Theoretical evaluation of structural models of the S2 state in the oxygen evolving complex of Photosystem II: protonation states and magnetic interactions

Substrate water exchange in the S2 state of photosystem II is dependent on the conformation of the Mn4Ca cluster

The structural flexibility of the Mn₄Ca cluster in photosystem II supports the exchange of the central O5 bridge.

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.

Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II

TyrZ oxidation state triggers hydrogen bond modification in the water oxidation catalysis.

Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA

BACKGROUND

The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach.

SCOPE OF REVIEW

Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described.

MAJOR CONCLUSIONS

XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data.

GENERAL SIGNIFICANCE

XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.

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.

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.

On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II

Understanding the structural modification experienced by the Mn₄ CaO₅ oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S-states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S₂ /S₁ infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra.

Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn4 OX (X = 5, 6) cluster in the Kok cycle Si (i = 0-3) of oxygen evolving complex of photosystem II

The optimized geometries of the CaMn₄ O_X (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the S_i (i = 0-3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the S_i intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S₃ state are investigated in detail in relation to recent SFX and XES experiments for the S₃ state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S₃ state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.

Assessment of Double-Hybrid Density Functional Theory for Magnetic Exchange Coupling in Manganese Complexes

Molecular systems containing magnetically interacting (exchange-coupled) manganese ions are important in catalysis, biomimetic chemistry, and molecular magnetism. The reliable prediction of exchange coupling constants with quantum chemical methods is key for tracing the relationships between structure and magnetic properties in these systems. Density functional theory (DFT) in the broken-symmetry approach has been employed extensively for this purpose and hybrid functionals with moderate levels of Hartree–Fock exchange admixture have often been shown to perform adequately. Double-hybrid density functionals that introduce a second-order perturbational contribution to the Kohn–Sham energy are generally regarded as a superior approach for most molecular properties, but their performance remains unexplored for exchange-coupled manganese systems. An assessment of various double-hybrid functionals for the prediction of exchange coupling constants is presented here using a set of experimentally characterized dinuclear manganese complexes that cover a wide range of exchange coupling situations. Double-hybrid functionals perform more uniformly compared to conventional DFT methods, but they fail to deliver improved accuracy or reliability in the prediction of exchange coupling constants. Reparametrized double-hybrid density functionals (DHDFs) perform no better, and most often worse, than the original B2-PLYP double-hybrid method. All DHDFs are surpassed by the hybrid-meta-generalized gradient approximation (GGA) TPSSh functional. Possible directions for future methodological developments are discussed.

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.

Tetranuclear [MnIIIMn3IVO4] Complexes as Spectroscopic Models of the S2 State of the Oxygen Evolving Complex in Photosystem II

Despite extensive biochemical, spectroscopic, and computational studies, the mechanism of biological water oxidation by the oxygen evolving complex (OEC) of Photosystem II remains a subject of significant debate. Mechanistic proposals are guided by the characterization of reaction intermediates such as the S₂ state, which features two characteristic EPR signals at g = 2 and g = 4.1. Two nearly isoenergetic structural isomers have been proposed as the source of these distinct signals, but relevant structure-electronic structure studies remain rare. Herein, we report the synthesis, crystal structure, electrochemistry, XAS, magnetic susceptibility, variable temperature CW-EPR, and pulse EPR data for a series of [Mn^IIIMn₃^IVO₄] cuboidal complexes as spectroscopic models of the S₂ state of the OEC. Resembling the oxidation state and EPR spectra of the S₂ state of the OEC, these model complexes show two EPR signals, a broad low field signal and a multiline signal, that are remarkably similar to the biological system. The effect of systematic changes in the nature of the bridging ligands on spectroscopy were studied. Results show that the electronic structure of tetranuclear Mn complexes is highly sensitive to even small geometric changes and the nature of the bridging ligands. Our model studies suggest that the spectroscopic properties of the OEC may also react very sensitively to small changes in structure; the effect of protonation state and other reorganization processes need to be carefully assessed.

