Evidence that the C-terminus of the D1 polypeptide of photosystem II is ligated to the manganese ion that undergoes oxidation during the S1 to S2 transition: an isotope-edited FTIR study

Reaction Mechanism of the Terminal Plastoquinone QB in Photosystem II as Revealed by Time-Resolved Infrared Spectroscopy

The secondary plastoquinone (PQ) electron acceptor QB in photosystem II (PSII) undergoes a two-step photoreaction through electron transfer from the primary PQ electron acceptor QA, converting into plastoquinol (PQH2). However, the detailed mechanism of the QB reactions remains elusive. Here, we investigated the reaction mechanism of QB in cyanobacterial PSII core complexes using two time-revolved infrared (TRIR) methods: dispersive-type TRIR spectroscopy and rapid-scan Fourier transform infrared spectroscopy. Upon the first flash, the ∼140 μs phase is attributed to electron transfer from QA•- to QB, while the ∼2.2 and ∼440 ms phases are assigned to the binding of an internal PQ in a nearby cavity to the vacant QB site and an external PQ traveling to the QB site through channels, respectively, followed by immediate electron transfer. The resultant QB•- is suggested to be in equilibrium with QBH•, which is protonated at the distal oxygen. Upon the second flash, the ∼130 μs and ∼3.3 ms phases are attributed to electron transfer to QBH• and the protonation of QB•- followed by electron transfer, respectively, forming QBH-, which then immediately accepts a proton from D1-H215 at the proximal oxygen to become QBH2. The resultant D1-H215 anion is reprotonated in ∼22 ms via a pathway involving the bicarbonate ligand. The final ∼490 ms phase may reflect the release of PQH2 and its replacement with PQ. The present results highlight the importance of time-resolved infrared spectroscopy in elucidating the mechanism of QB reactions in PSII.

Folic acid in carboxymethylcellulose/polyethylene oxide electrospun nanofibers: preparation, release and stability

BACKGROUND

Folic acid (FA), a synthetically produced compound analogous to vitamin B9, also referred to as vitamin folate, is an essential compound in human health and faces challenges in stability during food processing. This study explores the incorporation of FA into carboxymethylcellulose (CMC) nanofibers using electrospinning to enhance its stability.

RESULTS

In this study, optimization of both electrospinning and solution parameters facilitated the fabrication of nanofibers. Furthermore, incorporating FA into CMC/polyethylene oxide (PEO) nanofibers resulted in thinner fibers, with an average diameter of 88 nm, characterized by a flat shape and smooth surface. Fourier transform infrared spectroscopic analysis demonstrated substantial hydrogen bonding interactions between FA and the polar groups present in CMC. This interaction contributed to an encapsulation efficiency of 94.5%, with a yield exceeding 87%. Thermal analysis highlighted mutual interference between CMC and PEO, with FA enhancing the thermal stability and reducing the melting temperatures and enthalpies of PEO, while also increasing the reaction heats of CMC. The encapsulated FA remained stable in acidic conditions, with only 6% degradation over 30 days, demonstrating the efficacy of CMC/PEO nanofibers in safeguarding FA against acidic environments. Moreover, the nanofibers provided a protective barrier against UV radiation, thereby preserving the stability of FA.

CONCLUSION

This study emphasizes the efficacy of CMC/PEO nanofibers as a protective matrix against FA degradation. The findings indicate that this innovative approach could significantly diversify the applications of FA in food fortification, addressing concerns regarding its vulnerability to temperature and hydrolysis reactions during food processing. © 2024 Society of Chemical Industry.

Unravelling Mn4Ca cluster vibrations in the S1, S2 and S3 states of the Kok-Joliot cycle of photosystem II

Vibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok-Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To better analyze the computational data and assign spectral peaks, we introduce an approach based on dipole-dipole correlation function of cluster moieties of the reaction center. Our analysis reveals variation in the infrared signature of the Mn4Ca cluster along the Kok-Joliot cycle, attributed to its increasing symmetry and rigidity resulting from the rising oxidation state of the Mn ions. Furthermore, we successfully assign the debated contributions in the frequency range around 600 cm-1. This computational methodology provides valuable insights for deciphering experimental infrared spectra and understanding the water oxidation process in both biological and artificial systems.

