Mechanism of light induced water splitting in Photosystem II of oxygen evolving photosynthetic organisms

A Reappraisal of the S2 State of Nature's Water Oxidizing Complex in Its Low and High Spin Forms

Density functional theory calculated 14N hyperfine couplings are obtained for the Mn1 ligated π-N of residue His332 of the photosystem 2 water oxidizing complex. An open cubane, O4H, model closely matches the experimental coupling obtained for the high spin S = 5/2 form of the S2 state, supporting an open cubane structure for this state. We also investigate the unusual geometric features for the S2 state obtained by X-ray free electron laser structure determinations and rationalize it as an equilibrium occurring at room temperature between W1/O4 deprotonated and protonated forms of the open cubane structure.

The S1 to S2 and S2 to S3 state transitions in plant photosystem II: relevance to the functional and structural heterogeneity of the water oxidizing complex

In Photosystem II, light-induced water splitting occurs via the S state cycle of the CaMn4O5-cluster. To understand the role of various possible conformations of the CaMn4O5-cluster in this process, the temperature dependence of the S1 → S2 and S2 → S3 state transitions, induced by saturating laser flashes, was studied in spinach photosystem II membrane preparations under different conditions. The S1 → S2 transition temperature dependence was shown to be much dependent on the type of the cryoprotectant and presence of 3.5% methanol, resulting in the variation of transition half-inhibition temperature by 50 K. No similar effect was observed for the S2 → S3 state transition, for which we also show that both the low spin g = 2.0 multiline and high spin g = 4.1 EPR configurations of the S2 state advance with similar efficiency to the S3 state, both showing a transition half-inhibition temperature of 240 K. This was further confirmed by following the appearance of the Split S3 EPR signal. The results are discussed in relevance to the functional and structural heterogeneity of the water oxidizing complex intermediates in photosystem II.

The influence of cationic antiseptics on the processes of light energy conversion in various photosynthetic pigment-protein complexes

The widespread use of disinfectants and antiseptics, and consequently their release into the environment, determines the relevance of studying their potential impact on the main producers of organic matter on the planet-photosynthetic organisms. The review examines the effects of some biguanides and quaternary ammonium compounds, octenidine, miramistin, chlorhexidine, and picloxidine, on the functioning of the photosynthetic apparatus of various organisms (Strakhovskaya et al. in Photosynth Res 147:197-209, 2021; Knox et al. in Photosynth Res 153:103, 2022; Paschenko et al. in Photosynth Res 155:93-105, 2023a, Photosynth Res 2023b). A common feature of these antiseptics is the combination of hydrophobic and hydrophilic regions in the molecules, the latter carrying a positive charge(s). The comparison of the results obtained with intact bacterial membrane vesicles (chromatophores) and purified pigment-protein complexes (photosystem II and I) of oxygenic organisms allows us to draw conclusions about the mechanisms of the cationic antiseptic action on the functional properties of the components of the photosynthetic apparatus.

Evolution in the Design of Water Oxidation Catalysts with Transition-Metals: A Perspective on Biological, Molecular, Supramolecular, and Hybrid Approaches

Increased demand for a carbon-neutral sustainable energy scheme augmented by climatic threats motivates the design and exploration of novel approaches that reserve intermittent solar energy in the form of chemical bonds in molecules and materials. In this context, inspired by biological processes, artificial photosynthesis has garnered significant attention as a promising solution to convert solar power into chemical fuels from abundantly found H2O. Among the two redox half-reactions in artificial photosynthesis, the four-electron oxidation of water according to 2H2O → O2 + 4H+ + 4e- comprises the major bottleneck and is a severe impediment toward sustainable energy production. As such, devising new catalytic platforms, with traditional concepts of molecular, materials and biological catalysis and capable of integrating the functional architectures of the natural oxygen-evolving complex in photosystem II would certainly be a value-addition toward this objective. In this review, we discuss the progress in construction of ideal water oxidation catalysts (WOCs), starting with the ingenuity of the biological design with earth-abundant transition metal ions, which then diverges into molecular, supramolecular and hybrid approaches, blurring any existing chemical or conceptual boundaries. We focus on the geometric, electronic, and mechanistic understanding of state-of-the-art homogeneous transition-metal containing molecular WOCs and summarize the limiting factors such as choice of ligands and predominance of environmentally unrewarding and expensive noble-metals, necessity of high-valency on metal, thermodynamic instability of intermediates, and reversibility of reactions that create challenges in construction of robust and efficient water oxidation catalyst. We highlight how judicious heterogenization of atom-efficient molecular WOCs in supramolecular and hybrid approaches put forth promising avenues to alleviate the existing problems in molecular catalysis, albeit retaining their fascinating intrinsic reactivities. Taken together, our overview is expected to provide guiding principles on opportunities, challenges, and crucial factors for designing novel water oxidation catalysts based on a synergy between conventional and contemporary methodologies that will incite the expansion of the domain of artificial photosynthesis.

