Fourier transform infrared analysis of the photosynthetic oxygen-evolving center

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.

Experimentally quantifying small-molecule bond activation using valence-to-core X-ray emission spectroscopy

This work establishes the ability of valence-to-core X-ray emission spectroscopy (XES) to serve as a direct probe of N2 bond activation. A systematic series of iron-N2 complexes has been experimentally investigated and the energy of a valence-to-core XES peak was correlated with N-N bond length and stretching frequency. Computations demonstrate that, in a simple one-electron picture, this peak arises from the N2 2s2s σ* orbital, which becomes less antibonding as the N-N bond is weakened and broken. Changes as small as 0.02 Å in the N-N bond length may be distinguished using this approach. The results thus establish valence-to-core XES as an effective probe of small molecule activation, which should have broad applicability in transition-metal mediated catalysis.

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.

Effects of dehydration on light-induced conformational changes in bacterial photosynthetic reaction centers probed by optical and differential FTIR spectroscopy

Following light-induced electron transfer between the primary donor (P) and quinone acceptor (Q(A)) the bacterial photosynthetic reaction center (RC) undergoes conformational relaxations which stabilize the primary charge separated state P(+)Q(A)(-). Dehydration of RCs from Rhodobacter sphaeroides hinders these conformational dynamics, leading to acceleration of P(+)Q(A)(-) recombination kinetics [Malferrari et al., J. Phys. Chem. B 115 (2011) 14732-14750]. To clarify the structural basis of the conformational relaxations and the involvement of bound water molecules, we analyzed light-induced P(+)Q(A)(-)/PQ(A) difference FTIR spectra of RC films at two hydration levels (relative humidity r=76% and r=11%). Dehydration reduced the amplitude of bands in the 3700-3550cm(-1) region, attributed to water molecules hydrogen bonded to the RC, previously proposed to stabilize the charge separation by dielectric screening [Iwata et al., Biochemistry 48 (2009) 1220-1229]. Other features of the FTIR difference spectrum were affected by partial depletion of the hydration shell (r=11%), including contributions from modes of P (9-keto groups), and from NH or OH stretching modes of amino acidic residues, absorbing in the 3550-3150cm(-1) range, a region so far not examined in detail for bacterial RCs. To probe in parallel the effects of dehydration on the RC conformational relaxations, we analyzed by optical absorption spectroscopy the kinetics of P(+)Q(A)(-) recombination following the same photoexcitation used in FTIR measurements (20s continuous illumination). The results suggest a correlation between the observed FTIR spectral changes and the conformational rearrangements which, in the hydrated system, strongly stabilize the P(+)Q(A)(-) charge separated state over the second time scale.

Alternating electron and proton transfer steps in photosynthetic water oxidation

Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel-production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese-calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S(2) → S(3) transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (Y Z OX). The rate-determining elementary step (τ, approximately 30 µs at 20 °C) in the long-distance proton relocation toward the protein-water interface is characterized by a high activation energy (E(a) = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S(0) → S(1) transition are similar (τ, approximately 100 µs; E(a) = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

Structural models of the manganese complex of photosystem II and mechanistic implications

Photosynthetic water oxidation and O₂ formation are catalyzed by a Mn₄Ca complex bound to the proteins of photosystem II (PSII). The catalytic site, including the inorganic Mn₄CaO(n)H(x) core and its protein environment, is denoted as oxygen-evolving complex (OEC). Earlier and recent progress in the endeavor to elucidate the structure of the OEC is reviewed, with focus on recent results obtained by (i) X−ray spectroscopy (specifically by EXAFS analyses), and (ii) X-ray diffraction (XRD, protein crystallography). Very recently, an impressive resolution of 1.9Å has been achieved by XRD. Most likely however, all XRD data on the Mn₄CaO(n)H(x) core of the OEC are affected by X-ray induced modifications (radiation damage). Therefore and to address (important) details of the geometric and electronic structure of the OEC, a combined analysis of XRD and XAS data has been approached by several research groups. These efforts are reviewed and extended using an especially comprehensive approach. Taking into account XRD results on the protein environment of the inorganic core of the Mn complex, 12 alternative OEC models are considered and evaluated by quantitative comparison to (i) extended-range EXAFS data, (ii) polarized EXAFS of partially oriented PSII membrane particles, and (iii) polarized EXAFS of PSII crystals. We conclude that there is a class of OEC models that is in good agreement with both the recent crystallographic models and the XAS data. On these grounds, mechanistic implications for the O−O bond formation chemistry are discussed. This article is part of a Special Issue entitled: Photosystem II.