Independent Mutation of Two Bridging Carboxylate Ligands Stabilizes Alternate Conformers of the Photosynthetic O2-Evolving Mn4CaO5 Cluster in Photosystem II

The O2-evolving Mn4CaO5 cluster in photosystem II is ligated by six carboxylate residues. One of these is D170 of the D1 subunit. This carboxylate bridges between one Mn ion (Mn4) and the Ca ion. A second carboxylate ligand is D342 of the D1 subunit. This carboxylate bridges between two Mn ions (Mn1 and Mn2). D170 and D342 are located on opposite sides of the Mn4CaO5 cluster. Recently, it was shown that the D170E mutation perturbs both the intricate networks of H-bonds that surround the Mn4CaO5 cluster and the equilibrium between different conformers of the cluster in two of its lower oxidation states, S1 and S2, while still supporting O2 evolution at approximately 50% the rate of the wild type. In this study, we show that the D342E mutation produces much the same alterations to the cluster's FTIR and EPR spectra as D170E, while still supporting O2 evolution at approximately 20% the rate of the wild type. Furthermore, the double mutation, D170E + D342E, behaves similarly to the two single mutations. We conclude that D342E alters the equilibrium between different conformers of the cluster in its S1 and S2 states in the same manner as D170E and perturbs the H-bond networks in a similar fashion. This is the second identification of a Mn4CaO5 metal ligand whose mutation influences the equilibrium between the different conformers of the S1 and S2 states without eliminating O2 evolution. This finding has implications for our understanding of the mechanism of O2 formation in terms of catalytically active/inactive conformations of the Mn4CaO5 cluster in its lower oxidation states.

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

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.

Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II

Photosynthetic water oxidation takes place at the Mn₄CaO₅ cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S₀-S₄). Although the PSII structures have shown the presence of several channels around the Mn₄CaO₅ cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S₂ → S₃ transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S₃ → S₀ transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S₂ → S₃ transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S₃ → S₀ transition.

Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen

In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.

Alteration of the O2-Producing Mn4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand

The O₂-evolving Mn₄Ca cluster in photosystem II (PSII) is arranged as a distorted Mn₃Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn₄Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn₄Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn₄Ca cluster in the dark-stable S₁ state so that a high-spin form of the S₂ state is produced during the S₁-to-S₂ transition instead of the low-spin form that gives rise to the S₂ state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn₄Ca cluster without substantially eliminating O₂ evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn₄Ca cluster in the mechanism of O₂ formation.

Real-time isotopic methane detection using mid-infrared spectroscopy

A real-time, nondestructive mid-infrared (mid-IR) platform was proposed for isotopic methane detection. The measurement system consisted of a tunable mid-IR laser, a miniaturized gas chamber, and a mid-IR signal receiver. The isotope ratio of the ¹²CH₄/¹³CH₄ was identified by measuring the mid-IR spectrum at λ=3.2-3.5µm.In-situ¹²CH₄/¹³CH₄ monitoring was then achieved by tracing the characteristic mid-IR absorption peaks assigned to the ¹²CH₄ at λ=3.328µm and ¹³CH₄ at λ=3.340µm. The real-time methane isotope analysis can be applied to environmental monitoring and petroleum industries.

Molecular Binding of EuIII/CmIII by Stenotrophomonas bentonitica and Its Impact on the Safety of Future Geodisposal of Radioactive Waste

Microbial communities occurring in reference materials for artificial barriers (e.g., bentonites) in future deep geological repositories of radioactive waste can influence the migration behavior of radionuclides such as curium (Cm^III). This study investigates the molecular interactions between Cm^III and its inactive analogue europium (Eu^III) with the indigenous bentonite bacterium Stenotrophomonas bentonitica at environmentally relevant concentrations. Potentiometric studies showed a remarkably high concentration of phosphates at the bacterial cell wall compared to other bacteria, revealing the great potential of S. bentonitica for metal binding. Infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) confirmed the role of phosphates and carboxylate groups from the cell envelope in the bioassociation of Eu^III. Additionally, time-resolved laser-induced fluorescence spectroscopy (TRLFS) identified phosphoryl and carboxyl groups from bacterial envelopes, among other released complexing agents, to be involved in the Eu^III and Cm^III coordination. The ability of this bacterium to form a biofilm at the surface of bentonites allows them to immobilize trivalent lanthanide and actinides in the environment.