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.

Tuning of the ChlD1 and ChlD2 properties in photosystem II by site-directed mutagenesis of neighbouring amino acids

Photosystem II is the water/plastoquinone photo-oxidoreductase of photosynthesis. The photochemistry and catalysis occur in a quasi-symmetrical heterodimer, D1D2, that evolved from a homodimeric ancestor. Here, we studied site-directed mutants in PSII from the thermophilic cyanobacterium Thermosynechoccocus elongatus, focusing on the primary electron donor chlorophyll a in D1, ChlD1, and on its symmetrical counterpart in D2, ChlD2, which does not play a direct photochemical role. The main conserved amino acid specific to ChlD1 is D1/T179, which H-bonds the water ligand to its Mg2+, while its counterpart near ChlD2 is the non-H-bonding D2/I178. The symmetrical-swapped mutants, D1/T179I and D2/I178T, and a second ChlD2 mutant, D2/I178H, were studied. The D1 mutations affected the 686 nm absorption attributed to ChlD1, while the D2 mutations affected a 663 nm feature, tentatively attributed to ChlD2. The mutations had little effect on enzyme activity and forward electron transfer, reflecting the robustness of the overall enzyme function. In contrast, the mutations significantly affected photodamage and protective mechanisms, reflecting the importance of redox tuning in these processes. In D1/T179I, the radical pair recombination triplet on ChlD1 was shared onto a pheophytin, presumably PheD1 and the detection of 3PheD1 supports the proposed mechanism for the anomalously short lifetime of 3ChlD1; e.g. electron transfer quenching by QA- of 3PheD1 after triplet transfer from 3ChlD1. In D2/I178T, a charge separation could occur between ChlD2 and PheD2, a reaction that is thought to occur in ancestral precursors of PSII. These mutants help understand the evolution of asymmetry in PSII.

Pentanuclear iron complex for water oxidation: spectroscopic analysis of reactive intermediates in solution and catalyst immobilization into the MOF-based photoanode

Photoelectrochemical water splitting can produce green hydrogen for industrial use and CO2-neutral transportation, ensuring the transition from fossil fuels to green, renewable energy sources. The iron-based electrocatalyst [FeII4FeIII(μ-3-O)(μ-L)6]3+ (LH = 3,5-bis(2-pyridyl)pyrazole) (1), discovered in 2016, is one of the fastest molecular water oxidation catalysts (WOC) based on earth-abundant elements. However, its water oxidation reaction mechanism has not been yet fully elucidated. Here, we present in situ X-ray spectroscopy and electron paramagnetic resonance (EPR) analysis of electrochemical water oxidation reaction (WOR) promoted by (1) in water-acetonitrile solution. We observed transient reactive intermediates during the in situ electrochemical WOR, consistent with a coordination sphere expansion prior to the onset of catalytic current. At a pre-catalytic (~+1.1 V vs. Ag/AgCl) potential, the distinct g~2.0 EPR signal assigned to FeIII/FeIV interaction was observed. Prolonged bulk electrolysis at catalytic (~+1.6 V vs. Ag/AgCl) potential leads to the further oxidation of Fe centers in (1). At the steady state achieved with such electrolysis, the formation of hypervalent FeV=O and FeIV=O catalytic intermediates was inferred with XANES and EXAFS fitting, detecting a short Fe=O bond at ~1.6 Å. (1) was embedded into MIL-126 MOF with the formation of (1)-MIL-126 composite. The latter was tested in photoelectrochemical WOR and demonstrated an improvement of electrocatalytic current upon visible light irradiation in acidic (pH=2) water solution. The presented spectroscopic analysis gives further insight into the catalytic pathways of multinuclear systems and should help the subsequent development of more energy- and cost-effective catalysts of water splitting based on earth-abundant metals. Photoelectrocatalytic activity of (1)-MIL-126 confirms the possibility of creating an assembly of (1) inside a solid support and boosting it with solar irradiation towards industrial applications of the catalyst.

