Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins

Tracking the first electron transfer step at the donor side of oxygen-evolving photosystem II by time-resolved infrared spectroscopy

In oxygen-evolving photosystem II (PSII), the multi-phasic electron transfer from a redox-active tyrosine residue (TyrZ) to a chlorophyll cation radical (P680+) precedes the water-oxidation chemistry of the S-state cycle of the Mn4Ca cluster. Here we investigate these early events, observable within about 10 ns to 10 ms after laser-flash excitation, by time-resolved single-frequency infrared (IR) spectroscopy in the spectral range of 1310-1890 cm-1 for oxygen-evolving PSII membrane particles from spinach. Comparing the IR difference spectra at 80 ns, 500 ns, and 10 µs allowed for the identification of quinone, P680 and TyrZ contributions. A broad electronic absorption band assignable P680+ was used to trace largely specifically the P680+ reduction kinetics. The experimental time resolution was taken into account in least-square fits of P680+ transients with a sum of four exponentials, revealing two nanosecond phases (30-46 ns and 690-1110 ns) and two microsecond phases (4.5-8.3 µs and 42 µs), which mostly exhibit a clear S-state dependence, in agreement with results obtained by other methods. Our investigation paves the road for further insight in the early events associated with TyrZ oxidation and their role in the preparing the PSII donor side for the subsequent water oxidation chemistry.

Release of a Proton and Formation of a Low-Barrier Hydrogen Bond between Tyrosine D and D2-His189 in Photosystem II

In photosystem II (PSII), the second-lowest oxidation state (S₁) of the oxygen-evolving Mn₄CaO₅ cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S₀) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential (E _m) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The E _m depends on the H⁺ position along the low-barrier H-bond, e.g., 680 mV when the H⁺ is at the D2-His189 moiety and 800 mV when the H⁺ is at the TyrD moiety, which can explain why TyrD mediates both the S₀ to S₁ oxidation and the S₂ to S₁ reduction.

Phenotypic changes in microalgae at acidic pH mediate their tolerance to higher concentrations of transition metals

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Acid-tolerant microalgae were grown at pH 3.5 and 6.7 in presence of heavy metals (HMs).

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HMs-induced phenotypic changes in microalgae were evaluated by ATR-FTIR spectroscopy.

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Higher HMs bioavailability affected microalgae more at pH 6.7 than pH 3.5.

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Acclimation of microalgal strains to acidic pH significantly alleviates HMs toxicity.

Acclimatory phenotypic response is a common phenomenon in microalgae, particularly during heavy metal stress. It is not clear so far whether acclimating to one abiotic stressor can alleviate the stress imposed by another abiotic factor. The intent of the present study was to demonstrate the implication of acidic pH in effecting phenotypic changes that facilitate microalgal tolerance to biologically excess concentrations of heavy metals. Two microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were exposed to biologically excess concentrations of Cu (0.50 and 1.0 mg L^‒1), Fe (5 and 10 mg L^‒1), Mn (5 and 10 mg L^‒1) and Zn (2, 5 and 10 mg L^‒1) supplemented to the culture medium at pH 3.5 and 6.7. Chlorophyll autofluorescence and biochemical fingerprinting using FTIR-spectroscopy were used to assess the microalgal strains for phenotypic changes that mediate tolerance to metals. Both the strains responded to acidic pH by effecting differential changes in biochemicals such as carbohydrates, proteins, and lipids. Both the microalgal strains, when acclimated to low pH of 3.5, exhibited an increase in protein (< 2-fold) and lipid (> 1.5-fold). Strain MAS1 grown at pH 3.5 showed a reduction (1.5-fold) in carbohydrates while strain MAS3 exhibited a 17-fold increase in carbohydrates as compared to their growth at pH 6.7. However, lower levels of biologically excess concentrations of the selected transition metals at pH 6.7 unveiled positive or no effect on physiology and biochemistry in microalgal strains, whereas growth with higher metal concentrations at this pH resulted in decreased chlorophyll content. Although the bioavailability of free-metal ions is higher at pH 3.5, as revealed by Visual MINTEQ model, no adverse effect was observed on chlorophyll content in cells grown at pH 3.5 than at pH 6.7. Furthermore, increasing concentrations of Fe, Mn and Zn significantly upregulated the carbohydrate metabolism, but not protein and lipid synthesis, in both strains at pH 3.5 as compared to their growth at pH 6.7. Overall, the impact of pH 3.5 on growth response suggested that acclimation of microalgal strains to acidic pH alleviates metal toxicity by triggering physiological and biochemical changes in microalgae for their survival.

UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction

Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.

PCET-Based Ligand Limits Charge Recombination with an Ir(III) Photoredox Catalyst

Upon photoinitiated electron transfer, charge recombination limits the quantum yield of photoredox reactions for which the rates for the forward reaction and back electron transfer are competitive. Taking inspiration from a proton-coupled electron transfer (PCET) process in Photosystem II, a benzimidazole-phenol (BIP) has been covalently attached to the 2,2'-bipyridyl ligand of [Ir(dF(CF₃)ppy)₂(bpy)][PF₆] (dF(CF₃)ppy = 2-(2,4-difluorophenyl)-5-(trifluoromethyl)pyridine; bpy = 2,2'-bipyridyl). Excitation of the [Ir(dF(CF₃)ppy)₂(BIP-bpy)][PF₆] photocatalyst results in intramolecular PCET to form a charge-separated state with oxidized BIP. Subsequent reduction of methyl viologen dication (MV²⁺), a substrate surrogate, by the reducing moiety of the charge separated species demonstrates that the inclusion of BIP significantly slows the charge recombination rate. The effect of ∼24-fold slower charge recombination in a photocatalytic phthalimide ester reduction resulted in a greater than 2-fold increase in reaction quantum efficiency.

HYSCORE and DFT Studies of Proton-Coupled Electron Transfer in a Bioinspired Artificial Photosynthetic Reaction Center

The photosynthetic water-oxidation reaction is catalyzed by the oxygen-evolving complex in photosystem II (PSII) that comprises the Mn₄CaO₅ cluster, with participation of the redox-active tyrosine residue (Y_Z) and a hydrogen-bonded network of amino acids and water molecules. It has been proposed that the strong hydrogen bond between Y_Z and D1-His190 likely renders Y_Z kinetically and thermodynamically competent leading to highly efficient water oxidation. However, a detailed understanding of the proton-coupled electron transfer (PCET) at Y_Z remains elusive owing to the transient nature of its intermediate states involving Y_Z⋅. Herein, we employ a combination of high-resolution two-dimensional ¹⁴N hyperfine sublevel correlation spectroscopy and density functional theory methods to investigate a bioinspired artificial photosynthetic reaction center that mimics the PCET process involving the Y_Z residue of PSII. Our results underscore the importance of proximal water molecules and charge delocalization on the electronic structure of the artificial reaction center.

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Structural factors are critical in the design of artificial photosynthetic systems

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Correlation between hyperfine couplings of the N atoms and electron spin density

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Spin density distribution affected by charge delocalization and explicit waters

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Spin density modulation by electronic coupling as observed with P₆₈₀ and Y_Z in PSII

Probing the Proton-Loading Site of Cytochrome C Oxidase Using Time-Resolved Fourier Transform Infrared Spectroscopy

Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the “fast” kinetic spectra were found based on the following three requirements: (1) they are present in the “fast” phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the “slow” kinetic spectra in these mutants, and (3) they are absent in “fast” kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).