A Different hIAPP Polymorph Is Observed in Human Serum Than in Aqueous Buffer: Demonstration of a New Method for Studying Amyloid Fibril Structure Using Infrared Spectroscopy

There is enormous interest in measuring amyloid fibril structures, but most structural studies measure fibril formation in vitro using aqueous buffer. Ideally, one would like to measure fibril structure and mechanism under more physiological conditions. Toward this end, we have developed a method for studying amyloid fibril structure in human serum. Our approach uses isotope labeling, antibody depletion of the most abundant proteins (albumin and IgG), and infrared spectroscopy to measure aggregation in human serum with reduced protein content. Reducing the nonamyloid protein content enables the measurements by decreasing background signals but retains the full composition of salts, sugars, metal ions, etc. that are naturally present but usually missing from in vitro studies. We demonstrate the method by measuring the two-dimensional infrared (2D IR) spectra of isotopically labeled human islet amyloid polypeptide (hIAPP or amylin). We find that the fibril structure of hIAPP formed in serum differs from that formed via aggregation in aqueous buffer at residues Gly24 and Ala25, which reside in the putative "amyloidogenic core" or FGAIL region of the sequence. The spectra are consistent with extended parallel stacks of strands consistent with β-sheet-like structure, rather than a partially disordered loop that forms in aqueous buffer. These experiments provide a new method for using infrared spectroscopy to monitor the structure of proteins under physiological conditions and reveal the formation of a significantly different polymorph structure in the most important region of hIAPP.

Sorption and abiotic transformation of monensin by iron and manganese oxides

Monensin, an ionophore antibiotic, is commonly administered as a feed additive to cattle and poultry. A large percentage of the administered dose is excreted in animal waste, which is often applied to agricultural fields as fertilizer. The objective of this work is to gain insight into the fate of monensin in soil by investigating the interactions between monensin and common soil minerals, including sorption and transformation to unmonitored partial oxidation products. Batch sorption experiments across varying conditions (i.e., pH, ionic strength) and desorption experiments (i.e., methanol, PO₄^3-, methyl tert-butyl ether) were used to determine the extent to which a selection of common redox-active soil minerals [birnessite (δ-MnO₂), goethite (α-FeOOH), hematite (α-Fe₂O₃)] can bind and transform monensin. Monensin was bound by hematite (pH < 7.5, up to 7.5 mmol kg^-1), goethite (pH < 7.5, up to 3.4 mmol kg^-1), and birnessite (pH < 7, up to 0.1 mmol kg^-1). Combined sorption and transformation were the greatest for hematite and the lowest for birnessite. Sorption to hematite was more reversible than to goethite. Each desorption from goethite recovered <10% of sorbed monensin, whereas desorption from hematite recovered up to 69% of sorbed monensin, dependent on the solution. The potential for iron and manganese (hydr)oxides to abiotically transform monensin through reductive dissolution to partial oxidation products was evaluated by mass spectral analysis following sorption experiments. Additionally, the dominant sorption mechanism was inferred through ATR-FTIR spectroscopy, via examination of the carboxylate peak separation differences, on goethite and hematite to be bridging bidentate.