Nature of S-States in the Oxygen-Evolving Complex Resolved by High-Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy

Photosystem II, the water splitting enzyme of photosynthesis, utilizes the energy of sunlight to drive the four-electron oxidation of water to dioxygen at the oxygen-evolving complex (OEC). The OEC harbors a Mn4CaO5 cluster that cycles through five oxidation states Si (i = 0-4). The S3 state is the last metastable state before the O2 evolution. Its electronic structure and nature of the S2 → S3 transition are key topics of persisting controversy. Most spectroscopic studies suggest that the S3 state consists of four Mn(IV) ions, compared to the Mn(III)Mn(IV)3 of the S2 state. However, recent crystallographic data have received conflicting interpretations, suggesting either metal- or ligand-based oxidation, the latter leading to an oxyl radical or a peroxo moiety in the S3 state. Herein, we utilize high-energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy to obtain a highly resolved description of the Mn K pre-edge region for all S-states, paying special attention to use chemically unperturbed S3 state samples. In combination with quantum chemical calculations, we achieve assignment of specific spectroscopic features to geometric and electronic structures for all S-states. These data are used to confidently discriminate between the various suggestions concerning the electronic structure and the nature of oxidation events in all observable catalytic intermediates of the OEC. Our results do not support the presence of either peroxo or oxyl in the active configuration of the S3 state. This establishes Mn-centered storage of oxidative equivalents in all observable catalytic transitions and constrains the onset of the O-O bond formation until after the final light-driven oxidation event.

Theoretical elucidation of the structure, bonding, and reactivity of the CaMn4Ox clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation

This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.

Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography

The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.

Absorption changes in Photosystem II in the Soret band region upon the formation of the chlorophyll cation radical [PD1PD2]. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01049-3. [PMID: 37751034 DOI: 10.1007/s11120-023-01049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Flash-induced absorption changes in the Soret region arising from the [PD1PD2]+ state, the chlorophyll cation radical formed upon light excitation of Photosystem II (PSII), were measured in Mn-depleted PSII cores at pH 8.6. Under these conditions, TyrD is i) reduced before the first flash, and ii) oxidized before subsequent flashes. In wild-type PSII, when TyrD● is present, an additional signal in the [PD1PD2]+-minus-[PD1PD2] difference spectrum was observed when compared to the first flash when TyrD is not oxidized. The additional feature was "W-shaped" with troughs at 434 nm and 446 nm. This feature was absent when TyrD was reduced, but was present (i) when TyrD was physically absent (and replaced by phenylalanine) or (ii) when its H-bonding histidine (D2-His189) was physically absent (replaced by a Leucine). Thus, the simple difference spectrum without the double trough feature at 434 nm and 446 nm, seemed to require the native structural environment around the reduced TyrD and its H bonding partners to be present. We found no evidence of involvement of PD1, ChlD1, PheD1, PheD2, TyrZ, and the Cytb559 heme in the W-shaped difference spectrum. However, the use of a mutant of the PD2 axial His ligand, the D2-His197Ala, shows that the PD2 environment seems involved in the formation of "W-shaped" signal.

Solar energy conversion by photosystem II: principles and structures

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

Structural evidence for intermediates during O2 formation in photosystem II

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

Triplet Delocalization over the Reaction Center Chlorophylls in Photosystem II

The triplet state of chlorophyll formed by charge recombination in photosystem II (PSII) is a precursor of harmful singlet oxygen. Although main localization of the triplet state on the monomeric chlorophyll, Chl_D1, at cryogenic temperatures has been suggested, how the triplet state is delocalized on other chlorophylls remains unclear. Here, we investigated the distribution of the triplet state of chlorophyll in PSII using light-induced Fourier transform infrared (FTIR) difference spectroscopy. Measurements of triplet-minus-singlet FTIR difference spectra with PSII core complexes from cyanobacterial mutants, D1-V157H, D2-V156H, D2-H197A, and D1-H198A, in which the interactions of the 13¹-keto C═O groups of the reaction center chlorophylls, P_D1, P_D2, Chl_D1, and Chl_D2, respectively, were perturbed, identified the 13¹-keto C═O bands of the individual chlorophylls and showed that the triplet state is delocalized over all of these chlorophylls. It is suggested that the triplet delocalization plays important roles in the photoprotection and photodamage mechanisms in PSII.

Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs

Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4 CaO5 complex, in the intermediate Si (i = 0-4)-states of the Kok cycle, obtained using XFELs.

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.