Time-Resolved Infrared and Visible Spectroscopy on Cryptochrome aCRY: Basis for Red Light Reception

Cryptochromes function as flavin-binding photoreceptors in bacteria, fungi, algae, land plants, and insects. The discovery of an animal-like cryptochrome in the green alga Chlamydomonas reinhardtii has expanded the spectral range of sensitivity of these receptors from ultraviolet A/blue light to almost the complete visible spectrum. The broadened light response has been explained by the presence of the flavin neutral radical as a chromophore in the dark. Concomitant with photoconversion of the flavin, an unusually long-lived tyrosyl radical with a red-shifted ultraviolet-visible spectrum is formed, which is essential for the function of the receptor. In this study, the microenvironment of this key residue, tyrosine 373, was scrutinized using time-resolved Fourier transform infrared spectroscopy on several variants of animal-like cryptochrome and density functional theory for band assignment. The reduced tyrosine takes on distinct hydrogen bond scenarios depending on the presence of the C-terminal extension and of a neighboring cysteine. Upon radical formation, all variants showed a signal at 1400 cm^-1, which we assigned to the ν7'a marker band of the CO stretching mode. The exceptionally strong downshift of this band cannot be attributed to a loss of hydrogen bonding only. Time-resolved ultraviolet-visible spectroscopy on W322F, a mutant of the neighboring tryptophan residue, revealed a decrease of the tyrosyl radical lifetime by almost two orders of magnitude, along with a shift of the absorbance maximum from 416 to 398 nm. These findings strongly support the concept of a π-π stacking as an apolar interaction between Y373 and W322 to be responsible for the characteristics of the tyrosyl radical. This concept of radical stabilization has been unknown to cryptochromes so far but might be highly relevant for other homologs with a tetrad of tryptophans and tyrosines as electron donors.

Structure-Activity Relationships of Hierarchical Three-Dimensional Electrodes with Photosystem II for Semiartificial Photosynthesis

Semiartificial photosynthesis integrates photosynthetic enzymes with artificial electronics, which is an emerging approach to reroute the natural photoelectrogenetic pathways for sustainable fuel and chemical synthesis. However, the reduced catalytic activity of enzymes in bioelectrodes limits the overall performance and further applications in fuel production. Here, we show new insights into factors that affect the photoelectrogenesis in a model system consisting of photosystem II and three-dimensional indium tin oxide and graphene electrodes. Confocal fluorescence microscopy and in situ surface-sensitive infrared spectroscopy are employed to probe the enzyme distribution and penetration within electrode scaffolds of different structures, which is further correlated with protein film-photoelectrochemistry to establish relationships between the electrode architecture and enzyme activity. We find that the hierarchical structure of electrodes mainly influences the protein loading but not the enzyme activity. Photoactivity is more limited by light intensity and electronic communication at the biointerface. This study provides guidelines for maximizing the performance of semiartificial photosynthesis and also presents a set of methodologies to probe the photoactive biofilms in three-dimensional electrodes.

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.

Resonance Raman Analysis of the Tryptophan Cation Radical

Electron transfer (ET) reactions within proteins are accomplished by a broad set of redox-active molecules, including natural amino acids. Tryptophan participates in ET chemistry as both a cation and a neutral radical. Identification and characterization of the biologically relevant species is essential to understand efficient ET mechanisms in proteins. We present resonance Raman spectra and excitation profiles of the tryptophan cation radical generated by combining a strong oxidant, Ce(IV), with tryptophan model compounds in a fast-flow mixing device. Isotopically modified derivatives, coupled with calculations, allowed the assignment of the normal modes of this radical. Raman bands that are sensitive to protonation state and hydrogen bonding environment of the cation radical were identified. The present findings, along with resonance Raman spectra of the closed-shell and neutral radical counterparts, form a foundation for probing tryptophan-mediated ET reactions in proteins.

