David J. Vinyard

Photosystem II: The Reaction Center of Oxygenic Photosynthesis*

Photosystem II (PSII) uses light energy to split water into chemical products that power the planet. The stripped protons contribute to a membrane electrochemical potential before combining with the stripped electrons to make chemical bonds and releasing O2 for powering respiratory metabolisms. In this review, we provide an overview of the kinetics and thermodynamics of water oxidation that highlights the conserved performance of PSIIs across species. We discuss recent advances in our understanding of the site of water oxidation based upon the improved (1.9-Å resolution) atomic structure of the Mn4CaO5 water-oxidizing complex (WOC) within cyanobacterial PSII. We combine these insights with recent knowledge gained from studies of the biogenesis and assembly of the WOC (called photoassembly) to arrive at a proposed chemical mechanism for water oxidation.

Oxidized quinones signal onset of darkness directly to the cyanobacterial circadian oscillator

Synchronization of the circadian clock in cyanobacteria with the day/night cycle proceeds without an obvious photoreceptor, leaving open the question of its specific mechanism. The circadian oscillator can be reconstituted in vitro, where the activities of two of its proteins, KaiA and KaiC, are affected by metabolites that reflect photosynthetic activity: KaiC phosphorylation is directly influenced by the ATP/ADP ratio, and KaiA stimulation of KaiC phosphorylation is blocked by oxidized, but not reduced, quinones. Manipulation of the ATP/ADP ratio can reset the timing of KaiC phosphorylation peaks in the reconstituted in vitro oscillator. Here, we show that pulses of oxidized quinones reset the cyanobacterial circadian clock both in vitro and in vivo. Onset of darkness causes an abrupt oxidation of the plastoquinone pool in vivo, which is in contrast to a gradual decrease in the ATP/ADP ratio that falls over the course of hours until the onset of light. Thus, these two metabolic measures of photosynthetic activity act in concert to signal both the onset and duration of darkness to the cyanobacterial clock.

Binding of dinitrogen to an iron–sulfur–carbon site

Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron–molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe–S bond and binds N2. The product is the first synthetic Fe–N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe–S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.

Oxygen-evolving complex of Photosystem II: an analysis of second-shell residues and hydrogen-bonding networks.

The oxygen-evolving complex (OEC) is a Mn4O5Ca cluster embedded in the Photosystem II (PSII) protein complex. As the site of water oxidation, the OEC is connected to the lumen by channels that conduct water, oxygen, and/or protons during the catalytic cycle. The hydrogen-bond networks found in these channels also serve to stabilize the oxidized intermediates, known as the S states. We review recent developments in characterizing these networks via protein mutations, molecular inhibitors, and computational modeling. On the basis of these results, we highlight regions of the PSII protein in which changes have indirect effects on the S1, S2, and S3 oxidation states of the OEC while still allowing photosynthetic activity.

Analysis of the Radiation-Damage-Free X‑ray Structure of Photosystem II in Light of EXAFS and QM/MM Data

A recent femtosecond X-ray diffraction study produced the first high-resolution structural model of the oxygen-evolving complex of photosystem II that is free of radiation-induced manganese reduction (Protein Data Bank entries 4UB6 and 4UB8 ). We find, however, that the model does not match extended X-ray absorption fine structure and QM/MM data for the S1 state. This is attributed to uncertainty about the positions of oxygen atoms that remain partially unresolved, even at 1.95 Å resolution, next to the heavy manganese centers. In addition, the photosystem II crystals may contain significant amounts of the S0 state, because of extensive dark adaptation prior to data collection.

Comparison of dppf‐Supported Nickel Precatalysts for the Suzuki–Miyaura Reaction: The Observation and Activity of Nickel(I)

Ni-based precatalysts for the Suzuki-Miyaura reaction have potential chemical and economic advantages compared to commonly used Pd systems. Here, we compare Ni precatalysts for the Suzuki-Miyaura reaction supported by the dppf ligand in 3 oxidation states, 0, I and II. Surprisingly, at 80 °C they give similar catalytic activity, with all systems generating significant amounts of Ni(I) during the reaction. At room temperature a readily accessible bench-stable Ni(II) precatalyst is highly active and can couple synthetically important heterocyclic substrates. Our work conclusively establishes that Ni(I) species are relevant in reactions typically proposed to involve exclusively Ni(0) and Ni(II) complexes.

