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

Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography

Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions.

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.

Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation

In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.

Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors

The oxygen-evolving complex (OEC) of Photosystem II catalyzes the water-splitting reaction using solar energy. Thus, understanding the reaction mechanism will inspire the design of biomimetic artificial catalysts that convert solar energy to chemical energy. Conceptual Density Functional Theory (CDFT) focuses on understanding the reactivity of molecules and the atomic contribution to the overall nucleophilicity and electrophilicity of the molecule using quantum descriptors. However, this method has not been applied to the OEC before. Here, we use Fukui functions and the dual descriptor to provide quantitative measures of the nucleophilicity and electrophilicity of oxygens in the OEC for different models in different S states. Our results show that the μ-oxo bridges connected to terminal Mn4 are nucleophilic, and those in the cube formed by Mn1, Mn2, and Mn3 are mostly electrophilic. The dual descriptors of the bridging oxygens in the OEC showed a similar reactivity to that of bridging oxygens in Mn model compounds. However, the terminal water W1, which is bound to Mn4, showed very strong reactivity in some of the S3 models. Thus, our calculations support the model that proposes the formation of the O2 molecule through nucleophilic attack by a terminal water.

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.

Mutation of a metal ligand stabilizes the high-spin form of the S2 state in the O2-producing Mn4CaO5 cluster of photosystem II

The residue D1-D170 bridges Mn4 with the Ca ion in the O₂-evolving Mn₄CaO₅ cluster of Photosystem II. Recently, the D1-D170E mutation was shown to substantially alter the S_n+1-minus-S_n FTIR difference spectra [Debus RJ (2021) Biochemistry 60:3841-3855]. The mutation was proposed to alter the equilibrium between different Jahn-Teller conformers of the S₁ state such that (i) a different S₁ state conformer is stabilized in D1-D170E than in wild-type and (ii) the S₁ to S₂ transition in D1-D170E produces a high-spin form of the S₂ state rather than the low-spin form that is produced in wild-type. In this study, we employed EPR spectroscopy to test if a high-spin form of the S₂ state is formed preferentially in D1-D170E PSII. Our data show that illumination of dark-adapted D1-D170E PSII core complexes does indeed produce a high-spin form of the S₂ state rather than the low-spin multiline form that is produced in wild-type. This observation provides further experimental support for a change in the equilibrium between S state conformers in both the S₁ and S₂ states in a site-directed mutant that retains substantial O₂ evolving activity.

The electron-proton bottleneck of photosynthetic oxygen evolution

Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S₄ state-which was postulated half a century ago¹ and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O₂ formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O₂ formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S₄ state as the oxygen-radical state; its formation is followed by fast O-O bonding and O₂ release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O₂ formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.

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.

Post-translational amino acid conversion in photosystem II as a possible origin of photosynthetic oxygen evolution

Photosynthetic oxygen evolution is performed at the Mn cluster in photosystem II (PSII). The advent of this reaction on ancient Earth changed its environment by generating an oxygenic atmosphere. However, how oxygen evolution originated during the PSII evolution remains unknown. Here, we characterize the site-directed mutants at the carboxylate ligands to the Mn cluster in cyanobacterial PSII. A His residue replaced for D1-D170 is found to be post-translationally converted to the original Asp to recover oxygen evolution. Gln/Asn residues in the mutants at D1-E189/D1-D342 are also converted to Glu/Asp, suggesting that amino-acid conversion is a common phenomenon at the ligand sites of the Mn cluster. We hypothesize that post-translational generation of carboxylate ligands in ancestral PSII could have led to the formation of a primitive form of the Mn cluster capable of partial water oxidation, which could have played a crucial role in the evolutionary process of photosynthetic oxygen evolution.

How photosynthetic oxygen evolution is originated on ancient Earth is unknown. Here, the authors find that some amino acid residues at the ligand sites of the Mn cluster can be posttranslationally converted to the original carboxylate residues, which could have contributed to the evolutionary process of photosynthetic oxygen evolution.

Dangling Carboxylic Group That Participates in O-O Bond Formation Reaction to Promote Water Oxidation Catalyzed by a Ruthenium Complex: Experimental Evidence of an Oxide Relay Pathway