Fourier transform infrared detection of a polarizable proton trapped between photooxidized tyrosine YZ and a coupled histidine in photosystem II: relevance to the proton transfer mechanism of water oxidation

The redox-active tyrosine YZ (D1-Tyr161) in photosystem II (PSII) functions as an immediate electron acceptor of the Mn4Ca cluster, which is the catalytic center of photosynthetic water oxidation. YZ is also located in the hydrogen bond network that connects the Mn4Ca cluster to the lumen and hence is possibly related to the proton transfer process during water oxidation. To understand the role of YZ in the water oxidation mechanism, we have studied the hydrogen bonding interactions of YZ and its photooxidized neutral radical YZ(•) together with the interaction of the coupled His residue, D1-His190, using light-induced Fourier transform infrared (FTIR) difference spectroscopy. The YZ(•)-minus-YZ FTIR difference spectrum of Mn-depleted PSII core complexes exhibited a broad positive feature around 2800 cm(-1), which was absent in the corresponding spectrum of another redox-active tyrosine YD (D2-Tyr160). Analyses by (15)N and H/D substitutions, examination of the pH dependence, and density functional theory and quantum mechanics/molecular mechanics (QM/MM) calculations showed that this band arises from the N-H stretching vibration of the protonated cation of D1-His190 forming a charge-assisted strong hydrogen bond with YZ(•). This result provides strong evidence that the proton released from YZ upon its oxidation is trapped in D1-His190 and a positive charge remains on this His. The broad feature of the ~2800 cm(-1) band reflects a large proton polarizability in the hydrogen bond between YZ(•) and HisH(+). QM/MM calculations further showed that upon YZ oxidation the hydrogen bond network is rearranged and one water molecule moves toward D1-His190. From these data, a novel proton transfer mechanism via YZ(•)-HisH(+) is proposed, in which hopping of the polarizable proton of HisH(+) to this water triggers the transfer of the proton from substrate water to the luminal side. This proton transfer mechanism could be functional in the S2 → S3 transition, which requires proton release before electron transfer because of an excess positive charge on the Mn4Ca cluster.

Proton transfer reactions and hydrogen-bond networks in protein environments

In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.

Mechanism of tyrosine D oxidation in Photosystem II

Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II [Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473(7345):55-60], we investigated the H-bonding environment of the redox-active tyrosine D (TyrD) and obtained insights that help explain its slow redox kinetics and the stability of TyrD(•). The water molecule distal to TyrD, located ~4 Å away from the phenolic O of TyrD, corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to the phenolic O of TyrD, corresponds to the presence of the unoxidized tyrosine. The H(+) released on oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasiirreversible, explaining the great stability of the TyrD(•). A symmetry-related proton pathway associated with tyrosine Z is pointed out, and this is associated with one of the Cl(-) sites. This may represent a proton pathway functional in the water oxidation cycle.

Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations

The quantum yield of tryptophan (Trp) fluorescence was measured in 30 designed miniproteins (17 β-hairpins and 13 Trp-cage peptides), each containing a single Trp residue. Measurements were made in D(2)O and H(2)O to distinguish between fluorescence quenching mechanisms involving electron and proton transfer in the hairpin peptides, and at two temperatures to check for effects of partial unfolding of the Trp-cage peptides. The extent of folding of all the peptides also was measured by NMR. The fluorescence yields ranged from 0.01 in some of the Trp-cage peptides to 0.27 in some hairpins. Fluorescence quenching was found to occur by electron transfer from the excited indole ring of the Trp to a backbone amide group or the protonated side chain of a nearby histidine, glutamate, aspartate, tyrosine, or cysteine residue. Ionized tyrosine side chains quenched strongly by resonance energy transfer or electron transfer to the excited indole ring. Hybrid classical/quantum mechanical molecular dynamics simulations were performed by a method that optimized induced electric dipoles separately for the ground and excited states in multiple π-π* and charge-transfer (CT) excitations. Twenty 0.5 ns trajectories in the tryptophan's lowest excited singlet π-π* state were run for each peptide, beginning by projections from trajectories in the ground state. Fluorescence quenching was correlated with the availability of a CT or exciton state that was strongly coupled to the π-π* state and that matched or fell below the π-π* state in energy. The fluorescence yields predicted by summing the calculated rates of charge and energy transfer are in good accord with the measured yields.

