High-resolution structure of the photosynthetic Mn4Ca catalyst from X-ray spectroscopy

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn₄Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S₀-S₄). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this study, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S₂ state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the "narrow" channel is altered in D1-N87A PSII, allowing for the binding of deprotonated ¹³C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S₂ state. This has important implications on the mechanistic models for water oxidation in PSII.

Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA

BACKGROUND

The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach.

SCOPE OF REVIEW

Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described.

MAJOR CONCLUSIONS

XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data.

GENERAL SIGNIFICANCE

XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.

A DFT/B3LYP study of the mechanisms of the O2 formation reaction catalyzed by the [(terpy)(H2O)MnIII(O)2MnIV(OH2)(terpy)](NO3)3 complex: A paradigm for photosystem II

We present a theoretical study of the reaction pathway for dioxygen molecular formation catalyzed by the [(terpy)(H₂O)Mn^III(O)₂Mn^IV(OH₂) (terpy)](NO₃)₃ (terpy=2,2':6',2″-terpyridine) complex based on DFT-B3LYP calculations. In the initial state of the reaction, a partial oxido radical (0.44 spins) is formed ligated to Mn. This radical is involved in a nucleophylic attack by bulk water in the OO bond reaction formation step, in which the oxido fractional unpaired electron is delocalized toward the outermost Mn of the μ-oxo bridge, instead of the ligated Mn center. The reaction then follows with a series of proton-coupled electron transfer steps, in which the oxidation state, as well as the bond strength of the OO moiety increase, while the OOMn(1) bond gets weaker until O₂ is released. In this model, basic acetate ions from the buffer solution capture protons in the proton-transfer steps. In each step there is reduction of the OOMn(1) binding strength, with concomitant increase of the OO bond strength, which culminates with the release of O₂ in the last step. This last step is entropy driven, while formation of hydroperoxide and superoxide moieties is enthalpy driven. According with experiments, the rate-limiting step is the double oxidation of Mn(IV,III) or peroxymonosulfate binding, which occur prior to the OO bond formation step. This supports our findings that the barriers of all intermediate steps are below the experimental barrier of 19-21kcal/mol. The implications of these findings for understanding photosynthetic water-splitting catalysis are also discussed.

X-ray spectroscopy for chemical and energy sciences: the case of heterogeneous catalysis

Heterogeneous catalysis is the enabling technology for much of the current and future processes relevant for energy conversion and chemicals synthesis. The development of new materials and processes is greatly helped by the understanding of the catalytic process at the molecular level on the macro/micro-kinetic time scale and on that of the actual bond breaking and bond making. The performance of heterogeneous catalysts is inherently the average over the ensemble of active sites. Much development aims at unravelling the structure of the active site; however, in general, these methods yield the ensemble-average structure. A benefit of X-ray-based methods is the large penetration depth of the X-rays, enabling in situ and operando measurements. The potential of X-ray absorption and emission spectroscopy methods (XANES, EXAFS, HERFD, RIXS and HEROS) to directly measure the structure of the catalytically active site at the single nanoparticle level using nanometer beams at diffraction-limited storage ring sources is highlighted. The use of pump-probe schemes coupled with single-shot experiments will extend the time range from the micro/macro-kinetic time domain to the time scale of bond breaking and making.

Recent advances on ultrafast X-ray spectroscopy in the chemical sciences

Molecular snapshots obtained by ultrafast X-ray spectroscopy reveal new insight into fundamental reaction mechanisms at single electron and atomic levels.

Reflections on substrate water and dioxygen formation

This brief article aims at presenting a concise summary of all experimental findings regarding substrate water-binding to the Mn4CaO5 cluster in photosystem II. Mass spectrometric and spectroscopic results are interpreted in light of recent structural information of the water oxidizing complex obtained by X-ray crystallography, spectroscopy and theoretical modeling. Within this framework current proposals for the mechanism of photosynthetic water-oxidation are evaluated. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

Development of bioinspired Mn4O4-cubane water oxidation catalysts: lessons from photosynthesis