Herbicide effect on the photodamage process of photosystem II: fourier transform infrared study

The photodamage process of photosystem II by strong illumination was investigated by examining the herbicide effects on the photoinactivation of redox cofactors. O(2)-evolving photosystem II membranes from spinach in the absence of herbicide and in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and bromoxynil were subjected to strong white-light illumination at 298K, and the illumination-time dependence of the activities of Q(A), the Mn cluster, and P680 were monitored using light-induced Fourier transform infrared (FTIR) difference spectroscopy. The decrease in the Q(A) activity was suppressed and accelerated by DCMU and bromoxynil, respectively, in comparison with the sample without herbicide. The intensity change in the S(2)/S(1) FTIR signal of the Mn cluster exhibited a time course virtually identical to that in the Q(A) signal in all the three samples, suggesting that the loss of the S(1)→S(2) transition was ascribed to the Q(A) inactivation and hence the Mn cluster was inactivated not faster than Q(A). The decrease in the P680 signal was always slower than that of Q(A) keeping the tendency of the herbicide effect. Degradation of the D1 protein occurred after the P680 inactivation. These observations are consistent with the acceptor-side mechanism, in which double reduction of Q(A) triggers the formation of (1)O(2)* to promote further damage to other cofactors and the D1 protein, rather than the recently proposed mechanism that inactivation of the Mn cluster initiates the photodamage. Thus, the results of the present study support the view that the acceptor-side mechanism dominantly occurs in the photodamage to PSII by strong white-light illumination.

Interaction and inhibitory effect of ammonium cation in the oxygen evolving center of photosystem II

Photosynthetic O(2) evolution takes place at the Mn cluster in photosystem II (PSII) by oxidation of water. It has been proposed that ammonia, one of water analogues, functions as an inhibitor of O(2) evolution at alkaline pH. However, the detailed mechanism of inhibition has not been understood yet. In this study, we investigated the mechanism of ammonia inhibition by examining the NH(4)Cl-induced inhibition of O(2) evolution in a wide pH range (pH 5.0-8.0) and by detecting the interaction site using Fourier transform infrared (FTIR) spectroscopy. In addition to intact PSII membranes from spinach, PSII membranes depleted of the PsbP and PsbQ extrinsic proteins were used as samples to avoid the effect of the release of these proteins by salt treatments. In both types of samples, oxygen evolution activity decreased by approximately 40% by addition of 100 mM NH(4)Cl in the range of pH 5.0-8.0. The presence of inhibition at acidic pH without significant pH dependence strongly suggests that NH(4)(+) cation functions as a major inhibitor in the acidic pH region, where neutral NH(3) scarcely exists in the buffer. The NH(4)Cl treatment at pH 6.5 and 5.5 induced prominent changes in the COO(-) stretching regions in FTIR difference spectra upon the S(1) → S(2) transition measured at 283 K. The NH(4)Cl concentration dependence of the amplitude of the spectral changes showed a good correlation with that of the inhibition of O(2) evolution. From this observation, it is proposed that NH(4)(+) cation interacts with carboxylate groups coupled to the Mn cluster as direct ligands or proton transfer mediators, causing inhibition of the O(2) evolving reaction.

Participation of glutamate-354 of the CP43 polypeptide in the ligation of manganese and the binding of substrate water in photosystem II