Evidence of O-O Bond Formation in the Final Metastable S3 State of Nature's Water Oxidizing Complex Implying a Novel Mechanism of Water Oxidation

A novel mechanism for the final stages of Nature's photosynthetic water oxidation to molecular oxygen is proposed. This is based on a comparison of experimental and broken symmetry density functional theory (BS-DFT) calculated geometries and magnetic resonance properties of water oxidizing complex models in the final metastable oxidation state, S₃. We show that peroxo models of the S₃ state are in vastly superior agreement with the current experimental structural determinations compared with oxo-hydroxo models. Comparison of experimental and BS-DFT calculated ⁵⁵Mn hyperfine couplings for the electron paramagnetic resonance (EPR) visible form shows better agreement for the oxo-hydroxo model. An equilibrium between oxo-hydroxo and peroxo models is proposed for the S₃ state and the major implications for the final steps in the water oxidation mechanism are analyzed and discussed.

Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å

Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5-O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.

Resolving Ambiguous Protonation and Oxidation States in the Oxygen Evolving Complex of Photosystem II

Photosystem II (PSII) of photosynthetic organisms converts light energy into chemical energy by oxidizing water to dioxygen at the Mn₄CaO₅ oxygen-evolving complex (OEC). Extensive structural data have been collected on the resting dark state (nominally S₁ in the standard Kok nomenclature) from crystal diffraction and EXAFS studies but the protonation and Mn oxidation states are still uncertain. A "high-oxidation" model assigns the S₁ state to have the formal Mn oxidation level of (III, IV, IV, III), whereas the "low-oxidation" model posits two additional electrons. Generally, additional protons are expected to be associated with the low-oxidation model and were not fully investigated until now. Here we consider structural features of the S₀ and S₁ states using a quantum mechanics/molecular mechanics (QM/MM) method. We systematically alter the hydrogen-bonding network and the protonation states of bridging and terminal oxygens and His337 to investigate how they influence Mn-Mn and Mn-O distances, relative energetics, and the internal distribution of Mn oxidation states, in both high and low-oxidation state paradigms. The bridging oxygens (O1, O2, O3, O4) all need to be deprotonated (O^2-) to be compatible with available structural data, whereas the position of O5 (bridging Mn3, Mn4, and Ca) in the XFEL structure is more consistent with an OH^- under the low paradigm. We show that structures with two short Mn-Mn distances, which are sometimes argued to be diagnostic of a high oxidation state paradigm, can also arise in low oxidation-state models. We conclude that the low Mn oxidation state proposal for the OEC can closely fit all of the available structural data at accessible energies in a straightforward manner. Modeling at the 4 H⁺ protonation level of S₁ under the high paradigm predicts rearrangement of bidentate D1-Asp170 to H-bond to O5 (OH^-), a geometry found in artificial OEC catalysts.

Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism

The biological energy cycle of our planet is driven by photosynthesis whereby sunlight is absorbed by chlorophyll and other accessory pigments. The excitation energy is then efficiently transferred to a reaction centre where charge separation occurs in a few picoseconds. In the case of photosystem II (PSII), the energy of the charge transfer state is used to split water into oxygen and reducing equivalents. This is accomplished by the relatively low energy content of four photons of visible light. PSII is a large multi-subunit membrane protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Four high energy electrons, together with four protons (4H+), are used to reduce plastoquinone (PQ), the terminal electron acceptor of PSII, to plastoquinol (PQH2). PQH2 passes its reducing equivalents to an electron transfer chain which feeds into photosystem I (PSI) where they gain additional reducing potential from a second light reaction which is necessary to drive CO2 reduction. The catalytic centre of PSII consists of a cluster of four Mn ions and a Ca2+ linked by oxo bonds. In addition, there are seven amino acid ligands. In this Article, I discuss the structure of this metal cluster, its stability and the probability that an acid-base (nucleophilic-electrophilic) mechanism catalyses the water splitting reaction on the surface of the metal-cluster. Evidence for this mechanism is presented from studies on water splitting catalysts consisting of organo-complexes of ruthenium and manganese and also by comparison with the enzymology of carbon monoxide dehydrogenase (CODH). Finally the relevance of our understanding of PSII is discussed in terms of artificial photosynthesis with emphasis on inorganic water splitting catalysts as oxygen generating photoelectrodes.