FTIR Microspectroscopic Analysis of the Water Oxidation Reaction in a Single Photosystem II Microcrystal

Microcrystals of photosystem II (PSII) have recently been used to investigate the intermediate structures of the water oxidizing complex during water oxidation by serial femtosecond crystallography using X-ray free electron lasers. To clarify the water oxidation mechanism, it is crucial to know whether the reaction proceeds properly in the microcrystals. In this work, we monitored the water oxidation reaction in a single PSII microcrystal using Fourier transform infrared (FTIR) microspectroscopy with the transmission method. Flash-induced micro-FTIR difference spectra of S-state transitions in a PSII microcrystal showed features virtually identical to the corresponding spectra previously obtained using the attenuated total reflection method for multiple microcrystals, representing the reactions near the crystal surface, as well as the spectra in solution. This observation indicates that the reaction processes of water oxidation proceed with relatively high efficiencies retaining native intermediate structures in the entire inside of a PSII microcrystal.

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.

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.

Influence of a "Dangling" Co(II) Ion Bound to a [MnCo3O4] Oxo Cubane

Cobalt(II), in the presence of acetate and nitrate, quantitatively adds to the manganese-cobalt oxido cubane Mn^IVCo^III₃O₄(OAc)₅(py)₃ (1) to furnish the pentametallic dangler complex Mn^IVCo^III₃Co^IIO₄(OAc)₆(NO₃)(py)₃ (2). Complex 2 is structurally reminiscent of photosystem II's oxygen-evolving center, and is a rare example of a transition-metal "dangler" complex. Superconducting quantum interference device magnetometry and density functional theory calculations characterize 2 as having an S = 0 ground state arising from antiferromagnetic coupling between the Co^II and Mn^IV ions. At higher temperatures, an uncoupled state dominates. The voltammogram of 2 has four electrochemical events, two more than that of its parent cubane 1, suggesting that addition of the dangler increases available redox states. Structural, electrochemical, and magnetic comparisons of complexes 1 and 2 allow a better understanding of the dangler's influence on a cubane.

D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine YZ for proton exit during water oxidation

In photosynthetic water oxidation, two water molecules are converted into one oxygen molecule and four protons at the Mn₄CaO₅ cluster in photosystem II (PSII) via the S-state cycle. Efficient proton exit from the catalytic site to the lumen is essential for this process. However, the exit pathways of individual protons through the PSII proteins remain to be identified. In this study, we examined the involvement of a hydrogen-bond network near the redox-active tyrosine Y_Z in proton transfer during the S-state cycle. We focused on spectroscopic analyses of a site-directed variant of D1-Asn-298, a residue involved in a hydrogen-bond network near Y_Z We found that the D1-N298A mutant of Synechocystis sp. PCC 6803 exhibits an O₂ evolution activity of ∼10% of the wild-type. D1-N298A and the wild-type D1 had very similar features of thermoluminescence glow curves and of an FTIR difference spectrum upon Y_Z oxidation, suggesting that the hydrogen-bonded structure of Y_Z and electron transfer from the Mn₄CaO₅ cluster to Y_Z were little affected by substitution. In the D1-N298A mutant, however, the flash-number dependence of delayed luminescence showed a monotonic increase without oscillation, and FTIR difference spectra of the S-state cycle indicated partial and significant inhibition of the S₂ → S₃ and S₃ → S₀ transitions, respectively. These results suggest that the D1-N298A substitution inhibits the proton transfer processes in the S₂ → S₃ and S₃ → S₀ transitions. This in turn indicates that the hydrogen-bond network near Y_Z can be functional as a proton transfer pathway during photosynthetic water oxidation.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn₄O₅ inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O₂ evolution. The structure of the dark-stable S₁ state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S₁ state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S₁ state is exposed to light, the S₁ state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S₁ → S₂ transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S₂ → S₃ transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S₃ structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O₂ evolution.

Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II

During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO2, in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn4CaO5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S1 to S2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III)2Mn(IV)2, satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.

Deprotonation of Water/Hydroxo Ligands in Clusters Mimicking the Water Oxidizing Complex of PSII and Its Effect on the Vibrational Frequencies of Ligated Carboxylate Groups

The IR absorptions of several first-shell carboxylate ligands of the water oxidizing complex (WOC) have been experimentally shown to be unaffected by oxidation state changes in the WOC during its catalytic cycle. Several model clusters that mimic the Mn4O5Ca core of the WOC in the S1 state, with electronic configurations that correspond to both the so-called "high" and "low" oxidation paradigms, were investigated. Deprotonation at W2, W1, or O3 sites was found to strongly reduce carboxylate ligand frequency shifts on oxidation of the metal cluster. The frequency shifts were smallest in neutrally charged clusters where the initial mean Mn oxidation state was +3, with W2 as an hydroxide and O5 a water. Deprotonation also reduced and balanced the oxidation energy of all clusters in successive oxidations.

Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures

All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.

Effect of concomitant oxidation and deprotonation of hydrated Mn centres in rationalising the FTIR difference silence of D1-Asp170 in Photosystem II

The observation of negligible FTIR differences in carboxylate vibrational modes for the D1-Asp170 residue of Photosystem II (PSII) on successive one-electron oxidations of the Mn4CaO5 oxygen-evolving complex (OEC) is counterintuitive in light of the apparent ligation of D1-Asp170 to an oxidisable Mn ion in the X-ray crystallographic structures of PSII. Here, we show computational support for the hypothesis that suppression of the FTIR difference spectrum in the 1100cm(-1) to 1700cm(-1) region of D1-Asp170 occurs by concomitant Mn oxidation and deprotonation of water ligands bound to the ligated metal centre. Density functional theory calculations on the model species [Mn(II)Ca(COOH)(OH)2(H2O)2](+) over two successive oxidations of the Mn ion are performed, where those oxidations are accompanied by deprotonation of water and μ-hydroxo ligands coordinated to the Mn ion. In contrast, dramatically increased FTIR difference activity is observed where these oxidations are unaccompanied by proton loss.

Infrared Detection of a Proton Released from Tyrosine YD to the Bulk upon Its Photo-oxidation in Photosystem II

Photosystem II (PSII) has two symmetrically located, redox-active tyrosine residues, YZ and YD. Whereas YZ mediates the electron transfer from the water-oxidizing center to P680 in the main electron transfer pathway, YD functions as a peripheral electron donor to P680. To understand the mechanism of this functional difference between YZ and YD, it is essential to know where the proton is transferred upon its oxidation in the proton-coupled electron transfer process. In this study, we used Fourier transform infrared (FTIR) spectroscopy to examine whether the proton from YD is released from the protein into the bulk. The proton detection method previously used for water oxidation in PSII [Suzuki et al. (2009) J. Am. Chem. Soc. 131, 7849-7857] was applied to YD; a proton released into the bulk upon YD oxidation was trapped by a high-concentration Mes buffer, and the protonation reaction of Mes was monitored by FTIR difference spectroscopy. It was shown that 0.84 ± 0.10 protons are released into the bulk by oxidation of YD in one PSII center. This result indicates that the proton of YD is not transferred to the neighboring D2-His198 but is released from the protein; this is in sharp contrast to the YZ reaction, in which a proton is transferred to D1-His190 through a strong hydrogen bond. This functional difference is caused by differences in the hydrogen-bonded structures of YD and YZ, which are determined by the hydrogen bond partners at the Nπ sites of these His residues, i.e., D2-Arg294 and D1-Asn298, which function as a hydrogen bond donor and acceptor, respectively. This FTIR spectroscopy result supports the recent theoretical prediction [Saito et al. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 7690-7695] based on the X-ray crystallographic structure of PSII and explains the different rates of the redox reactions of YD and YZ.

Towards a mechanistic understanding of carbon stabilization in manganese oxides

Minerals stabilize organic carbon (OC) in sediments, thereby directly affecting global climate at multiple scales, but how they do it is far from understood. Here we show that manganese oxide (Mn oxide) in a water treatment works filter bed traps dissolved OC as coatings build up in layers around clean sand grains at 3%w/wC. Using spectroscopic and thermogravimetric methods, we identify two main OC fractions. One is thermally refractory (>550 °C) and the other is thermally more labile (<550 °C). We postulate that the thermal stability of the trapped OC is due to carboxylate groups within it bonding to Mn oxide surfaces coupled with physical entrapment within the layers. We identify a significant difference in the nature of the surface-bound OC and bulk OC . We speculate that polymerization reactions may be occurring at depth within the layers. We also propose that these processes must be considered in future studies of OC in natural systems.