In the current X-ray crystallographic structural models of photosystem II, Glu354 of the CP43 polypeptide is the only amino acid ligand of the oxygen-evolving Mn(4)Ca cluster that is not provided by the D1 polypeptide. To further explore the influence of this structurally unique residue on the properties of the Mn(4)Ca cluster, the CP43-E354Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray absorption, FTIR, and mass spectrometry. 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, correlating with the mutant's lower steady-state rate (approximately 20% compared to wild type). Experiments conducted with H(2)(18)O showed that the fast and slow phases of substrate water exchange in CP43-E354Q thylakoid membranes were accelerated 8.5- and 1.8-fold, respectively, in the S(3) state compared to wild type. Purified oxygen-evolving CP43-E354Q PSII core complexes exhibited a slightly altered S(1) state Mn-EXAFS spectrum, a slightly altered S(2) state multiline EPR signal, a substantially altered S(2)-minus-S(1) FTIR difference spectrum, and an unusually long lifetime for the S(2) state (>10 h) in a substantial fraction of reaction centers. In contrast, the S(2) state Mn-EXAFS spectrum was nearly indistinguishable from that of wild type. The S(2)-minus-S(1) FTIR difference spectrum showed alterations throughout the amide and carboxylate stretching regions. Global labeling with (15)N and specific labeling with l-[1-(13)C]alanine revealed that the mutation perturbs both amide II and carboxylate stretching modes and shifts the symmetric carboxylate stretching modes of the α-COO(-) group of D1-Ala344 (the C-terminus of the D1 polypeptide) to higher frequencies by 3-4 cm(-1) in both the S(1) and S(2) states. The EPR and FTIR data implied that 76-82% of CP43-E354Q PSII centers can achieve the S(2) state and that most of these can achieve the S(3) state, but no evidence for advancement beyond the S(3) state was observed in the FTIR data, at least not in a majority of PSII centers. Although the X-ray absorption and EPR data showed that the CP43-E354Q mutation only subtly perturbs the structure and spin state of the Mn(4)Ca cluster in the S(2) state, the FTIR and H(2)(18)O exchange data show that the mutation strongly influences other properties of the Mn(4)Ca cluster, altering the response of numerous carboxylate and amide groups to the increased positive charge that develops on the cluster during the S(1) to S(2) transition and weakening the binding of both substrate water molecules (or water-derived ligands), especially the one that exchanges rapidly in the S(3) state. The FTIR data provide evidence that CP43-Glu354 coordinates to the Mn(4)Ca cluster in the S(1) state as a bridging ligand between two metal ions but provide no compelling evidence that this residue changes its coordination mode during the S(1) to S(2) transition. The H(2)(18)O exchange data provide evidence that CP43-Glu354 interacts with the Mn ion that ligates the substrate water molecule (or water-derived ligand) that is in rapid exchange in the S(3) state.

Zwitterion modulation of O(2)-evolving activity of cyanobacterial photosystem II

Photosystem II (PSII) is the only enzyme in nature that can catalyze the challenging catalytic photooxidation of H(2)O into four protons, four electrons, and O(2). Slowing down turnover of the O(2)-evolving complex (OEC) is a plausible approach to gain mechanistic information on the reaction. However, modulating the kinetics of the reaction without perturbing the active site is a challenge. In this study, it is shown that the steady-state activity of cyanobacterial PSII is inhibited by small zwitterions, such as glycine betaine and β-alanine. We show that the binding of zwitterions is nondenaturing, is highly reversible, and results in the decrease of the rate of catalytic turnover by ∼50% in the presence of excess zwitterion. Control measurements of photoinduced electron transfer in O(2)-inactive PSII show that the inhibition by zwitterions is the result of a specific decrease in the rate of catalytic turnover of the OEC. Recovery of activity upon addition of an exogenous proton carrier (HCO(3)(-)) provides evidence that proton-transfer pathways, thought to be essential for the relay of protons from the OEC to the lumen, are affected. Interestingly, no inhibition is observed for spinach PSII, suggesting that zwitterions act specifically by binding to the extrinsic proteins on the lumenal side of PSII, which differ significantly between plants and cyanobacteria, to slow proton transfer on the electron donor side of PSII.

Evidence from FTIR difference spectroscopy of an extensive network of hydrogen bonds near the oxygen-evolving Mn(4)Ca cluster of photosystem II involving D1-Glu65, D2-Glu312, and D1-Glu329