Comparison of Experimental and Broken Symmetry Density Functional Theory Calculated Electron Paramagnetic Resonance Parameters for the Manganese Catalase Active Site in the Superoxidized MnIII/MnIV State

Broken symmetry density functional theory has been used to calculate g-tensor, ⁵⁵Mn, ¹⁴N, and ¹⁷O hyperfine couplings for active site models of superoxidized Mn^III/Mn^IV manganese catalase both in its native and azide-inhibited form. While a good agreement is found between the calculated and experimental g-tensor and ⁵⁵Mn hyperfine couplings for all models, the active site geometry and Mn ion oxidation state can only be readily distinguished based on a comparison of the calculated and experimental ¹⁴N azide and ¹⁷O HFCs. This comparison shows that only models containing a Jahn-Teller distorted 5-coordinate (Mn^III)₂ site and a 6-coordinate (Mn^IV)₁ site can satisfactorily reproduce the experimental ¹⁴N and ¹⁷O hyperfine couplings.

The S2 to S3 transition for water oxidation in PSII (photosystem II), revisited

The formation of O₂ from water requires four transitions, each one after the absorption of one light flash.

Quantum Chemical Modeling of Homogeneous Water Oxidation Catalysis

The design of efficient and robust water oxidation catalysts has proven challenging in the development of artificial photosynthetic systems for solar energy harnessing and storage. Tremendous progress has been made in the development of homogeneous transition-metal complexes capable of mediating water oxidation. To improve the efficiency of the catalyst and to design new catalysts, a detailed mechanistic understanding is necessary. Quantum chemical modeling calculations have been successfully used to complement the experimental techniques to suggest a catalytic mechanism and identify all stationary points, including transition states for both O-O bond formation and O₂ release. In this review, recent progress in the applications of quantum chemical methods for the modeling of homogeneous water oxidation catalysis, covering various transition metals, including manganese, iron, cobalt, nickel, copper, ruthenium, and iridium, is discussed.

Discovery of Open Cubane Core Structures for Biomimetic LnCo3 (OR)4 Water Oxidation Catalysts

Bio-mimetic catalysts such as LnCo₃ (OR)₄ (Ln=Er, Tm; OR=alkoxide) cubanes have recently been in the focus of research for artificial water oxidation processes. Previously, the remarkable adaptability with respect to ligand shell, nuclear structure as well as protonation and oxidation states of those catalysts has been shown to be beneficial for the water oxidation process. We further explored the structural flexibility of those catalysts and present here a series of novel structures in which one metal center is pulled out of the cubane cage. This leads to an open cubane core, which is to some extent reminiscent of observed open/closed cubane-core forms of the oxygen-evolving complex in nature's photosystem II. We investigate how those open cubane core models alter the thermodynamics of the water oxidation cycle and how different solvation approaches influence their stability.

Effects of Static Correlation between Spin Centers in Multicenter Transition Metal Complexes

Multicenter transition metal complexes are the key moieties of many processes in chemistry, biochemistry, and materials science such as in the active sites of enzymes, molecular catalysts, and biological electron carriers. Their electronic structure, often characterized by high-spin-polarized metal sites, is a challenge for theoretical chemists because of their high degree of dynamical and static correlation. Static correlation is necessary both for the appropriate description of the metal-ligand bonding and for a correct description of the multideterminant character arising from the magnetic interactions between spin centers. Density functional theory (DFT) is usually applied using a single-determinant broken-symmetry state that is lacking the correct spin symmetry when the ground state has total low-spin character. To alleviate this drawback, we use the extended broken-symmetry (EBS) approach to derive approximate ground-state energies and, for the first time, forces for the correctly symmetric ground state of an arbitrary number of spin centers within the framework of the Heisenberg-Dirac-van Vleck Hamiltonian. Remarkably, the proposed procedure supplies relaxed geometries that are fully consistent with the calculated J-coupling constants. We apply the method to investigate the relaxed geometrical structure of the low-spin ground state of iron-sulfur clusters with two, three, and four iron centers. We observed significant differences in both geometrical parameters and coupling constant J between the symmetrized ground state, the high-spin, and the broken-symmetry optimized structures. These changes are often comparable with the differences observed by using different functionals, and the use of EBS always improves the description of the studied systems. It will be therefore important to include it in any DFT attempt to quantitatively describe multicenter transition metal complexes in the future.

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.

Cluster size convergence for the energetics of the oxygen evolving complex in PSII

Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated. However, recently results were published by Isobe et al., suggesting that very different results could be obtained if the model was extended from 200 to 340 atoms. The present study aims at understanding where this difference comes from. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.