Magnetic and Electronic Structural Properties of the S3 State of Nature's Water Oxidizing Complex: A Combined Study in ELDOR-Detected Nuclear Magnetic Resonance Spectral Simulation and Broken-Symmetry Density Functional Theory

ELDOR-detected nuclear magnetic resonance (EDNMR) spectral simulations combined with broken-symmetry density functional theory (BS-DFT) calculations are used to obtain and to assign the ⁵⁵Mn hyperfine coupling constants (hfcs) for modified forms of the water oxidizing complex in the penultimate S₃ state of the water oxidation cycle. The study shows that an open cubane form of the core Mn₄CaO₆ cluster explains the magnetic properties of the dominant S = 3 species in all cases studied experimentally with no need to invoke a closed cubane intermediate possessing a distorted pentacoordinate Mn₄ ion as recently suggested. EDNMR simulations found that both the experimental bandwidth and multinuclear transitions may alter relative EDNMR peak intensities, potentially leading to incorrect assignment of hfcs. The implications of these findings for the water oxidation mechanism are discussed.

How Nature Makes O2: an Electronic Level Mechanism for Water Oxidation in Photosynthesis

In this paper, we combine broken symmetry density functional calculations and electron paramagnetic resonance analysis to obtain the electronic structure of the penultimate S₃ state of nature's water-oxidizing complex and determine the electronic pathway of O-O bond formation. Analysis of the electronic structure changes along the reaction path shows that two spin crossovers, facilitated by the geometry and magnetism of the water-oxidizing complex, are used to provide a unique low-energy pathway. The pathway is facilitated via the formation and stabilization of the [O₂]^3- ion. This ion is formed between ligated deprotonated substrate waters, O5 and O6, and is stabilized by antiferromagnetic interaction with the Mn ions of the complex. Combining the computational, crystallographic, and spectroscopic data, we show that an equilibrium exists between the O5 oxo and O6 hydroxo forms with an S = 3 spin state and a deprotonated O6 form containing a two-center one-electron bond in [O5O6]^3- which we identify as the form detected using crystallography. This form corresponds to an S = 6 spin state which we demonstrate gives rise to a low-intensity EPR spectrum compared with the accompanying S = 3 state, making its detection via EPR difficult and overshadowed by the S = 3 form. Simulations using 70% of the S = 6 component give rise to a superior fit to the experimental W-band EPR spectral envelope compared with an S = 3 only form. Analyses of the most recent X-ray emission spectroscopy first moment changes for solution and time-resolved crystal data are also shown to support the model. The computational, crystallographic, and spectroscopic data are shown to coalesce to the same picture of a predominant S = 6 species containing the first one-electron oxidation product of two water molecules, that is, [O5O6]^3-. Progression of this form to the two-electron-oxidized peroxo and three-electron-oxidized superoxo forms, leading eventually to the evolution of triplet O₂, is proposed to be the pathway nature adopts to oxidize water. The study reveals the key electronic, magnetic, and structural design features of nature's catalyst which facilitates water oxidation to O₂ under ambient conditions.

An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana

Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating ¹⁵ N isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future ¹⁵ N-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.

Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae

The paper presents the results of recent work at the Department of Biophysics of the Biological Faculty, Lomonosov Moscow State University on the kinetic and multiparticle modeling of processes in the photosynthetic membrane. The detailed kinetic models and the rule-based kinetic Monte Carlo models allow to reproduce the fluorescence induction curves and redox transformations of the photoactive pigment P700 in the time range from 100 ns to dozens of seconds and make it possible to reveal the role of individual carriers in their formation for different types of photosynthetic organisms under different illumination regimes, in the presence of inhibitors, under stress conditions. The fitting of the model curves to the experimental data quantifies the reaction rate constants that cannot be directly measured experimentally, including the non-radiative thermal relaxation reactions. We use the direct multiparticle models to explicitly describe the interactions of mobile photosynthetic carrier proteins with multienzyme complexes both in solution and in the biomembrane interior. An analysis of these models reveals the role of diffusion and electrostatic factors in the regulation of electron transport, the influence of ionic strength and pH of the cellular environment on the rate of electron transport reactions between carrier proteins. To describe the conformational intramolecular processes of formation of the final complex, in which the actual electron transfer occurs, we use the methods of molecular dynamics. The results obtained using kinetic and molecular models supplement our knowledge of the mechanisms of organization of the photosynthetic electron transport processes at the cellular and molecular levels.

Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation

Photosynthetic water oxidation is catalyzed by a manganese–calcium oxide cluster, which experiences five “S-states” during a light-driven reaction cycle. The unique “distorted chair”-like geometry of the Mn₄CaO₅₍₆₎ cluster shows structural flexibility that has been frequently proposed to involve “open” and “closed”-cubane forms from the S₁ to S₃ states. The isomers are interconvertible in the S₁ and S₂ states, while in the S₃ state, the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples. In this work, using density functional theory calculations, we go beyond the S₃⁺Y_z state to the S₃ⁿY_z^• → S₄⁺Y_z step, and report for the first time that the reversible isomerism, which is suppressed in the S₃⁺Y_z state, is fully recovered in the ensuing S₃ⁿY_z^• state due to the proton release from a manganese-bound water ligand. The altered coordination strength of the manganese–ligand facilitates formation of the closed-cubane form, in a dynamic equilibrium with the open-cubane form. This tautomerism immediately preceding dioxygen formation may constitute the rate limiting step for O₂ formation, and exert a significant influence on the water oxidation mechanism in photosystem II.

pH-Dependent Regulation of Electron Flow in Photosystem II by a Histidine Residue at the Stromal Surface

In photosystem II (PSII), the secondary plastoquinone electron acceptor Q_B functions as a substrate that converts into plastoquinol upon its double reduction by electrons abstracted from water. It has been suggested that a histidine residue, D1-H252, which is located at the stromal surface near Q_B, is involved in the pH-dependent regulation of electron flow and proton transfer to Q_B. However, definitive evidence for the involvement of D1-H252 in the Q_B reactions has not been obtained yet. Here, we studied the roles of D1-H252 in PSII using a cyanobacterial mutant, in which D1-H252 was replaced with Ala. Delayed luminescence (DL) measurement upon a single flash showed a faster Q_B^- decay at higher pH in the thylakoids from the wild-type strain due to the downshift of the redox potential of Q_B [E_m(Q_B^-/Q_B)]. This pH dependence of the Q_B^- decay was lost in the D1-H252A mutant. The experimental E_m(Q_B^-/Q_B) changes were well reproduced by the density functional theory calculations for models with different protonation states of D1-H252 and with Ala replaced for H252. It was further shown that the period-four oscillation of the DL intensity by successive flashes was significantly diminished in the D1-H252A mutant, suggesting the inhibition of plastoquinone exchange at the Q_B pocket in this mutant. It is thus concluded that D1-H252 is a key amino acid residue that regulates electron flow in PSII by sensing pH in the stroma and stabilizes the Q_B binding site to facilitate the quinone exchange reaction.

From manganese oxidation to water oxidation: assembly and evolution of the water-splitting complex in photosystem II

The manganese cluster of photosystem II has been the focus of intense research aiming to understand the mechanism of H₂O-oxidation. Great effort has also been applied to investigating its oxidative photoassembly process, termed photoactivation that involves the light-driven incorporation of metal ions into the active Mn₄CaO₅ cluster. The knowledge gained on these topics has fundamental scientific significance, but may also provide the blueprints for the development of biomimetic devices capable of splitting water for solar energy applications. Accordingly, synthetic chemical approaches inspired by the native Mn cluster are actively being explored, for which the native catalyst is a useful benchmark. For both the natural and artificial catalysts, the assembly process of incorporating Mn ions into catalytically active Mn oxide complexes is an oxidative process. In both cases this process appears to share certain chemical features, such as producing an optimal fraction of open coordination sites on the metals to facilitate the binding of substrate water, as well as the involvement of alkali metals (e.g., Ca²⁺) to facilitate assembly and activate water-splitting catalysis. This review discusses the structure and formation of the metal cluster of the PSII H₂O-oxidizing complex in the context of what is known about the formation and chemical properties of different Mn oxides. Additionally, the evolutionary origin of the Mn₄CaO₅ is considered in light of hypotheses that soluble Mn²⁺ was an ancient source of reductant for some early photosynthetic reaction centers ('photomanganotrophy'), and recent evidence that PSII can form Mn oxides with structural resemblance to the geologically abundant birnessite class of minerals. A new functional role for Ca²⁺ to facilitate sustained Mn²⁺ oxidation during photomanganotrophy is proposed, which may explain proposed physiological intermediates during the likely evolutionary transition from anoxygenic to oxygenic photosynthesis.

Molecular basis for turnover inefficiencies (misses) during water oxidation in photosystem II

