Native-like Photosystem II Superstructure at 2.44 Å Resolution through Detergent Extraction from the Protein Crystal

Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes?

Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.

Towards understanding the crystallization of photosystem II: influence of poly(ethylene glycol) of various molecular sizes on the micelle formation of alkyl maltosides

The influence of poly(ethylene glycol) (PEG) polymers H-(O-CH2-CH2)p-OH with different average molecular sizes p on the micelle formation of n-alkyl-β-D-maltoside detergents with the number of carbon atoms in the alkyl chain ranging from 10 to 12 is investigated with the aim to learn more about the detergent behavior under conditions suitable for the crystallization of the photosynthetic pigment-protein complex photosystem II. PEG is shown to increase the critical micelle concentration (CMC) of all three detergents in the crystallization buffer in a way that the free energy of micelle formation increases linearly with the concentration of oxyethylene units (O-CH2-CH2) irrespective of the actual molecular weight of the polymer. The CMC shift is modeled by assuming for simplicity that it is dominated by the interaction between PEG and detergent monomers and is interpreted in terms of an increase of the transfer free energy of a methylene group of the alkyl chain by 0.2 kJ mol-1 per 1 mol L-1 increase of the concentration of oxyethylene units at 298 K. Implications of this effect for the solubilization and crystallization of protein-detergent complexes as well as detergent extraction from crystals are discussed.

Coherences of Photoinduced Electron Spin Qubit Pair States in Photosystem I

This publication presents the first comprehensive experimental study of electron spin coherences in photosynthetic reaction center proteins, specifically focusing on photosystem I (PSI). The ultrafast electron transfer in PSI generates spin-correlated radical pairs (SCRPs), which are entangled spin pairs formed in well-defined spin states (Bell states). Since their discovery in our group in the 1980s, SCRPs have been extensively used to enhance our understanding of structure-function relationships in photosynthetic proteins. More recently, SCRPs have been utilized as tools for quantum sensing. Electron spin decoherence poses a significant challenge in realizing practical applications of electron spin qubits, particularly the creation of quantum entanglement between multiple electron spins. This work is focused on the systematic characterization of decoherence in SCRPs of PSI. These decoherence times were measured as electron spin echo decay times, termed phase memory times (TM), at various temperatures. Decoherence was recorded on both transient SCRP states P700+A1- and thermalized states. Our study reveals that TM exhibits minimal dependence on the biological species, biochemical treatment, and paramagnetic species. The analysis indicates that nuclear spin diffusion and instantaneous diffusion mechanisms alone cannot explain the observed decoherence. As a plausible explanation we discuss the assumption that the low-temperature dynamics of methyl groups in the protein surrounding the unpaired electron spin centers is the main factor governing the loss of the spin coherence in PSI.

Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography

The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the 'water wheel' to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421-425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831-15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

Room temperature crystallography and X-ray spectroscopy of metalloenzymes

The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.

Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography

Structural dynamics of water and its hydrogen-bonding networks play an important role in enzyme function via the transport of protons, ions, and substrates. To gain insights into these mechanisms in the water oxidation reaction in Photosystem II (PS II), we have performed crystalline molecular dynamics (MD) simulations of the dark-stable S1 state. Our MD model consists of a full unit cell with 8 PS II monomers in explicit solvent (861 894 atoms), enabling us to compute the simulated crystalline electron density and to compare it directly with the experimental density from serial femtosecond X-ray crystallography under physiological temperature collected at X-ray free electron lasers (XFELs). The MD density reproduced the experimental density and water positions with high fidelity. The detailed dynamics in the simulations provided insights into the mobility of water molecules in the channels beyond what can be interpreted from experimental B-factors and electron densities alone. In particular, the simulations revealed fast, coordinated exchange of waters at sites where the density is strong, and water transport across the bottleneck region of the channels where the density is weak. By computing MD hydrogen and oxygen maps separately, we developed a novel Map-based Acceptor-Donor Identification (MADI) technique that yields information which helps to infer hydrogen-bond directionality and strength. The MADI analysis revealed a series of hydrogen-bond wires emanating from the Mn cluster through the Cl1 and O4 channels; such wires might provide pathways for proton transfer during the reaction cycle of PS II. Our simulations provide an atomistic picture of the dynamics of water and hydrogen-bonding networks in PS II, with implications for the specific role of each channel in the water oxidation reaction.