Analyses of the refined X-ray crystallographic structures of photosystem II (PSII) at 2.9-3.5 A have revealed the presence of possible channels for the removal of protons from the catalytic Mn(4)Ca cluster during the water-splitting reaction. As an initial attempt to verify these channels experimentally, the presence of a network of hydrogen bonds near the Mn(4)Ca cluster was probed with FTIR difference spectroscopy in a spectral region sensitive to the protonation states of carboxylate residues and, in particular, with a negative band at 1747 cm(-1) that is often observed in the S(2)-minus-S(1) FTIR difference spectrum of PSII from the cyanobacterium Synechocystis sp. PCC 6803. On the basis of its 4 cm(-1) downshift in D(2)O, this band was assigned to the carbonyl stretching vibration (C horizontal lineO) of a protonated carboxylate group whose pK(a) decreases during the S(1) to S(2) transition. The positive charge that forms on the Mn(4)Ca cluster during the S(1) to S(2) transition presumably causes structural perturbations that are transmitted to this carboxylate group via electrostatic interactions and/or an extended network of hydrogen bonds. In an attempt to identify the carboxylate group that gives rise to this band, the FTIR difference spectra of PSII core complexes from the mutants D1-Asp61Ala, D1-Glu65Ala, D1-Glu329Gln, and D2-Glu312Ala were examined. In the X-ray crystallographic models, these are the closest carboxylate residues to the Mn(4)Ca cluster that do not ligate Mn or Ca and all are highly conserved. The 1747 cm(-1) band is present in the S(2)-minus-S(1) FTIR difference spectrum of D1-Asp61Ala but absent from the corresponding spectra of D1-Glu65Ala, D2-Glu312Ala, and D1-Glu329Gln. The band is also sharply diminished in magnitude in the wild type when samples are maintained at a relative humidity of </=85%. It is proposed that D1-Glu65, D2-Glu312, and D1-Glu329 participate in a common network of hydrogen bonds that includes water molecules and the carboxylate group that gives rise to the 1747 cm(-1) band. It is further proposed that the mutation of any of these three residues, or partial dehydration caused by maintaining samples at a relative humidity of <or=85%, disrupts the network sufficiently that the structural perturbations associated with the S(1) to S(2) transition are no longer transmitted to the carboxylate group that gives rise to the 1747 cm(-1) band. Because D1-Glu329 is located approximately 20 A from D1-Glu65 and D2-Glu312, the postulated network of hydrogen bonds must extend for at least 20 A across the lumenal face of the Mn(4)Ca cluster. The D1-Asp61Ala, D1-Glu65Ala, and D2-Glu312Ala mutations also appear to substantially decrease the fraction of PSII reaction centers that undergo the S(3) to S(0) transition in response to a saturating flash. This behavior is consistent with D1-Asp61, D1-Glu65, and D2-Glu312 participating in a dominant proton egress channel that links the Mn(4)Ca cluster with the thylakoid lumen.

Is Mn-Bound Substrate Water Protonated in the S(2) State of Photosystem II?

In spite of great progress in resolving the geometric structure of the water-splitting Mn(4)O(x)Ca cluster in photosystem II, the binding sites and modes of the two substrate water molecules are still insufficiently characterized. While time-resolved membrane-inlet mass spectrometry measurements indicate that both substrate water molecules are bound to the oxygen-evolving complex (OEC) in the S(2) and S(3) states (Hendry and Wydrzynski in Biochemistry 41:13328-13334, 2002), it is not known (1) if they are both Mn-bound, (2) if they are terminal or bridging ligands, and (3) in what protonation state they are bound in the different oxidation states S(i) (i = 0, 1, 2, 3, 4) of the OEC. By employing (17)O hyperfine sublevel correlation (HYSCORE) spectroscopy we recently demonstrated that in the S(2) state there is only one (type of) Mn-bound oxygen that is water exchangeable. We therefore tentatively identified this oxygen as one substrate 'water' molecule, and on the basis of the finding that it has a hyperfine interaction of about 10 MHz with the electron spin of the Mn(4)O(x)Ca cluster, we suggest that it is bound as a Mn-O-Mn bridge within a bis-mu(2) oxo-bridged unit (Su et al. in J Am Chem Soc 130:786-787, 2008). Employing pulse electron paramagnetic resonance, (1)H/(2)H Mims electron-nuclear double resonance and (2)H-HYSCORE spectroscopies together with (1)H/(2)H-exchange here, we test this hypothesis by probing the protonation state of this exchangeable oxygen. We conclude that this oxygen is fully deprotonated. This result is discussed in the light of earlier reports in the literature.

Validation of broken-symmetry density functional methods for the calculation of electron paramagnetic resonance parameters of dinuclear mixed-valence MnIVMnIII complexes