Minerals are known to stabilize organic carbon in sediments, affecting biogeochemical cycles and global climate, but the mechanism is not understood. Here, the authors suggest that manganese oxides can trap organic carbon and may act as a ‘mineral pump', transforming carbon between labile and refractory forms.

Light-dependent production of dioxygen in photosynthesis

Oxygen, that supports all aerobic life, is abundant in the atmosphere because of its constant regeneration by photosynthetic water oxidation, which is catalyzed by a Mn₄CaO₅ cluster in photosystem II (PS II), a multi subunit membrane protein complex. X-ray and other spectroscopy studies of the electronic and geometric structure of the Mn₄CaO₅ cluster as it advances through the intermediate states have been important for understanding the mechanism of water oxidation. The results and interpretations, especially from X-ray spectroscopy studies, regarding the geometric and electronic structure and the changes as the system proceeds through the catalytic cycle will be summarized in this review. This review will also include newer methodologies in time-resolved X-ray diffraction and spectroscopy that have become available since the commissioning of the X-ray free electron laser (XFEL) and are being applied to study the oxygen-evolving complex (OEC). The femtosecond X-ray pulses of the XFEL allows us to outrun X-ray damage at room temperature, and the time-evolution of the photo-induced reaction can be probed using a visible laser-pump followed by the X-ray-probe pulse. XFELs can be used to simultaneously determine the light-induced protein dynamics using crystallography and the local chemistry that occurs at the catalytic center using X-ray spectroscopy under functional conditions. Membrane inlet mass spectrometry has been important for providing direct information about the exchange of substrate water molecules, which has a direct bearing on the mechanism of water oxidation. Moreover, it has been indispensable for the time-resolved X-ray diffraction and spectroscopy studies and will be briefly reviewed in this chapter. Given the role of PS II in maintaining life in the biosphere and the future vision of a renewable energy economy, understanding the structure and mechanism of the photosynthetic water oxidation catalyst is an important goal for the future.

Structural changes in the oxygen-evolving complex of photosystem II induced by the S1 to S2 transition: A combined XRD and QM/MM study

The S₁ → S₂ transition of the oxygen-evolving complex (OEC) of photosystem II does not involve the transfer of a proton to the lumen and occurs at cryogenic temperatures. Therefore, it is commonly thought to involve only Mn oxidation without any significant change in the structure of the OEC. Here, we analyze structural changes upon the S₁ → S₂ transition, as revealed by quantum mechanics/molecular mechanics methods and the isomorphous difference Fourier method applied to serial femtosecond X-ray diffraction data. We find that the main structural change in the OEC is in the position of the dangling Mn and its coordination environment.

Warwick Hillier: a tribute

Warwick Hillier (October 18, 1967-January 10, 2014) made seminal contributions to our understanding of photosynthetic water oxidation employing membrane inlet mass spectrometry and FTIR spectroscopy. This article offers a collection of historical perspectives on the scientific impact of Warwick Hillier's work and tributes to the personal impact his life and ideas had on his collaborators and colleagues.

FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in Photosystem II

The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn₄CaO₅ cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn₄CaO₅ cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn₄CaO₅ cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn₄CaO₅ cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn₄CaO₅ catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Fourier transform infrared difference and time-resolved infrared detection of the electron and proton transfer dynamics in photosynthetic water oxidation

Photosynthetic water oxidation, which provides the electrons necessary for CO₂ reduction and releases O₂ and protons, is performed at the Mn₄CaO₅ cluster in photosystem II (PSII). In this review, studies that assessed the mechanism of water oxidation using infrared spectroscopy are summarized focusing on electron and proton transfer dynamics. Structural changes in proteins and water molecules between intermediates known as Si states (i=0-3) were detected using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Electron flow in PSII and proton release from substrate water were monitored using the infrared changes in ferricyanide as an exogenous electron acceptor and Mes buffer as a proton acceptor. Time-resolved infrared (TRIR) spectroscopy provided information on the dynamics of proton-coupled electron transfer during the S-state transitions. In particular, a drastic proton movement during the lag phase (~200μs) before electron transfer in the S3→S0 transition was detected directly by monitoring the infrared absorption of a polarizable proton in a hydrogen bond network. Furthermore, the proton release pathways in the PSII proteins were analyzed by FTIR difference measurements in combination with site-directed mutagenesis, isotopic substitutions, and quantum chemical calculations. Therefore, infrared spectroscopy is a powerful tool for understanding the molecular mechanism of photosynthetic water oxidation. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