Hydrogen is the most promising fuel of the future owing to its carbon-free, high-energy content and potential to be efficiently converted into either electrical or thermal energy. The greatest technical barrier to accessing this renewable resource remains the inability to create inexpensive catalysts for the solar-driven oxidation of water. To date, the most efficient system that uses solar energy to oxidize water is the photosystem II water-oxidizing complex (PSII-WOC), which is found within naturally occurring photosynthetic organisms. The catalytic core of this enzyme is a CaMn(4)O(x) cluster, which is present in all known species of oxygenic phototrophs and has been conserved since the emergence of this type of photosynthesis about 2.5 billion years ago. The key features that facilitate the catalytic success of the PSII-WOC offer important lessons for the design of abiological water oxidation catalysts. In this Account, we examine the chemical principles that may govern the PSII-WOC by comparing the water oxidation capabilities of structurally related synthetic manganese-oxo complexes, particularly those with a cubical Mn(4)O(4) core ("cubanes"). We summarize this research, from the self-assembly of the first such clusters, through the elucidation of their mechanism of photoinduced rearrangement to release O(2), to recent advances highlighting their capability to catalyze sustained light-activated electrolysis of water. The [Mn(4)O(4)](6+) cubane core assembles spontaneously in solution from monomeric precursors or from [Mn(2)O(2)](3+) core complexes in the presence of metrically appropriate bidentate chelates, for example, diarylphosphinates (ligands of Ph(2)PO(2)(-) and 4-phenyl-substituted derivatives), which bridge pairs of Mn atoms on each cube face (Mn(4)O(4)L(6)). The [Mn(4)O(4)](6+) core is enlarged relative to the [Mn(2)O(2)](3+) core, resulting in considerably weaker Mn-O bonds. Cubanes are ferocious oxidizing agents, stronger than analogous complexes with the [Mn(2)O(2)](3+) core, as demonstrated both by the range of substrates they dehydrogenate or oxygenate (unactivated alkanes, for example) and the 25% larger O-H bond enthalpy of the resulting mu(3)-OH bridge. The cubane core topology is structurally suited to releasing O(2), and it does so in high yield upon removal of one phosphinate by photoexcitation in the gas phase or thermal excitation in the solid state. This is quite unlike other Mn-oxo complexes and can be attributed to the elongated Mn-O bond lengths and low-energy transition state to the mu-peroxo precursor. The photoproduct, [Mn(4)O(2)L(5)](+), an intact nonplanar butterfly core complex, is poised for oxidative regeneration of the cubane core upon binding of two water molecules and coupling to an anode. Catalytic evolution of O(2) and protons from water exceeding 1000 turnovers can be readily achieved by suspending the oxidized cubane, [Mn(4)O(4)L(6)](+), into a proton-conducting membrane (Nafion) preadsorbed onto a conducting electrode and electroxidizing the photoreduced butterfly complexes by the application of an external bias. Catalytic water oxidation can be achieved using sunlight as the only source of energy by replacing the external electrical bias with redox coupling to a photoanode incorporating a Ru(bipyridyl) dye.

The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).

A combined picture from theory and experiments on water oxidation, oxygen reduction and proton pumping

In order to illustrate how theory and experiments can be combined, examples are taken from two projects that have been going on for a decade. The goal is to obtain the full mechanistic picture of water oxidation in photosystem II and proton pumping in cytochrome c oxidase. It is argued that for obtaining a complete description of these processes, both experiments and theoretical calculations are needed. It is obvious that there are aspects, which are out of reach for computations, but there are also key aspects that can not be obtained by experiments. This concerns very short-lived species but also, in the case of photosynthesis in particular, structural information that is presently out of reach. The main contributions from theory in the present cases, is for photosynthesis a mechanism for O-O bond formation including new and improved structures for all S-states, and for proton pumping a plausible and simple mechanism for proton gating. The examples also illustrate that sometimes rather qualitative experimental information can be of highest importance.

A structure-consistent mechanism for dioxygen formation in photosystem II

In recent DFT studies a new mechanism for O-O bond formation at the oxygen evolving center (OEC) in photosystem II has been suggested. With the structure of the S(4) state required for that mechanism, the structures of the lower S states are investigated herein by adding protons and electrons. A model was used including the full amino acids for the ones ligating the OEC, and in which the backbone positions were held fixed from the X-ray structure. The only charged second-shell ligand Arg357 was also included. An optimized structure for the S(1) state was reached with a large similarity to one of those suggested by EXAFS. A full catalytic cycle was derived which can rationalize the structural relaxation in the S(2) to S(3) transition, and the fact that only an electron leaves in the transition before. Water is suggested to bind to the OEC in the S(2) to S(3), and S(4) to S(0) transitions. A new possibility for water exchange is suggested from the final energy diagram. The optimal O-O bond formation occurs between an oxygen radical and an oxo ligand. The alternative mechanism, where the oxygen radical reacts with an external water, has a barrier about 20 kcal mol(-1) higher.