. The EPR parameters of a series of dinuclear manganese(III,IV) complexes with mono(μ-oxo), bis(μ-oxo), (μ-oxo)(μ-carboxylato), bis(μ-oxo)(μ-carboxylato), and (μ-oxo)bis(μ-carboxylato) bridges were studied by broken-symmetry density functional (DFT) methods. The influence of the exchange-correlation functional on the agreement with experiment has been evaluated systematically for g tensors; 55Mn, 14N, and 1H hyperfine coupling tensors; and Heisenberg exchange couplings. 14N and 1H hyperfine couplings, 55Mn hyperfine anisotropies, g tensors, and exchange couplings are well described by hybrid functionals with moderate exact-exchange admixtures such as B3LYP. The isotropic 55Mn hyperfine couplings require larger exact-exchange admixtures. However, the errors of the B3LYP calculations are systematic and may be corrected by a constant scaling factor, providing good predictive power for a wide range of EPR parameters with broken-symmetry DFT and standard functionals. The influence of terminal and bridging ligands on structure, spin-density distributions, and EPR parameters are evaluated systematically. Computed hyperfine and g tensors are not covariant to each other. This may have consequences for spectra simulations. The nature of the broken-symmetry state and the origin of its spin contamination were analyzed by an expansion into restricted determinants, based on paired orbitals.

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.

FTIR evidence that the PsbP extrinsic protein induces protein conformational changes around the oxygen-evolving Mn cluster in photosystem II

Extrinsic proteins of photosystem II (PSII) regulate the oxygen-evolving reaction performed at the Mn cluster by controlling the binding properties of the indispensable cofactors Ca(2+) and Cl(-). However, the molecular mechanism underlying this regulation is not yet understood. We have investigated the structural couplings of the extrinsic proteins PsbO, PsbP, and PsbQ of higher plants with the Mn cluster using Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon the S(1) --> S(2) transition were measured using spinach PSII membranes, and the effects of the selective depletion of extrinsic proteins were examined. Depletion of the PsbP and PsbQ proteins by NaCl washing revealed clear changes in the amide I bands with no appreciable changes in the bands of carboxylate and imidazole groups, whereas the depletion of all three proteins by CaCl(2) washing did not cause further changes. The original amide I features were recovered by reconstitution of the NaCl-washed PSII with PsbP, and the same recovery was observed with (13)C-labeled PsbP. These results indicate that the PsbP protein, but not PsbQ and PsbO, affects the protein conformation around the Mn cluster in the intrinsic proteins without changing the ligand structure. Reconstitution with Delta15-PabP, in which the 15 N-terminal residues were truncated, did not restore the amide I bands, indicating that the interaction of the N-terminal region induces the conformational changes. This observation correlates well with a previous finding that Delta15-PabP did not restore the Ca(2+) and Cl(-) retention ability upon rebinding to PSII [Ifuku, K., et al. (2005) Photosynth. Res. 84, 251-255]. Therefore, the evidence strongly suggests that protein conformational changes around the Mn cluster induced by PsbP through its N-terminal region affect the binding properties of Ca(2+) and Cl(-) and enhance their retention.

Monitoring water reactions during the S-state cycle of the photosynthetic water-oxidizing center: detection of the DOD bending vibrations by means of Fourier transform infrared spectroscopy

Photosynthetic water oxidation takes place in the water-oxidizing center (WOC) of photosystem II (PSII). To clarify the mechanism of water oxidation, detecting water molecules in the WOC and monitoring their reactions at the molecular level are essential. In this study, we have for the first time detected the DOD bending vibrations of functional D 2O molecules during the S-state cycle of the WOC by means of Fourier transform infrared (FTIR) difference spectroscopy. Flash-induced FTIR difference spectra upon S-state transitions were measured using the PSII core complexes from Thermosynechococcus elongatus moderately deuterated with D 2 (16)O and D 2 (18)O. D 2 (16)O-minus-D 2 (18)O double difference spectra at individual S-state transitions exhibited six to eight peaks arising from the D (16)OD/D (18)OD bending vibrations in the 1250-1150 cm (-1) region. This observation indicates that at least two water molecules, not in any deprotonated forms, participate in the reaction at each S-state transition throughout the cycle. Most of the peaks exhibited clear counter peaks with opposite signs at different transitions, reflecting a series of reactions of water molecules at the catalytic site. In contrast, negative bands at approximately 1240 cm (-1) in the S 2 --> S 3, S 3 --> S 0, and possibly S 0 --> S 1 transitions, for which no clear counter peaks were found in other transitions, can be interpreted as insertion of substrate water into the WOC from a water cluster in the proteins. The characteristics of the weakly D-bonded OD stretching bands were consistent with the insertion of substrate from internal water molecules in the S 2 --> S 3 and S 3 --> S 0 transitions. The results of this study show that FTIR detection of the DOD bending vibrations is a powerful method for investigating the molecular mechanism of photosynthetic water oxidation as well as other enzymatic reactions involving functional water molecules.