ATR-FTIR spectroscopic evidence for biomolecular phosphorus and carboxyl groups facilitating bacterial adhesion to iron oxides

Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy has been used to probe the binding of bacteria to hematite (α-Fe2O3) and goethite (α-FeOOH). In situ ATR-FTIR experiments with bacteria (Pseudomonas putida, Pseudomonas aeruginosa, Escherichia coli), mixed amino acids, polypeptide extracts, deoxyribonucleic acid (DNA), and a suite of model compounds were conducted. These compounds represent carboxyl, catecholate, amide, and phosphate groups present in siderophores, amino acids, polysaccharides, phospholipids, and DNA. Due in part to the ubiquitous presence of carboxyl groups in biomolecules, numerous IR peaks corresponding to outer-sphere or unbound (1400 cm(-1)) and inner-sphere (1310-1320 cm(-1)) coordinated carboxyl groups are noted following reaction of bacteria and biomolecules with α-Fe2O3 and α-FeOOH. However, the data also reveal that the presence of low-level amounts (i.e., 0.45-0.79%) of biomolecular phosphorous groups result in strong IR bands at ∼1043 cm(-1), corresponding to inner-sphere Fe-O-P bonds, underscoring the importance of bacteria associated P-containing groups in biomolecule and cell adhesion. Spectral comparisons also reveal slightly greater P-O-Fe contributions for bacteria (Pseudomonad, E. coli) deposited on α-FeOOH, as compared to α-Fe2O3. This data demonstrates that slight differences in bacterial adhesion to Fe oxides can be attributed to bacterial species and Fe-oxide minerals. However, more importantly, the strong binding affinity of phosphate in all bacteria samples to both Fe-oxides results in the formation of inner-sphere Fe-O-P bonds, signifying the critical role of biomolecular P in the initiation of bacterial adhesion.

Ab Initio modeling of the effect of oxidation coupled with HnO deprotonation on carboxylate ligands in Mn/Ca clusters

Oxidation of some manganese complexes containing both carboxylate and water/hydroxo ligands does not result in changes to the carboxylate stretching frequencies. The water oxidizing complex of photosystem II is one motivating example. On the basis of electronic structure theory calculations, we here suggest that the deprotonation of water or hydroxo ligands minimizes changes in the vibrational frequencies of coligating carboxylates, rendering the carboxylate modes "invisible" in FTIR difference spectroscopy. This deprotonation of water/hydroxo ligands was also found to balance the redox potentials of the Mn(II)/Mn(III) and Mn(III)/Mn(IV) couples, allowing the possibility for successive manganese oxidations at a relatively constant redox potential.

Participation of glutamate-333 of the D1 polypeptide in the ligation of the Mn₄CaO₅ cluster in photosystem II