Solvent effects on the physicochemical properties of the cross-linked histidine-tyrosine ligand of cytochrome c oxidase

Density functional theory was used to explore the effects of aqueous solvation on the structure, vibrational frequencies, and the electronic absorption spectrum of 2-(4-methylimidazol-1-yl)-phenol (Me-ImPhOH), a chemical analogue of the cross-linked histidine-tyrosine Cu(B) ligand of cytochrome c oxidase. In addition, the phenolic-OH pK(a), the anodic redox potential for the biring radical/anion couple, and the phenolic-OH bond dissociation energy were calculated relative to phenol using a series of isodesmic reactions. In the gas phase, the imidazole moiety stabilizes the biring anion for all the models and greatly decreases the phenolic-OH pK(a) relative to phenol. Moreover, the conductor-like polarizable continuum model (C-PCM)-water-solvated reactions predict Delta pK(a) values that are five times smaller than the gas-phase reactions, in agreement with the proposed role of the cross-linked histidine-tyrosine as a proton donor in the enzyme. For the neutral biring radical solvation models, the imidazole moiety induces a high degree of asymmetry into the phenol ring when compared to unmodified phenoxyl radical. The biring radical pi-bonds of the imidazole ring are more localized when compared to unmodified 1-methylimidazole and Me-ImPhOH solvation models, suggesting reduced aromaticity for all biring radical solvation models. The C-PCM-water-solvated reactions predict relative biring radical reduction potentials that are an order of magnitude smaller than the gas-phase reactions. The biring O-H bond is weakened relative to phenol by less than 4 kcal/mol for all the reactions studied, suggesting that the imidazole moiety does not facilitate H-atom abstraction in the enzyme. Together, these results demonstrate the sensitive nature of the proton and electron donating ability of the histidine-tyrosine cross-linked ligand in cytochrome c oxidase and suggest that for quantitative predictions of reaction energies and thermodynamic properties, models of this ligand should take care to account for changes in environment and, more specifically, hydrogen bonding interactions.

Three redox states of Trypanosoma brucei alternative oxidase identified by infrared spectroscopy and electrochemistry

Electrochemistry coupled with Fourier transform infrared (IR) spectroscopy was used to investigate the redox properties of recombinant alternative ubiquinol oxidase from Trypanosoma brucei, the organism responsible for African sleeping sickness. Stepwise reduction of the fully oxidized resting state of recombinant alternative ubiquinol oxidase revealed two distinct IR redox difference spectra. The first of these, signal 1, titrates in the reductive direction as an n = 2 Nernstian component with an apparent midpoint potential of 80 mV at pH 7.0. However, reoxidation of signal 1 in the same potential range under anaerobic conditions did not occur and only began with potentials in excess of 500 mV. Reoxidation by introduction of oxygen was also unsuccessful. Signal 1 contained clear features that can be assigned to protonation of at least one carboxylate group, further perturbations of carboxylic and histidine residues, bound ubiquinone, and a negative band at 1554 cm(-1) that might arise from a radical in the fully oxidized protein. A second distinct IR redox difference spectrum, signal 2, appeared more slowly once signal 1 had been reduced. This component could be reoxidized with potentials above 100 mV. In addition, when both signals 1 and 2 were reduced, introduction of oxygen caused rapid oxidation of both components. These data are interpreted in terms of the possible active site structure and mechanism of oxygen reduction to water.

Fourier transform infrared (FTIR) spectroscopy

Fourier transform infrared (FTIR) spectroscopy probes the vibrational properties of amino acids and cofactors, which are sensitive to minute structural changes. The lack of specificity of this technique, on the one hand, permits us to probe directly the vibrational properties of almost all the cofactors, amino acid side chains, and of water molecules. On the other hand, we can use reaction-induced FTIR difference spectroscopy to select vibrations corresponding to single chemical groups involved in a specific reaction. Various strategies are used to identify the IR signatures of each residue of interest in the resulting reaction-induced FTIR difference spectra. (Specific) Isotope labeling, site-directed mutagenesis, hydrogen/deuterium exchange are often used to identify the chemical groups. Studies on model compounds and the increasing use of theoretical chemistry for normal modes calculations allow us to interpret the IR frequencies in terms of specific structural characteristics of the chemical group or molecule of interest. This review presents basics of FTIR spectroscopy technique and provides specific important structural and functional information obtained from the analysis of the data from the photosystems, using this method.