Photosynthesis stores solar light as chemical energy and efficiency of this process is highly important. The electrons required for CO₂ reduction are extracted from water in a reaction driven by light-induced charge separations in the Photosystem II reaction center and catalyzed by the CaMn₄O₅-cluster. This cyclic process involves five redox intermediates known as the S₀–S₄ states. In this study, we quantify the flash-induced turnover efficiency of each S state by electron paramagnetic resonance spectroscopy. Measurements were performed in photosystem II membrane preparations from spinach in the presence of an exogenous electron acceptor at selected temperatures between −10 °C and +20 °C and at flash frequencies of 1.25, 5 and 10 Hz. The results show that at optimal conditions the turnover efficiencies are limited by reactions occurring in the water oxidizing complex, allowing the extraction of their S state dependence and correlating low efficiencies to structural changes and chemical events during the reaction cycle. At temperatures 10 °C and below, the highest efficiency (i.e. lowest miss parameter) was found for the S₁ → S₂ transition, while the S₂ → S₃ transition was least efficient (highest miss parameter) over the whole temperature range. These electron paramagnetic resonance results were confirmed by measurements of flash-induced oxygen release patterns in thylakoid membranes and are explained on the basis of S state dependent structural changes at the CaMn₄O₅-cluster that were determined recently by femtosecond X-ray crystallography. Thereby, possible “molecular errors” connected to the e⁻ transfer, H⁺ transfer, H₂O binding and O₂ release are identified.

Temperature dependence of the transition inefficiencies (misses) for the water oxidation process in photosystem II were studied by EPR spectroscopy and are explained on the basis of S state dependent structural changes at the CaMn₄O₅-cluster.

The exchange of the fast substrate water in the S2 state of photosystem II is limited by diffusion of bulk water through channels - implications for the water oxidation mechanism

The molecular oxygen we breathe is produced from water-derived oxygen species bound to the Mn4CaO5 cluster in photosystem II (PSII). Present research points to the central oxo-bridge O5 as the 'slow exchanging substrate water (Ws)', while, in the S2 state, the terminal water ligands W2 and W3 are both discussed as the 'fast exchanging substrate water (Wf)'. A critical point for the assignment of Wf is whether or not its exchange with bulk water is limited by barriers in the channels leading to the Mn4CaO5 cluster. In this study, we measured the rates of H2 16O/H2 18O substrate water exchange in the S2 and S3 states of PSII core complexes from wild-type (WT) Synechocystis sp. PCC 6803, and from two mutants, D1-D61A and D1-E189Q, that are expected to alter water access via the Cl1/O4 channels and the O1 channel, respectively. We found that the exchange rates of Wf and Ws were unaffected by the E189Q mutation (O1 channel), but strongly perturbed by the D61A mutation (Cl1/O4 channel). It is concluded that all channels have restrictions limiting the isotopic equilibration of the inner water pool near the Mn4CaO5 cluster, and that D61 participates in one such barrier. In the D61A mutant this barrier is lowered so that Wf exchange occurs more rapidly. This finding removes the main argument against Ca-bound W3 as fast substrate water in the S2 state, namely the indifference of the rate of Wf exchange towards Ca/Sr substitution.

S3 State Models of Nature's Water Oxidizing Complex: Analysis of Bonding and Magnetic Exchange Pathways, Assessment of Experimental Electron Paramagnetic Resonance Data, and Implications for the Water Oxidation Mechanism

Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr²⁺ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn₁ and Mn₂ ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated ⁵⁵Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.

Mechanism of Oxygen Evolution and Mn4CaO5 Cluster Restoration in the Natural Water-Oxidizing Catalyst

Water oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn₄Ca cluster located in the core of Photosystem II and proceeds along the five steps (S₀-S₄) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn₄Ca cluster in the S₀ state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S₀ state.

Bonding and Magnetic Exchange Pathways in Nature's Water-Oxidizing Complex

The nature of the bonding and magnetic exchange pathways of the water-oxidizing complex of photosystem 2 is explored using broken symmetry density functional theory. The electronic structure and superexchange pathways are illustrated and analyzed using corresponding orbitals and intrinsic bond orbitals. These demonstrate a dominating influence on the bonding and magnetic interactions by both the geometrical structure of the Mn₄CaO₅ core complex and the ionic interactions of the oxo bridges with the neighboring Ca²⁺ ion. The demonstrated ionic nature of the Ca²⁺ bonds is proposed to contribute to the stabilization of the oxygen atoms participating in O-O bond formation.

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.

Redox-Inactive Metal Ions That Enhance the Nucleophilic Reactivity of an Alkylperoxocopper(II) Complex