A Multi-iron System Capable of Rapid N2 Formation and N2 Cleavage

The six-electron oxidation of two nitrides to N2 is a key step of ammonia synthesis and decomposition reactions on surfaces. In molecular complexes, nitride coupling has been observed with terminal nitrides, but not with bridging nitride complexes that more closely resemble catalytically important surface species. Further, nitride coupling has not been reported in systems where the nitrides are derived from N2. Here, we show that a molecular diiron(II) diiron(III) bis(nitride) complex reacts with Lewis bases, leading to the rapid six-electron oxidation of two bridging nitrides to form N2. Surprisingly, these mild reagents generate high yields of iron(I) products from the iron(II/III) starting material. This is the first molecular system that both breaks and forms the triple bond of N2 at room temperature. These results highlight the ability of multi-iron species to decrease the energy barriers associated with the activation of strong bonds.

Natural Variants of Photosystem II Subunit D1 Tune Photochemical Fitness to Solar Intensity

Background: Cyanobacteria use multiple PSII-D1 isoforms to adapt to environmental conditions. Results: D1:2 achieves higher quantum efficiency of water oxidation and biomass accumulation rate at high light versus D1:1; the latter is more efficient at low light due to less charge recombination. Conclusion: A functional advantage for D1:1 is revealed for the first time. Significance: Improved photochemical efficiency at low light suggests an evolutionary advantage to retain D1:1. Photosystem II (PSII) is composed of six core polypeptides that make up the minimal unit capable of performing the primary photochemistry of light-driven charge separation and water oxidation in all oxygenic phototrophs. The D1 subunit of this complex contains most of the ligating amino acid residues for the Mn4CaO5 core of the water-oxidizing complex (WOC). Most cyanobacteria have 3–5 copies of the psbA gene coding for at least two isoforms of D1, whereas algae and plants have only one isoform. Synechococcus elongatus PCC 7942 contains two D1 isoforms; D1:1 is expressed under low light conditions, and D1:2 is up-regulated in high light or stress conditions. Using a heterologous psbA expression system in the green alga Chlamydomonas reinhardtii, we have measured growth rate, WOC cycle efficiency, and O2 yield as a function of D1:1, D1:2, or the native algal D1 isoform. D1:1-PSII cells outcompete D1:2-PSII cells and accumulate more biomass in light-limiting conditions. However, D1:2-PSII cells easily outcompete D1:1-PSII cells at high light intensities. The native C. reinhardtii-PSII WOC cycles less efficiently at all light intensities and produces less O2 than either cyanobacterial D1 isoform. D1:2-PSII makes more O2 per saturating flash than D1:1-PSII, but it exhibits lower WOC cycling efficiency at low light intensities due to a 40% faster charge recombination rate in the S3 state. These functional advantages of D1:1-PSII and D1:2-PSII at low and high light regimes, respectively, can be explained by differences in predicted redox potentials of PSII electron acceptors that control kinetic performance.

NH3 Binding to the S2 State of the O2-Evolving Complex of Photosystem II: Analogue to H2O Binding during the S2 → S3 Transition.

Ammonia binds directly to the oxygen-evolving complex of photosystem II (PSII) upon formation of the S2 intermediate, as evidenced by electron paramagnetic resonance spectroscopy. We explore the binding mode by using quantum mechanics/molecular mechanics methods and simulations of extended X-ray absorption fine structure spectra. We find that NH3 binds as an additional terminal ligand to the dangling Mn4, instead of exchanging with terminal water. Because water and ammonia are electronic and structural analogues, these findings suggest that water binds analogously during the S2 → S3 transition, leading to rearrangement of ligands in a carrousel around Mn4.

Experimental Support for a Single Electron-Transfer Oxidation Mechanism in Firefly Bioluminescence

Firefly luciferase produces light by converting substrate beetle luciferin into the corresponding adenylate that it subsequently oxidizes to oxyluciferin, the emitter of bioluminescence. We have confirmed the generally held notions that the oxidation step is initiated by formation of a carbanion intermediate and that a hydroperoxide (anion) is involved. Additionally, structural evidence is presented that accounts for the delivery of oxygen to the substrate reaction site. Herein, we report key convincing spectroscopic evidence of the participation of superoxide anion in a related chemical model reaction that supports a single electron-transfer pathway for the critical oxidative process. This mechanism may be a common feature of bioluminescence processes in which light is produced by an enzyme in the absence of cofactors.