Probing the coupling between proton and electron transfer in photosystem II core complexes containing a 3-fluorotyrosine

The catalytic cycle of numerous enzymes involves the coupling between proton transfer and electron transfer. Yet, the understanding of this coordinated transfer in biological systems remains limited, likely because its characterization relies on the controlled but experimentally challenging modifications of the free energy changes associated with either the electron or proton transfer. We have performed such a study here in Photosystem II. The driving force for electron transfer from Tyr(Z) to P(680)(*+) has been decreased by approximately 80 meV by mutating the axial ligand of P(680), and that for proton transfer upon oxidation of Tyr(Z) by substituting a 3-fluorotyrosine (3F-Tyr(Z)) for Tyr(Z). In Mn-depleted Photosystem II, the dependence upon pH of the oxidation rates of Tyr(Z) and 3F-Tyr(Z) were found to be similar. However, in the pH range where the phenolic hydroxyl of Tyr(Z) is involved in a H-bond with a proton acceptor, the activation energy of the oxidation of 3F-Tyr(Z) is decreased by 110 meV, a value which correlates with the in vitro finding of a 90 meV stabilization energy to the phenolate form of 3F-Tyr when compared to Tyr (Seyedsayamdost et al. J. Am. Chem. Soc. 2006, 128,1569-1579). Thus, when the phenol of Y(Z) acts as a H-bond donor, its oxidation by P(680)(*+) is controlled by its prior deprotonation. This contrasts with the situation prevailing at lower pH, where the proton acceptor is protonated and therefore unavailable, in which the oxidation-induced proton transfer from the phenolic hydroxyl of Tyr(Z) has been proposed to occur concertedly with the electron transfer to P(680)(*+). This suggests a switch between a concerted proton/electron transfer at pHs < 7.5 to a sequential one at pHs > 7.5 and illustrates the roles of the H-bond and of the likely salt-bridge existing between the phenolate and the nearby proton acceptor in determining the coupling between proton and electron transfer.

QM/MM vibrational mode tracking

Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of biomolecules. When small subsystems of large molecules such as active centers of enzymes are studied, quantum chemical calculations based on quantum mechanics/molecular mechanics (QM/MM) coupling schemes are a valuable means to interpret the spectra. The goal of this work is a methodological pilot study on how to selectively and thus efficiently extract certain vibrational information for extended molecular systems described by QM/MM methods. This is achieved by an extension of the mode tracking algorithm and a comparison with the partial Hessian diagonalization approach. After validating the methodology for the CO stretching vibration of 2-butanone and a delocalized CO stretch in acetylacetone, the stretching and bending modes of the CO ligand in CO myoglobin are tracked. Such systems represent an ideal application for mode tracking, because only a few strongly localized vibrations are sought for, while the large remainder of the molecule is of interest only as far as it affects these local vibrations. This influence is treated exactly by mode tracking.

Time-resolved X-ray spectroscopy leads to an extension of the classical S-state cycle model of photosynthetic oxygen evolution

In oxygenic photosynthesis, a complete water oxidation cycle requires absorption of four photons by the chlorophylls of photosystem II (PSII). The photons can be provided successively by applying short flashes of light. Already in 1970, Kok and coworkers [Photochem Photobiol 11:457-475, 1970] developed a basic model to explain the flash-number dependence of O2 formation. The third flash applied to dark-adapted PSII induces the S3-->S4-->S0 transition, which is coupled to dioxygen formation at a protein-bound Mn4Ca complex. The sequence of events leading to dioxygen formation and the role of Kok's enigmatic S4-state are only incompletely understood. Recently we have shown by time-resolved X-ray spectroscopy that in the S3-->S0 transition an interesting intermediate is formed, prior to the onset of O-O bond formation [Haumann et al. Science 310:1019-1021, 2005]. The experimental results of the time-resolved X-ray experiments are discussed. The identity of the reaction intermediate is considered and the question is addressed how the novel intermediate is related to the S4-state proposed in 1970 by Bessel Kok. This leads us to an extension of the classical S-state cycle towards a basic model which describes sequence and interplay of electron and proton abstraction events at the donor side of PSII [Dau and Haumann, Science 312:1471-1472, 2006].

