of 0.19-0.20 cm^-1 under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (S = 1) atoms displayed a single, small ZFS (±0.30 cm^-1) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm^-1) were observed in the dehydrated samples. Although the magnetically dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g., by simple vacuum drying) is an important step toward identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials.

Promoting hole transfer for photoelectrochemical water oxidation through a manganese cluster catalyst bioinspired by natural photosystem II

A Mn₄O₄–cubane molecule bioinspired by the natural photosystem II was used as a co-catalyst in photoelectrochemical water oxidation.

Water oxidation in photosystem II

Biological water oxidation, performed by a single enzyme, photosystem II, is a central research topic not only in understanding the photosynthetic apparatus but also for the development of water splitting catalysts for technological applications. Great progress has been made in this endeavor following the report of a high-resolution X-ray crystallographic structure in 2011 resolving the cofactor site (Umena et al. in Nature 473:55-60, 2011), a tetra-manganese calcium complex. The electronic properties of the protein-bound water oxidizing Mn4OxCa complex are crucial to understand its catalytic activity. These properties include: its redox state(s) which are tuned by the protein matrix, the distribution of the manganese valence and spin states and the complex interactions that exist between the four manganese ions. In this short review we describe how magnetic resonance techniques, particularly EPR, complemented by quantum chemical calculations, have played an important role in understanding the electronic structure of the cofactor. Together with isotope labeling, these techniques have also been instrumental in deciphering the binding of the two substrate water molecules to the cluster. These results are briefly described in the context of the history of biological water oxidation with special emphasis on recent work using time resolved X-ray diffraction with free electron lasers. It is shown that these data are instrumental for developing a model of the biological water oxidation cycle.

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.

Electron Transfer on the Donor Side of Manganese-Depleted Photosystem 2

After removal of manganese ions responsible for light-driven water oxidation, redox-active tyrosine Y_Z (tyrosine 161 of the D1 subunit) still remains the dominant electron donor to the photooxidized chlorophyll P₆₈₀ (P₆₈₀⁺) in the reaction center of photosystem 2 (PS2). Here, we investigated P₆₈₀⁺ reduction by Y_Z under single-turnover flashes in Mn-depleted PS2 core complexes in the presence of weak acids and NH₄Cl. Analysis of changes in the light-induced absorption at 830 nm (reflecting P₆₈₀ redox transitions) at pH 6.0 showed that P₆₈₀⁺ reduction is well approximated by two kinetic components with the characteristic times (τ) of ~7 and ~31 μs and relative contributions of ~54 and ~37%, respectively. In contrast to the very small effect of sodium formate (200 mM), addition of sodium acetate and NH₄Cl increased the rate of electron transfer between Y_Z and P₆₈₀⁺ approx. by a factor of 5. The suggestion that direct electron transfer from Y_Z to P₆₈₀⁺ has a biphasic kinetics and reflects the presence of two different populations of PS2 centers was confirmed by the data obtained using direct electrometrical technique. It was demonstrated that the submillisecond two-phase kinetics of the additional electrogenic phase in the kinetics of photoelectric response due to the electron transfer between Y_Z and P₆₈₀⁺ is significantly accelerated in the presence of acetate or ammonia. These results contribute to the understanding of the mechanism of interaction between the oxidized tyrosine Y_Z and exogenous substances (including synthetic manganese-containing compounds) capable of photooxidation of water molecule in the manganese-depleted PS2 complexes.

Five-coordinate MnIV intermediate in the activation of nature's water splitting cofactor

Nature's water splitting cofactor passes through a series of catalytic intermediates (S₀-S₄) before O-O bond formation and O₂ release. In the second last transition (S₂ to S₃) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all Mn^IV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S₄ How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S₃') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (>50%) in (i) chemical-modified cofactors in which Ca²⁺ is exchanged with Sr²⁺; the Mn₄O₅Sr cofactor remains active, but the S₂-S₃ and S₃-S₀ transitions are slower than for the Mn₄O₅Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S₃' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S₃ signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S₂ state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S₃' cofactor is similar to the high spin form of the preceding S₂ state, which contains a cuboidal Mn₃O₄Ca unit tethered to an external, 5-coordinate Mn ion (Mn4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn4. The interaction of ammonia with the cofactor is also discussed.

The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation

The catalytic cycle of the oxygen-evolving complex (OEC) of photosystem II (PSII) comprises five intermediate states Si (i = 0–4), from the most reduced S0 state to the most oxidized S4, which spontaneously evolves dioxygen. The precise geometric and electronic structure of the Si states, and hence the mechanism of O–O bond formation in the OEC, remain under investigation, particularly for the final steps of the catalytic cycle. Recent advances in protein crystallography based on X-ray free-electron lasers (XFELs) have produced new structural models for the S3 state, which indicate that two of the oxygen atoms of the inorganic Mn4CaO6 core of the OEC are in very close proximity. This has been interpreted as possible evidence for “early-onset” O–O bond formation in the S3 state, as opposed to the more widely accepted view that the O–O bond is formed in the final state of the cycle, S4. Peroxo or superoxo formation in S3 has received partial support from computational studies. Here, a brief overview is provided of spectroscopic information, recent crystallographic results, and computational models for the S3 state. Emphasis is placed on computational S3 models that involve O–O formation, which are discussed with respect to their agreement with structural information, experimental evidence from various spectroscopic studies, and substrate exchange kinetics. Despite seemingly better agreement with some of the available crystallographic interpretations for the S3 state, models that implicate early-onset O–O bond formation are hard to reconcile with the complete line of experimental evidence, especially with X-ray absorption, X-ray emission, and magnetic resonance spectroscopic observations. Specifically with respect to quantum chemical studies, the inconclusive energetics for the possible isoforms of S3 is an acute problem that is probably beyond the capabilities of standard density functional theory.