Two mononuclear ruthenium(II) complexes of the types [Ru(trpy)(HL¹)(OH₂)]²⁺ (1^Aq) and [Ru(trpy)(L²-κ-N²O)] (2) [where trpy = 2,2':6',2″-terpyridine, HL¹ = 2-(2-pyridyl)benzimidazole, H₂L² = 2-(pyridin-2-yl)-1H-benzo[d]imidazole-4-carboxylic acid] have been synthesized and thoroughly characterized by analytical and spectroscopic [UV-vis, NMR, high-resolution mass spectrometry, and IR] techniques. Complex 1^Aq has been further characterized by X-ray crystallography. In an acidic aqueous medium (pH 1), complex 2 undergoes carboxylate/water exchange readily to form an aqua-ligated complex, [Ru(trpy)(H₂L²-κ-N²)(OH₂)]²⁺ (2^Aq), having a dangling carboxylic group. This exchange phenomenon has been followed by IR, ¹H NMR, and UV-vis spectroscopic techniques. Electrochemical analyses of 1^Aq and 2^Aq (Pourbaix diagram) suggest the generation of a formal Ru^V═O species that can potentially promote the oxidation of water. A comparative study of the water oxidation activity catalyzed by 1^Aq and 2^Aq is reported here to see the effect of a dangling carboxylic group in the catalytic performance. Complex 2^Aq shows an enormously higher rate of reaction than 1^Aq. The pendant carboxylic group in 2^Aq participates in an intramolecular O-O bond formation reaction with the reactive formal Ru^V═O unit to form a percarboxylate intermediate and provides an electron-deficient carbon center where water nucleophilic attack takes place. The isotope labeling experiment using ¹⁸O-labeled water verifies the attack of water at the carbon center of the carboxylic group rather than a direct attack at the oxo of the formal Ru^V═O unit. The present work provides experimental evidence of the uncommon functionality of the carboxylic group, the oxide relay, in molecular water oxidation chemistry.

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm⁻¹ region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm⁻¹ originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm⁻¹ to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm⁻¹, and in some cases of ∼1 cm⁻¹. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.

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.

Effects of Stromal and Lumenal Side Perturbations on the Redox Potential of the Primary Quinone Electron Acceptor QA in Photosystem II

The primary quinone electron acceptor Q_A is a key component in the electron transfer regulation in photosystem II (PSII), and hence accurate estimation of its redox potential, E_m(Q_A^-/Q_A), is crucial in understanding the regulatory mechanism. Although fluorescence detection has been extensively used for monitoring the redox state of Q_A, it was recently suggested that this method tends to provide a higher E_m(Q_A^-/Q_A) estimate depending on the sample status due to the effect of measuring light [Kato et al. (2019) Biochim. Biophys. Acta 1860, 148082]. In this study, we applied the Fourier transform infrared (FTIR) spectroelectrochemistry, which uses non-reactive infrared light to monitor the redox state of Q_A, to investigate the effects of stromal- and lumenal-side perturbations on E_m(Q_A^-/Q_A) in PSII. It was shown that replacement of bicarbonate bound to the non-heme iron with formate upshifted E_m(Q_A^-/Q_A) by ∼55 mV, consistent with the previous fluorescence measurement. In contrast, an E_m(Q_A^-/Q_A) difference between binding of 3-(3,4-dichlorophenyl)-1,1-dimethylurea and bromoxynil was found to be ∼30 mV, which is much smaller than the previous estimate, ∼100 mV, by the fluorescence method. This ∼30 mV difference was verified by the decay kinetics of the S₂Q_A^- recombination. On the lumenal side, Mn depletion hardly affected the E_m(Q_A^-/Q_A), confirming the previous FTIR result. However, removal of the extrinsic proteins by NaCl or CaCl₂ wash downshifted the E_m(Q_A^-/Q_A) by 14-20 mV. These results suggest that electron flow through Q_A is regulated by changes both on the stromal and lumenal sides of PSII.

Proton and Water Transfer Pathways in the S2 → S3 Transition of the Water-Oxidizing Complex in Photosystem II: Time-Resolved Infrared Analysis of the Effects of D1-N298A Mutation and NO3- Substitution

Photosynthetic water oxidation is performed through a light-driven cycle of five intermediates (S₀-S₄ states) in photosystem II (PSII). The S₂ → S₃ transition, which involves concerted water and proton transfer, is a key process for understanding the water oxidation mechanism. Here, to identify the water and proton transfer pathways during the S₂ → S₃ transition, we examined the effects of D1-N298A mutation and NO₃^- substitution for Cl^-, which perturbed the O1 and Cl channels, respectively, on the S₂ → S₃ kinetics using time-resolved infrared spectroscopy. The S₂ → S₃ transition was retarded both upon NO₃^- substitution and upon D1-N298A mutation, whereas it was unaffected by further NO₃^- substitution in N298A PSII. The H/D kinetic isotope effect in N298A PSII was relatively small, revealing that water transfer is a rate-limiting step in this mutant. From these results, it was suggested that during the S₂ → S₃ transition, water delivery and proton release occur through the O1 and Cl channels, respectively.

Activation energies for two steps in the S2→ S3 transition of photosynthetic water oxidation from time-resolved single-frequency infrared spectroscopy