Oxidative photosynthetic water splitting: energetics, kinetics and mechanism

This minireview is an attempt to summarize our current knowledge on oxidative water splitting in photosynthesis. Based on the extended Kok model (Kok, Forbush, McGloin (1970) Photochem Photobiol 11:457-476) as a framework, the energetics and kinetics of two different types of reactions comprising the overall process are discussed: (i) P680+* reduction by the redox active tyrosine YZ of polypeptide D1 and (ii) Yz (ox) induced oxidation of the four step sequence in the water oxidizing complex (WOC) leading to the formation of molecular oxygen. The mode of coupling between electron transport (ET) and proton transfer (PT) is of key mechanistic relevance for the redox turnover of YZ and the reactions within the WOC. The peculiar energetics of the oxidation steps in the WOC assure that redox state S1 is thermodynamically most stable. This is a general feature in all oxygen evolving photosynthetic organisms and assumed to be of physiological relevance. The reaction coordinate of oxidative water splitting is discussed on the basis of the available information about the Gibbs energy differences between the individual redox states Si+1 and Si and the data reported for the activation energies of the individual oxidation steps in the WOC. Finally, an attempt is made to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and on the active role of the protein in tuning the local proton activity that depends on time and redox state Si. The O-O linkage is assumed to take place at the level of a complexed peroxide.

Eight steps preceding O-O bond formation in oxygenic photosynthesis--a basic reaction cycle of the Photosystem II manganese complex

In oxygenic photosynthesis, water is split at a Mn(4)Ca complex bound to the proteins of photosystem II (PSII). Powered by four quanta of visible light, four electrons and four protons are removed from two water molecules before dioxygen is released. By this process, water becomes an inexhaustible source of the protons and electrons needed for primary biomass formation. On the basis of structural and spectroscopic data, we recently have introduced a basic reaction cycle of water oxidation which extends the classical S-state cycle [B. Kok, B. Forbush, M. McGloin, Cooperation of charges in photosynthetic O2 evolution- I. A linear four-step mechanism, Photochem. Photobiol. 11 (1970) 457-475] by taking into account also the role and sequence of deprotonation events [H. Dau, M. Haumann, Reaction cycle of photosynthetic water oxidation in plants and cyanobacteria, Science 312 (2006) 1471-1472]. We propose that the outwardly convoluted and irregular events of the classical S-state cycle are governed by a simple underlying principle: protons and electrons are removed strictly alternately from the Mn complex. Starting in I(0), eight successive steps of alternate proton and electron removal lead to I(8) and only then the O-O bond is formed. Thus not only four oxidizing equivalents, but also four bases are accumulated prior to the onset of dioxygen formation. After reviewing the kinetic properties of the individual S-state transition, we show that the proposed basic model explains a large body of experimental results straightforwardly. Furthermore we discuss how the I-cycle model addresses the redox-potential problem of PSII water oxidation and we propose that the accumulated bases facilitate dioxygen formation by acting as proton acceptors.