The importance of redox-inactive metal ions in modulating the reactivity of redox-active biological systems is a subject of great current interest. In this work, the effect of redox-inactive metal ions (M³⁺ = Sc³⁺, Y³⁺, Yb³⁺, La³⁺) on the nucleophilic reactivity of a mononuclear ligand-based alkylperoxocopper(II) complex, [Cu(ⁱPr₂-tren-C(CH₃)₂O₂)]⁺ (1), was examined. 1 was prepared by the addition of hydrogen peroxide and triethylamine to the solution of [Cu(ⁱPr₃-tren)(CH₃CN)]⁺ (ⁱPr₃-tren = tris[2-(isopropylamino)ethyl]amine) via the formation of [Cu(ⁱPr₃-tren)(O₂H)]⁺ (2) in methanol (CH₃OH) at 30 °C. 1 was characterized using density functional theory (DFT) calculations and spectroscopic methods such as UV-vis, resonance Raman (rR), and electron paramagnetic resonance (EPR). DFT calculations support the electronic structure of 1 with an intermediate geometry between the trigonal-bipyramidal and square-pyramidal geometries, which is consistent with the observed EPR signal exhibiting a signal with g_⊥ = 2.03 (A_⊥ = 16 G) and g_|| = 2.19 (A_|| = 158 G). The Cu-O bond stretching frequency of 1 was observed at 507 cm^-1 for ¹⁶O₂ species (486 cm^-1 for ¹⁸O₂ species), and its O-O vibrational energy was determined to be 799 cm^-1 for ¹⁶O₂ species (759 cm^-1 for ¹⁸O₂ species) by rR spectroscopy. The reactivity of 1 was investigated in oxidative nucleophilic reactions. The positive slope of the Hammett plot (ρ = 2.3(1)) with para-substituted benzaldehydes and the reactivity order with 1°-, 2°-, and 3°-CHO demonstrate well the nucleophilic character of this copper(II) ligand-based alkylperoxo complex. The Lewis acidity of M³⁺ improves the oxidizing ability of 1. The modulated reactivity of 1 with M³⁺ was revealed to be an opposite trend of the Lewis acidity of M³⁺ in aldehyde deformylation.

Bicarbonate-Mediated CO2 Formation on Both Sides of Photosystem II

The effect of bicarbonate (HCO3-) on photosystem II (PSII) activity was discovered in the 1950s, but only recently have its molecular mechanisms begun to be clarified. Two chemical mechanisms have been proposed. One is for the electron-donor side, in which mobile HCO3- enhances and possibly regulates water oxidation by acting as proton acceptor, after which it dissociates into CO2 and H2O. The other is for the electron-acceptor side, in which (i) reduction of the QA quinone leads to the release of HCO3- from its binding site on the non-heme iron and (ii) the Em potential of the QA/QA•- couple increases when HCO3- dissociates. This suggested a protective/regulatory role of HCO3- as it is known that increasing the Em of QA decreases the extent of back-reaction-associated photodamage. Here we demonstrate, using plant thylakoids, that time-resolved membrane-inlet mass spectrometry together with 13C isotope labeling of HCO3- allows donor- and acceptor-side formation of CO2 by PSII to be demonstrated and distinguished, which opens the door for future studies of the importance of both mechanisms under in vivo conditions.

Electron and energy transfer in a porphyrin-oxoporphyrinogen-fullerene triad, ZnP-OxP-C60

A multichromophoric triad, ZnP-OxP-C60 containing porphyrin (ZnTPP hereafter ZnP), oxoporphyrinogen (OxP) and fullerene (C60) has been synthesized to probe the intramolecular dynamics of its electron and energy transfer in relation to the presence of the closely linked electron deficient OxP-C60 'special pair', constructed as a mimic of the naturally occurring photosynthetic antenna-reaction center. The DFT optimized structure of the triad reveals the relative spatial remoteness of the ZnP entity with proximal OxP/C60 entities. Free-energetics of different energy and electron transfer events were estimated using spectral, computational and electrochemical studies, according to the Rehm-Weller approach. Femtosecond transient absorption spectral studies revealed energy transfer from 1ZnP* to OxP to yield ZnP-1OxP*-C60, and electron transfer to yield ZnP˙+-OxP-C60˙- and/or ZnP-OxP˙+-C60˙- charge seperated states. That is, the ZnP entity in the triad operates as both antenna and electron donor to generate relatively long-lived charge separated states thus mimicking the early photoevents of natural photosynthesis.

Molecular Identification of a High-Spin Deprotonated Intermediate during the S2 to S3 Transition of Nature's Water-Oxidizing Complex

The identity of a key intermediate in the S₂ to S₃ transition of nature's water-oxidizing complex (WOC) in Photosystem 2 is presented. Broken-symmetry density functional theory (BS-DFT) calculations and Heisenberg-Dirac-van Vleck (HDvV) spin ladder calculations show that an S₂ state open cubane model of the WOC containing a μ-hydroxo O4 changes from an S = ⁵/₂ form to an S = ⁷/₂, form upon deprotonation of W1. Combined with X-band electron paramagnetic resonance (EPR) spectral analysis, this indicates that the g = 4.1 EPR signal corresponds to an S = ⁵/₂ form of the WOC with W1 present as a water ligand to Mn₄, while the g = 4.8/4.9 form observed at high pH values corresponds to an S = ⁷/₂ form, with W1 as a hydroxo ligand. The latter is also likely to represent the form needed to progress to S₃ in the functioning enzyme.

