Evaluation of new low-valent computational models for the oxygen-evolving complex of photosystem II

Cryo-EM meets crystallography: A model-independent view of the heteronuclear Mn4Ca cluster structure of photosystem II

Photosynthesis converts solar energy to chemical energy by splitting water molecules and carbon dioxide to produce oxygen and carbohydrates with an efficiency that engineers working on solar energy device can only dream of. Photosystem II (PSII) is the enzyme that catalyzes the light-driven oxidation of water that occurs during photosynthesis. This oxygen-producing reaction occurs in the Mn4Ca cluster found inside the enzyme's oxygen-evolving center (OEC). Even though the structure and mechanism of action of the OEC have been intensively investigated for many decades, questions still remain about both. The Mn4Ca cluster stores the high-energy oxidizing equivalents required for water oxidation so that its own oxidation state depends on its chemical composition, i.e., the number of its oxygen ligands. The issue addressed here is the number of oxygen ligands associated with the Mn4Ca cluster after PSII has been exposed to two of the four flashes of light necessary for it to produce an oxygen molecule, PSII 2F. Comparisons of recently published cryo-EM maps and crystallographic OEC-omit maps described here reveal the OEC structure of PSII 2F contains only five internal oxygen ligands, and that the sixth O ligand identified earlier in PSII 2F crystal structures is an artifact caused by model bias. This finding should have a significant impact on our understanding of the mechanism of water oxidation that is catalyzed by PSII because it is incompatible with prevailing high valence paradigm (HVP) models for this process.

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.

Probing the proton release by Photosystem II in the S1 to S2 high-spin transition

The stoichiometry and kinetics of the proton release were investigated during each transition of the S-state cycle in Photosystem II (PSII) from Thermosynechococcus elongatus containing either a Mn₄CaO₅ (PSII/Ca) or a Mn₄SrO₅ (PSII/Sr) cluster. The measurements were done at pH 6.0 and pH 7.0 knowing that, in PSII/Ca at pH 6.0 and pH 7.0 and in PSII/Sr at pH 6.0, the flash-induced S₂-state is in a low-spin configuration (S₂^LS) whereas in PSII/Sr at pH 7.0, the S₂-state is in a high-spin configuration (S₂^HS) in half of the centers. Two measurements were done; the time-resolved flash dependent i) absorption of either bromocresol purple at pH 6.0 or neutral red at pH 7.0 and ii) electrochromism in the Soret band of P_D1 at 440 nm. The fittings of the oscillations with a period of four indicate that one proton is released in the S₁ to S₂^HS transition in PSII/Sr at pH 7.0. It has previously been suggested that the proton released in the S₂^LS to S₃ transition would be released in a S₂^LSTyr_Z^• → S₂^HSTyr_Z^• transition before the electron transfer from the cluster to Tyr_Z^• occurs. The release of a proton in the S₁Tyr_Z^• → S₂^HSTyr_Z transition would logically imply that this proton release is missing in the S₂^HSTyr_Z^• to S₃Tyr_Z transition. Instead, the proton release in the S₁ to S₂^HS transition in PSII/Sr at pH 7.0 was mainly done at the expense of the proton release in the S₃ to S₀ and S₀ to S₁ transitions. However, at pH 7.0, the electrochromism of P_D1 seems larger in PSII/Sr when compared to PSII/Ca in the S₃ state. This points to the complex link between proton movements in and immediately around the Mn₄ cluster and the mechanism leading to the release of protons into the bulk.

Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II

Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O₂ into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn₄O₅Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyr_z (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca²⁺-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn₄O₅Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn₄O₅Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O₂ formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.

Redox Isomerism in the S3 State of the Oxygen-Evolving Complex Resolved by Coupled Cluster Theory

The electronic and geometric structures of the water-oxidizing complex of photosystem II in the steps of the catalytic cycle that precede dioxygen evolution remain hotly debated. Recent structural and spectroscopic investigations support contradictory redox formulations for the active-site Mn4 CaOx cofactor in the final metastable S3 state. These range from the widely accepted MnIV 4 oxo-hydroxo model, which presumes that O-O bond formation occurs in the ultimate transient intermediate (S4 ) of the catalytic cycle, to a MnIII 2 MnIV 2 peroxo model representative of the contrasting "early-onset" O-O bond formation hypothesis. Density functional theory energetics of suggested S3 redox isomers are inconclusive because of extreme functional dependence. Here, we use the power of the domain-based local pair natural orbital approach to coupled cluster theory, DLPNO-CCSD(T), to present the first correlated wave function theory calculations of relative stabilities for distinct redox-isomeric forms of the S3 state. Our results enabled us to evaluate conflicting models for the S3 state of the oxygen-evolving complex (OEC) and to quantify the accuracy of lower-level theoretical approaches. Our assessment of the relevance of distinct redox-isomeric forms for the mechanism of biological water oxidation strongly disfavors the scenario of early-onset O-O formation advanced by literal interpretations of certain crystallographic models. This work serves as a case study in the application of modern coupled cluster implementations to redox isomerism problems in oligonuclear transition metal systems.

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.

Identification of a Na+-Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions and one redox-inactive Ca²⁺ ion, with two nearby bound Cl^- ions. Sodium is a common counterion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Here, we find that the oxygen-evolution activity of spinach PSII increases with Na⁺ concentration, particularly at high pH. A Na⁺-specific binding site next to the OEC, becomes available after deprotonation of the D1-H337 amino acid residue, is suggested by the analysis of two recently published PSII cryo-electron microscopy maps in combination with quantum mechanical calculations and multiconformation continuum electrostatics simulations.