The mechanism of water oxidation by the Photosystem II (PSII) protein-cofactor complex is of high interest, but specifically, the crucial coupling of protonation dynamics to electron transfer (ET) and dioxygen chemistry remains insufficiently understood. We drove spinach-PSII membranes by nanosecond-laser flashes synchronously through the water-oxidation cycle and traced the PSII processes by time-resolved single-frequency infrared (IR) spectroscopy in the spectral range of symmetric carboxylate vibrations of protein side chains. After the collection of IR-transients from 100 ns to 1 s, we analyzed the proton-removal step in the S₂ ⇒ S₃ transition, which precedes the ET that oxidizes the Mn₄CaO_x-cluster. Around 1400 cm^-1, pronounced changes in the IR-transients reflect this pre-ET process (∼40 µs at 20 °C) and the ET step (∼300 µs at 20 °C). For transients collected at various temperatures, unconstrained multi-exponential simulations did not provide a coherent set of time constants, but constraining the ET time constants to previously determined values solved the parameter correlation problem and resulted in an exceptionally high activation energy of 540 ± 30 meV for the pre-ET step. We assign the pre-ET step to deprotonation of a group that is re-protonated by accepting a proton from the substrate-water, which binds concurrently with the ET step. The analyzed IR-transients disfavor carboxylic-acid deprotonation in the pre-ET step. Temperature-dependent amplitudes suggest thermal equilibria that determine how strongly the proton-removal step is reflected in the IR-transients. Unexpectedly, the proton-removal step is only weakly reflected in the 1400 cm^-1 transients of PSII core complexes of a thermophilic cyanobacterium (T. elongatus).

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

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.

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

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

Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

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.

Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II

Photosynthetic water oxidation is performed in photosystem II (PSII) through a light-driven cycle of intermediates called S states (S₀-S₄) at the water oxidizing center. Time-resolved serial femtosecond crystallography (SFX) has recently been applied to the microcrystals of PSII to obtain the structural information on these intermediates. However, it remains unanswered whether the reactions efficiently proceed throughout the S-state cycle retaining the native structures of the intermediates in PSII crystals. We investigated the water oxidation reactions in the PSII microcrystals using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. In comparison with the FTIR spectra in solution, it was shown that all of the metastable intermediates in the microcrystals retained their native structures, and the efficiencies of the S-state transitions remained relatively high, although those of the S₂ → S₃ and S₃ → S₀ transitions were slightly lowered possibly due to some restriction of water movement in the crystals.

Inhibitory and Non-Inhibitory NH3 Binding at the Water-Oxidizing Manganese Complex of Photosystem II Suggests Possible Sites and a Rearrangement Mode of Substrate Water Molecules

The identity and rearrangements of substrate water molecules in photosystem II (PSII) water oxidation are of great mechanistic interest and addressed herein by comprehensive analysis of NH₄⁺/NH₃ binding. Time-resolved detection of O₂ formation and recombination fluorescence as well as Fourier transform infrared (FTIR) difference spectroscopy on plant PSII membrane particles reveals the following. (1) Partial inhibition in NH₄Cl buffer occurs with a pH-independent binding constant of ∼25 mM, which does not result from decelerated O₂ formation, but from complete blockage of a major PSII fraction (∼60%) after reaching the Mn(IV)₄ (S₃) state. (2) The non-inhibited PSII fraction advances through the reaction cycle, but modified nuclear rearrangements are suggested by FTIR difference spectroscopy. (3) Partial inhibition can be explained by anticooperative (mutually exclusive) NH₃ binding to one inhibitory and one non-inhibitory site; these two sites may correspond to two water molecules terminally bound to the "dangling" Mn ion. (4) Unexpectedly strong modifications of the FTIR difference spectra suggest that in the non-inhibited PSII, ammonia binding obliterates the need for some of the nuclear rearrangements occurring in the S₂-S₃ transition as well as their reversal in the O₂ formation transition, in line with the carousel mechanism [Askerka, M., et al. (2015) Biochemistry 54, 5783]. (5) We observe the same partial inhibition of PSII by NH₄Cl also for thylakoid membranes prepared from mesophilic and thermophilic cyanobacteria, suggesting that the results described above are valid for plant and cyanobacterial PSII.

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.

Genetically introduced hydrogen bond interactions reveal an asymmetric charge distribution on the radical cation of the special-pair chlorophyll P680

The special-pair chlorophyll (Chl) P680 in photosystem II has an extremely high redox potential (E_m ) to enable water oxidation in photosynthesis. Significant positive-charge localization on one of the Chl constituents, P_D1 or P_D2, in P680⁺ has been proposed to contribute to this high E_m To identify the Chl molecule on which the charge is mainly localized, we genetically introduced a hydrogen bond to the 13¹-keto C=O group of P_D1 and P_D2 by changing the nearby D1-Val-157 and D2-Val-156 residues to His, respectively. Successful hydrogen bond formation at P_D1 and P_D2 in the obtained D1-V157H and D2-V156H mutants, respectively, was monitored by detecting 13¹-keto C=O vibrations in Fourier transfer infrared (FTIR) difference spectra upon oxidation of P680 and the symmetrically located redox-active tyrosines Y_Z and Y_D, and they were simulated by quantum-chemical calculations. Analysis of the P680⁺/P680 FTIR difference spectra of D1-V157H and D2-V156H showed that upon P680⁺ formation, the 13¹-keto C=O frequency upshifts by a much larger extent in P_D1 (23 cm^-1) than in P_D2 (<9 cm^-1). In addition, thermoluminescence measurements revealed that the D1-V157H mutation increased the E_m of P680 to a larger extent than did the D2-V156H mutation. These results, together with the previous results for the mutants of the His ligands of P_D1 and P_D2, lead to a definite conclusion that a charge is mainly localized to P_D1 in P680<sup/>.