Structure of the Mn4-Ca cluster as derived from X-ray diffraction

Core atoms escape from the shell: reverse segregation of Pb-Al core-shell nanoclusters via nanoscale melting

Melting is a phase transition that profoundly affects the fabrication and diverse applications of metal nanoclusters. Core-shell clusters offer distinctive properties and thus opportunities compared with other classes of nano-alloys. Molecular dynamics simulations have been employed to investigate the melting behaviour of Pb-Al core-shell clusters containing a fixed Pb147 core and varying shell thickness. Our results show that the core and shell melt separately. Surprisingly, core melting always drives the core Pb atoms to break out the shell and coat the nanoclusters in a reversed segregation process at the nanoscale. The melting point of the core increases with the shell thickness to exceed that of the bare core cluster, but the thinnest shell always supresses the core melting point. These results can be a reference for the future fabrication, manipulation, and exploitation of the core-shell nanoalloys chosen. The system chosen is ideally suited for experimental observations.

The diversity and distribution of D1 proteins in cyanobacteria

The psbA gene family in cyanobacteria encodes different forms of the D1 protein that is part of the Photosystem II reaction centre. We have identified a phylogenetically distinct D1 group that is intermediate between previously identified G3-D1 and G4-D1 proteins (Cardona et al. Mol Biol Evol 32:1310-1328, 2015). This new group contained two subgroups: D1^INT, which was frequently in the genomes of heterocystous cyanobacteria and D1^FR that was part of the far-red light photoacclimation gene cluster of cyanobacteria. In addition, we have identified subgroups within G3, the micro-aerobically expressed D1 protein. There are amino acid changes associated with each of the subgroups that might affect the function of Photosystem II. We show a phylogenetically broad range of cyanobacteria have these D1 types, as well as the genes encoding the G2 protein and chlorophyll f synthase. We suggest identification of additional D1 isoforms and the presence of multiple D1 isoforms in phylogenetically diverse cyanobacteria supports the role of these proteins in conferring a selective advantage under specific conditions.

Preparation and Properties of an MnIV-Hydroxide Complex: Proton and Electron Transfer at a Mononuclear Manganese Site and its Relationship to the Oxygen Evolving Complex within Photosystem II

Photosynthetic water oxidation is catalyzed by a Mn4O5Ca cluster with an unprecedented arrangement of metal ions in which a single manganese center is bonded to a distorted Mn3O4Ca cubane-like structure. Several mechanistic proposals describe the unique manganese center as a site for water binding and subsequent formation of a high valent Mn-oxo center that reacts with a M-OH unit (M = Mn or CaII) to form the O-O bond. The conversion of low valent Mn-OHn (n = 1,2) to a Mn-oxo species requires that a single manganese site be able to accommodate several oxidation states as the water ligand is deprotonated. To study these processes, the preparation and characterization of a new monomeric MnIV-OH complex is described. The MnIV-OH complex completes a series of well characterized Mn-OH and Mn-oxo complexes containing the same primary and secondary coordination spheres; this work thus demonstrates that a single ligand can support mononuclear Mn complexes spanning four different oxidation states (II through V) with oxo and hydroxo ligands that are derived from water. Moreover, we have completed a thermodynamic analysis based on this series of manganese complexes to predict the formation of high valent Mn-oxo species; we demonstrated that the conversion of a MnIV-OH species to a MnV-oxo complex would likely occur via a stepwise proton transfer-electron transfer mechanism. The large dissociation energy for the MnIVO-H bond (~95 kcal/mol) diminished the likelihood that other pathways are operative within a biological context. Furthermore, these studies showed that reactions between Mn-OH and Mn-oxo complexes lead to non-productive, one-electron processes suggesting that initial O-O bond formation with the OEC does not involve an Mn-OH unit.

Structure of gamma-secretase and its trimeric pre-activation intermediate by single-particle electron microscopy

The γ-secretase membrane protein complex is responsible for proteolytic maturation of signaling precursors and catalyzes the final step in the production of the amyloid β-peptides implicated in the pathogenesis of Alzheimer disease. The incorporation of PEN-2 (presenilin enhancer 2) into a pre-activation intermediate, composed of the catalytic subunit presenilin and the accessory proteins APH-1 (anterior pharynx-defective 1) and nicastrin, triggers the endoproteolysis of presenilin and results in an active tetrameric γ-secretase. We have determined the three-dimensional reconstruction of a mature and catalytically active γ-secretase using single-particle cryo-electron microscopy. γ-Secretase has a cup-like shape with a lateral belt of ∼40-50 Å in height that encloses a water-accessible internal chamber. Active site labeling with a gold-coupled transition state analog inhibitor suggested that the γ-secretase active site faces this chamber. Comparison with the structure of a trimeric pre-activation intermediate suggested that the incorporation of PEN-2 might contribute to the maturation of the active site architecture.

Light-induced quinone reduction in photosystem II

The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.

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.

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.