In the 1.9 Å structural model of photosystem II (PDB: 3ARC), the amino acid residue Glu333 of the D1 polypeptide coordinates to the oxygen-evolving Mn₄CaO₅ cluster. This residue appears to be highly significant in that it bridges the two Mn ions (Mn(B3) and the "dangling" Mn(A4)) that are also bridged by the oxygen atom O5. This oxygen atom has been proposed to be derived from one of two substrate water molecules and to become incorporated into the product dioxygen molecule during the final step in the catalytic cycle. In addition, the backbone nitrogen of D1-Glu333 interacts directly with a nearby Cl⁻ atom. To further explore the influence of this structurally unique residue on the properties of the Mn₄CaO₅ cluster, the D1-E333Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray absorption, and FTIR difference spectroscopy. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild-type. In addition, the oxygen flash yields exhibited normal period-four oscillations having normal S state parameters, although the yields were lower, indicative of the mutant's lower steady-state dioxygen evolution rate of approximately 30% compared to that of the wild-type. The S₁ state Mn-XANES and Mn-EXAFS and S₂ state multiline EPR signals of purified D1-E333Q PSII core complexes closely resembled those of wild-type, aside from having lower amplitudes. The S(n+1)-minus-S(n) FTIR difference spectra showed only minor alterations to the carbonyl, amide, and carboxylate stretching regions. However, the mutation eliminated a negative peak at 3663 cm⁻¹ in the weakly H-bonding O-H stretching region of the S₂-minus-S₁ FTIR difference spectrum and caused an approximately 9 cm⁻¹ downshift of the negative feature in this region of the S₁-minus-S₀ FTIR difference spectrum. We conclude that fully functional Mn₄CaO₅ clusters assemble in the presence of the D1-E333Q mutation but that the mutation decreases the yield of assembled clusters and alters the H-bonding properties of one or more water molecules or hydroxide groups that are located on or near the Mn₄CaO₅ cluster and that either deprotonate or form stronger hydrogen bonds during the S₀ to S₁ and S₁ to S₂ transitions.

Functional roles of D2-Lys317 and the interacting chloride ion in the water oxidation reaction of photosystem II as revealed by fourier transform infrared analysis

Photosynthetic water oxidation in plants and cyanobacteria is catalyzed by a Mn4CaO5 cluster within the photosystem II (PSII) protein complex. Two Cl(-) ions bound near the Mn4CaO5 cluster act as indispensable cofactors, but their functional roles remain to be clarified. We have investigated the role of the Cl(-) ion interacting with D2-K317 (designated Cl-1) by Fourier transform infrared spectroscopy (FTIR) analysis of the D2-K317R mutant of Synechocystis sp. PCC 6803 in combination with Cl(-)/NO3(-) replacement. The D2-K317R mutation perturbed the bands in the regions of the COO(-) stretching and backbone amide vibrations in the FTIR difference spectrum upon the S1 → S2 transition. In addition, this mutation altered the (15)N isotope-edited NO3(-) bands in the spectrum of NO3(-)-treated PSII. These results provide the first experimental evidence that the Cl-1 site is coupled with the Mn4CaO5 cluster and its interaction is affected by the S1 → S2 transition. It was also shown that a negative band at 1748 cm(-1) arising from COOH group(s) was altered to a positive intensity by the D2-K317R mutation as well as by NO3(-) treatment, suggesting that the Cl-1 site affects the pKa of COOH/COO(-) group(s) near the Mn4CaO5 cluster in a common hydrogen bond network. Together with the observation that the efficiency of the S3 → S0 transition significantly decreased in the core complexes of D2-K317R upon moderate dehydration, it is suggested that D2-K317 and Cl-1 are involved in a proton transfer pathway from the Mn4CaO5 cluster to the lumen, which functions in the S3 → S0 transition.

Structural changes of the oxygen-evolving complex in photosystem II during the catalytic cycle

The oxygen-evolving complex (OEC) in the membrane-bound protein complex photosystem II (PSII) catalyzes the water oxidation reaction that takes place in oxygenic photosynthetic organisms. We investigated the structural changes of the Mn4CaO5 cluster in the OEC during the S state transitions using x-ray absorption spectroscopy (XAS). Overall structural changes of the Mn4CaO5 cluster, based on the manganese ligand and Mn-Mn distances obtained from this study, were incorporated into the geometry of the Mn4CaO5 cluster in the OEC obtained from a polarized XAS model and the 1.9-Å high resolution crystal structure. Additionally, we compared the S1 state XAS of the dimeric and monomeric form of PSII from Thermosynechococcus elongatus and spinach PSII. Although the basic structures of the OEC are the same for T. elongatus PSII and spinach PSII, minor electronic structural differences that affect the manganese K-edge XAS between T. elongatus PSII and spinach PSII are found and may originate from differences in the second sphere ligand atom geometry.