Electronic-Level View of O-O Bond Formation in Nature's Water Oxidizing Complex

The crucial O-O bond forming step in the water oxidizing complex (WOC) of photosystem II is modeled using density functional theory calculations and compared with structural X-ray free electron laser (XFEL) determinations for the penultimate S₃ state. Concerted electron flow between the Mn₄O5 and Mn₁O6 bonds of the complex and the nascent O-O bond is monitored using intrinsic bond orbital analysis along the reaction path. Concerted transfer to Mn₁ and Mn₄ of two electrons from the reactant oxos, O5 and O6, resulting in an unoccupied antibonding σ_2p* orbital is the key to low barrier O-O bond formation. The potential energy surface for O-O bond formation shows a rather broad energy minimum for the oxo-oxo form ranging from 2.4-2.0 Å which may explain the relatively short O5-O6 bond distance reported in experimental structure studies. Alternatively the short O5-O6 bond distance may reflect a dynamic equilibrium model across the whole O-O potential energy surface.

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.

The role of photoinduced charge transfer for photocatalysis, photoelectrocatalysis and luminescence sensing in metal–organic frameworks

Understanding PCT taking place within MOFs is crucial for designing porous photo/electrocatalysts and luminescent sensors. Unique features of PCT in MOFs and recent progress along with state-of-the-art characterization methods are discussed in the context of its applications.

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.

Proton Isomers Rationalize the High- and Low-Spin Forms of the S2 State Intermediate in the Water-Oxidizing Reaction of Photosystem II

A new paradigm for the high- and low-spin forms of the S₂ state of nature's water-oxidizing complex in Photosystem II is found. Broken symmetry density functional theory calculations combined with Heisenberg-Dirac-van Vleck spin ladder calculations show that an open cubane form of the water-oxidizing complex changes from a low-spin, S = 1/2, to a high-spin, S = 5/2, form on protonation of the bridging O4 oxo. We show that such models are fully compatible with structural determinations of the S₂ state by X-ray free-electron laser crystallography and extended X-ray absorption fine structure and provide a clear rationale for the effect of various treatments on the relative populations of each form observed experimentally in electron paramagnetic resonance studies.

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.

Evolutionary Analysis of Unicellular Species in Chlamydomonadales Through Chloroplast Genome Comparison With the Colonial Volvocine Algae

This study is the first determination of six chloroplast genomes of colonial volvocine algae, Colemanosphaera charkowiensis, Volvulina compacta, Pandorina colemaniae, Pandorina morum, Colemanosphaera angeleri, and Yamagishiella unicocca. Based on 55 chloroplast protein-coding genes, we compared the nonsynonymous (dN) and synonymous (dS) substitution rates between colonial volvocine algae and the other unicellular Chlamydomonadales species. When refer to the dN, we found 27 genes were significantly different, among them, 19 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). When refer to the dS, we found 10 genes were significantly different, among them, 6 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). Then we identified 14 putative fast-evolving genes and 11 putative positively selected genes of unicellular species, we analyzed the function of positively selected sites of the overlap genes of putative fast-evolving and positively selected genes, and found some sites were close to the important functional region of the proteins. Photosynthesis is the process to transform and store solar energy by chloroplast, it plays a vital role in the survival of algae, this study is the first to use the chloroplast genomes to analysis the evolutionary relationship between colonial and unicellular species in Chlamydomonadales. We found more genes have higher substitution rates in unicellular species and proposed that the fast-evolving and positively selected two genes, psbA and psbC, may help to improve the photosynthetic efficiency of unicellular species in Chlamydomonadales.

Structural isomers of the S2 state in photosystem II: do they exist at room temperature and are they important for function?

In nature, an oxo-bridged Mn₄ CaO₅ cluster embedded in photosystem II (PSII), a membrane-bound multi-subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light-induced charge separations in the reaction center of PSII. The Mn₄ CaO₅ cluster accumulates four oxidizing equivalents to enable the four-electron four-proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S-states, S₀  - S₄ in the Kok cycle. One important question related to the catalytic mechanism of the oxygen-evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S-states and if such equilibria are essential for the mechanism of the O-O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S₂ state of PSII with structural data collected of the S₁ , S₂ and S₃ states by serial crystallography at neutral pH (∼6.5) using an X-ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S₂ state, the room temperature crystallography data can be well-described by just one S₂ structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.

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.