An alternative method for calcium depletion of the oxygen evolving complex of photosystem II as revealed by the dark-stable multiline EPR signal

The dark-stable multiline EPR signal of photosystem II (PSII) is associated with a slow-decaying S(2) state that is due to Ca(2+) loss from the oxygen evolving complex. Formation of the signal was observed in intact PSII in the presence of 100-250 mM NaCl at pH 5.5. Both moderately high NaCl concentration and decreased pH were required for its appearance in intact PSII. It was estimated that only a portion of oxygen evolving complexes was responsible for the signal (about 20% in 250 mM NaCl), based on the loss of the normal S(2)-state multiline signal. The formation of the dark-stable multiline signal in intact PSII at pH 5.5 could be reversed by addition of 15 mM Ca(2+) in the presence of moderately high NaCl, confirming that it was the absence of Ca(2+) that led to its appearance. Formation of the dark-stable multiline signal in NaCl-washed PSII, which lacks the PsbP (23 kDa) and PsbQ (17 kDa) subunits, was observed in about 80% of the sample in the presence of 150 mM NaCl at pH 5.5, but some signal was also observed under normal buffer conditions. In both intact and NaCl-washed PSII, the S(2)Y(Z). signal, which is also characteristic of Ca(2+) depletion, appeared upon subsequent illumination. Formation of the dark-stable multiline signal took place in the absence of Ca(2+) chelator or polycarboxylic acids, indicating that the signal did not require their direct binding as has been proposed previously. The conditions used here were milder than those used to produce the signal in previous studies and included a preillumination protocol to maximize the dark-stable S(2) state. Based on these conditions, it is suggested that Ca(2+) release occurred through protonation of key residues that coordinate Ca(2+) at low pH, followed by displacement of Ca(2+) with Na(+) by mass action at the moderately high NaCl concentration.

Magnetic and spectroscopic properties of mixed valence manganese(III,IV) dimers: a systematic study using broken symmetry density functional theory

Exchange coupling parameters and isotropic (55)Mn hyperfine couplings of fourteen mixed-valence Mn(III)-Mn(IV) dimers are determined using broken-symmetry density functional theory (DFT) and spin projection techniques. A systematic evaluation of density functional approaches shows that the TPSSh functional yields the best exchange coupling constants among all investigated methods, with deviations from experiment of the order of approximately 10-15%. For the prediction of (55)Mn hyperfine couplings the deficiencies of DFT in the description of core-level spin-polarization and the neglect of scalar relativistic effects lead to systematic deviations between theory and experiment that can be compensated through the use of a universal scaling factor. We determine this scaling factor to be 1.49 and demonstrate that the (55)Mn hyperfine couplings in mixed-valence Mn(III,IV) dimers can be successfully and systematically predicted with the TPSSh functional and the proposed spin projection techniques. The dependence of isotropic (55)Mn hyperfine couplings on the Mn(III) zero-field splitting values is studied in detail using a dimer for which the strong exchange approximation breaks down. In this case we apply a rigorous form of our spin projection technique that incorporates zero-field splitting contributions to the site spin expectation values. These results form the basis for future studies that aim at deducing unknown structures on the basis of computed spectroscopic parameters.

A new quantum chemical approach to the magnetic properties of oligonuclear transition-metal complexes: application to a model for the tetranuclear manganese cluster of photosystem II

The reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition-metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken-symmetry density functional theory (BS-DFT) calculations on clusters. Using the geometry-optimized tetranuclear manganese complex [Mn(4)O(6)(bpy)(6)](4+/3+) as a model, we first examine in detail the calculation of exchange coupling constants J through the BS-DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of (55)Mn HFCs of the Mn(III,IV,IV,IV) state of the complex, which is similar to the S(2) state of the oxygen-evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero-oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.

The dynamics of photosynthesis

Despite recent elucidation of the three-dimensional structure of major photosynthetic complexes, our understanding of light energy conversion in plant chloroplasts and microalgae under physiological conditions requires exploring the dynamics of photosynthesis. The photosynthetic apparatus is a flexible molecular machine that can acclimate to metabolic and light fluctuations in a matter of seconds and minutes. On a longer time scale, changes in environmental cues trigger acclimation responses that elicit intracellular signaling between the nucleo-cytosol and chloroplast resulting in modification of the biogenesis of the photosynthetic machinery. Here we attempt to integrate well-established knowledge on the functional flexibility of light-harvesting and electron transfer processes, which has greatly benefited from genetic approaches, with data derived from the wealth of recent transcriptomic and proteomic studies of acclimation responses in photosynthetic eukaroytes.