Light-induced FTIR difference spectroscopy as a powerful tool toward understanding the molecular mechanism of photosynthetic oxygen evolution

The molecular mechanism of photosynthetic oxygen evolution remains a mystery in photosynthesis research. Although recent X-ray crystallographic studies of the photosystem II core complex at 3.0-3.5 A resolutions have revealed the structure of the oxygen-evolving center (OEC), with approximate positions of the Mn and Ca ions and the amino acid ligands, elucidation of its detailed structure and the reactions during the S-state cycle awaits further spectroscopic investigations. Light-induced Fourier transform infrared (FTIR) difference spectroscopy was first applied to the OEC in 1992 as detection of its structural changes upon the S(1)-->S(2) transition, and spectra during the S-state cycle induced by consecutive flashes were reported in 2001. These FTIR spectra provide extensive structural information on the amino acid side groups, polypeptide chains, metal core, and water molecules, which constitute the OEC and are involved in its reaction. FTIR spectroscopy is thus becoming a powerful tool in investigating the reaction mechanism of photosynthetic oxygen evolution. In this mini-review, the measurement method of light-induced FTIR spectra of OEC is introduced and the results obtained thus far using this technique are summarized.

Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis

This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron (ET) and proton transfer (PT) reactions is shown to be of key mechanistic relevance for the redox turnover of Y(Z) and the reactions within the WOC. The WOC is characterized by peculiar energetics of its oxidation steps in the WOC. In all oxygen evolving photosynthetic organisms the redox state S(1) is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S(i+1) and S(i) and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem II (PS II). Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S(i). The O-O linkage is assumed to take place within a multistate equilibrium at the redox level of S(3), comprising both redox isomerism and proton tautomerism. It is proposed that one state, S(3)(P), attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through S(3)(P) oxidation by Y(Z)(ox).

The mystery of oxygen evolution: analysis of structure and function of photosystem II, the water-plastoquinone oxido-reductase

Photosystem II (PS II) of thylakoid membrane of photosynthetic organisms has drawn attention of researchers over the years because it is the only system on Earth that provides us with oxygen that we breathe. In the recent past, structure of PS II has been the focus of research in plant science. The report of X-ray crystallographic structure of PS II complex by the research groups of James Barber and So Iwata in UK is a milestone in the area of research in photosynthesis. It follows the pioneering and elegant work from the laboratories of Horst Witt and W. Saenger in Germany, and J. Shen in Japan. It is time to analyze the historic events during the long journey made by the researchers to arrive at this point. This review makes an attempt to critically review the growth of the advancement of concepts and knowledge on the photosystem in the background of technological development. We conclude the review with perspectives on research and technology that should reveal the complete story of PS II of thylakoid in the future.

Formate binding near the redox-active tyrosineD in photosystem II: consequences on the properties of tyrD

Formate and phosphate affect substantially the rate of tyrosine D (TyrD) oxidation and the stability of the radical TyrD* in Photosystem II [Hienerwadel R, Boussac A, Breton J and Berthomieu C (1996) Biochemistry 35: 15447-15460]. This observation prompted us to analyze the influence of formate and phosphate on the environment of TyrD using FTIR spectroscopy. The nu (CO) IR mode of TyrD* at 1503 cm-1 remains unchanged whatever the buffer used at pH 6 and whether formate is present or not in the sample. Similarly, the main IR mode of reduced TyrD remains at approximately 1250 cm-1 in all tested conditions. We thus conclude that formate does not modify the hydrogen-bonded interactions of TyrD and TyrD* with neighbouring D2His189 and D2Gln164. In the TyrD-state, an IR mode of formate significantly different from that observed in solution, is detected using 13C-formate, showing that formate forms a strong electrostatic interaction within PS II. The presence of formate affects also IR bands that may be assigned to an arginine side chain. Upon TyrD* formation, formate does not protonate but its binding interaction weakens. A proton uptake by Mes or phosphate buffer is detected, which is not observed when BisTris is used as a buffer. In these latter conditions, IR bands characteristic of the protonation of a carboxylate group of the protein are detected instead. The present IR data and the recent structural model of the TyrD environment proposed by Ferreira KN, Iverson TM, Maghlaoui K, Barber J and Iwata S [(2004) Science 303: 1831-1838], suggest that the proton released upon TyrD* formation is shared within a hydrogen bonding network including D2Arg294, and CP47Glu364 and that perturbation of this network by formate - possibly binding near D2Arg294 - substantially affects the properties of TyrD.