Mediator-assisted water oxidation by the ruthenium "blue dimer" cis,cis-[(bpy)2(H2O)RuORu(OH2)(bpy)2]4+

Light-driven water oxidation occurs in oxygenic photosynthesis in photosystem II and provides redox equivalents directed to photosystem I, in which carbon dioxide is reduced. Water oxidation is also essential in artificial photosynthesis and solar fuel-forming reactions, such as water splitting into hydrogen and oxygen (2 H(2)O + 4 h nu --> O(2) + 2 H(2)) or water reduction of CO(2) to methanol (2 H(2)O + CO(2) + 6 h nu --> CH(3)OH + 3/2 O(2)), or hydrocarbons, which could provide clean, renewable energy. The "blue ruthenium dimer," cis,cis-[(bpy)(2)(H(2)O)Ru(III)ORu(III)(OH(2))(bpy)(2)](4+), was the first well characterized molecule to catalyze water oxidation. On the basis of recent insight into the mechanism, we have devised a strategy for enhancing catalytic rates by using kinetically facile electron-transfer mediators. Rate enhancements by factors of up to approximately 30 have been obtained, and preliminary electrochemical experiments have demonstrated that mediator-assisted electrocatalytic water oxidation is also attainable.

Structural and functional aspects of the MSP (PsbO) and study of its differences in thermophilic versus mesophilic organisms

The Manganese Stabilizing Protein (MSP) of Photosystem II (PSII) is a so-called extrinsic subunit, which reversibly associates with the other membrane-bound PSII subunits. The MSP is essential for maximum rates of O(2) production under physiological conditions as stabilizes the catalytic [Mn(4)Ca] cluster, which is the site of water oxidation. The function of the MSP subunit in the PSII complex has been extensively studied in higher plants, and the structure of non-PSII associated MSP has been studied by low-resolution biophysical techniques. Recently, crystal structures of PSII from the thermophilic cyanobacterium Thermosynechococcus elongatus have resolved the MSP subunit in its PSII-associated state. However, neither any crystal structure is available yet for MSP from mesophilic organisms, higher plants or algae nor has the non-PSII associated form of MSP been crystallized. This article reviews the current understanding of the structure, dynamics, and function of MSP, with a particular focus on properties of the MSP from T. elongatus that may be attributable to the thermophilic ecology of this organism rather than being general features of MSP.

The inhibitory effects of acidification and augmented oxygen pressure on water oxidation

Cyanobacteria, algae, and plants produce dioxygen from water. Driven and clocked by light quanta, the catalytic Mn(4)Ca Tyrosine centre accumulates four oxidizing equivalents before it abstracts four electrons from water and liberates dioxygen and protons. Intermediates of this reaction cascade are short-lived (<100 micros) and difficult to detect. By application of high oxygen pressure to cyanobacterial PSII-core-complexes, we have previously suppressed the transition from the highest oxidation state of the centre to the lowest by stabilizing a (peroxy) intermediate. Here, we investigated the inhibitory interplay of acidification and augmented oxygen pressure. Starting from pH 6.5, acidification increasingly inhibited the reduction of the highest oxidized state and resulted in a lower oxygen partial pressure for half inhibition. Oxygen and proton interfere with different steps of the reaction cascade.

Structure of Photosystems I and II

Photosynthesis is the major process that converts solar energy into chemical energy on Earth. Two and a half billion years ago, the ancestors of cyanobacteria were able to use water as electron source for the photosynthetic process, thereby evolving oxygen and changing the atmosphere of our planet Earth. Two large membrane protein complexes, Photosystems I and II, catalyze the primary step in this energy conversion, the light-induced charge separation across the photosynthetic membrane. This chapter describes and compares the structure of two Photosystems and discusses their function in respect to the mechanism of light harvesting, electron transfer and water splitting.

The terminal reaction cascade of water oxidation: proton and oxygen release

In cyanobacteria, algae and plants Photosystem II produces the oxygen we breathe. Driven and clocked by light quanta, the catalytic Mn(4)Ca-tyrosine centre accumulates four oxidising equivalents before it abstracts four electrons from water, liberating dioxygen and protons. Aiming at intermediates of the terminal four-electron cascade, we previously have suppressed this reaction by elevating the oxygen pressure, thereby stabilising one redox intermediate. Here, we established a similar suppression by increasing the proton concentration. Data were analysed in terms of only one (peroxy) redox intermediate between the fourfold oxidised Mn(4)Ca-tyrosine centre and oxygen release. The surprising result was that the release into the bulk of one proton per dioxygen is linked to the first and rate-limiting electron transfer in the cascade rather than to the second which produces free oxygen. The penultimate intermediate might thus be conceived as a fully deprotonated peroxy-moiety.

Crystal structure of cyanobacterial photosystem II at 3.0 A resolution: a closer look at the antenna system and the small membrane-intrinsic subunits

Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the water splitting reaction during oxygenic photosynthesis. In the first part of this review, we describe the current state of the crystal structure at 3.0 A resolution of cyanobacterial PSII from Thermosynechococcus elongatus [B. Loll et al., Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-1044] with emphasis on the core antenna subunits CP43 and CP47 and the small membrane-intrinsic subunits. The second part describes first the general theory of optical spectra and excitation energy transfer and how the parameters of the theory can be obtained from the structural data. Next, structure-function relationships are discussed that were identified from stationary and time-resolved experiments and simulations of optical spectra and energy transfer processes.