Structural evidence for intermediates during O2 formation in photosystem II

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn's oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S₁ state. However, significant discrepancies are observed for the excited XFEL states (S₂, S_3, and S₀) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Refined definition of the critical micelle concentration and application to alkyl maltosides used in membrane protein research

The critical micelle concentration (CMC) of nonionic detergents is defined as the breaking point in the monomer concentration as a function of the total detergent concentration, identified by setting the third derivate of this function to zero. Combined with a mass action model for micelle formation, this definition yields analytic formulae for the concentration ratio of monomers to total detergent at the CMC and the relationship between the CMC and the free energy of micellization g mic. The theoretical breaking point is shown to coincide with the breaking point of the experimental titration curve, if the fluorescence enhancement of 8-anilino-1-naphthalene-sulfonic acid (ANS) or a similar probe dye is used to monitor micelle formation. Application to a series of n-alkyl-β-d-maltosides with the number of carbon atoms in the alkyl chain ranging from 8 to 12 demonstrates the good performance of a molecular thermodynamic model, in which the free energy of micellization is given by g mic = σΦ + g pack + g st. In this model, σ is a fit parameter with the dimension of surface tension, Φ represents the change in area of hydrophobic molecular surfaces in contact with the aqueous phase, and g pack and g st are contributions, respectively, from alkyl chain packing in the micelle interior and steric repulsion of detergent head groups. The analysis of experimental data from different sources shows that varying experimental conditions such as co-solutes in the aqueous phase can be accounted for by adapting only σ, if the co-solutes do not bind to the detergent to an appreciable extent. The model is considered a good compromise between theory and practicability to be applied in the context of in vitro investigations of membrane proteins.

Functional Water Networks in Fully Hydrated Photosystem II

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone Q_B. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.

Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster

Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in proton transporters, deliver protons to an internal site. The protonation-coupled dynamics of bulk-exposed carboxylate clusters, also known as proton antennas, is poorly described. An essential open question is how water-mediated bridges between sidechains of the cluster respond to protonation change and facilitate transient proton storage. To address this question, here I studied the protonation-coupled dynamics at the proton-binding antenna of PsbO, a small extrinsinc subunit of the photosystem II complex, with atomistic molecular dynamics simulations and systematic graph-based analyses of dynamic protein and protein-water hydrogen-bond networks. The protonation of specific carboxylate groups is found to impact the dynamics of their local protein-water hydrogen-bond clusters. Regardless of the protonation state considered for PsbO, carboxylate pairs that can sample direct hydrogen bonding, or bridge via short hydrogen-bonded water chains, anchor to nearby basic or polar protein sidechains. As a result, carboxylic sidechains of the hypothesized antenna cluster are part of dynamic hydrogen bond networks that may rearrange rapidly when the protonation changes.

Investigation of Photosystem II Functional Size in Higher Plants under Physiological and Stress Conditions Using Radiation Target Analysis and Sucrose Gradient Ultracentrifugation

The photosystem II (PSII) reaction centre is the critical supramolecular pigment-protein complex in the chloroplast which catalyses the light-induced transfer of electrons from water to plastoquinone. Structural studies have demonstrated the existence of an oligomeric PSII. We carried out radiation inactivation target analysis (RTA), together with sucrose gradient ultracentrifugation (SGU) of PSII, to study the functional size of PSII in diverse plant species under physiological and stress conditions. Two PSII populations, made of dimeric and monomeric core particles, were revealed in Pisum sativum, Spinacea oleracea, Phaseulus vulgaris, Medicago sativa, Zea mais and Triticum durum. However, this core pattern was not ubiquitous in the higher plants since we found one monomeric core population in Vicia faba and a dimeric core in the Triticum durum yellow-green strain, respectively. The PSII functional sizes measured in the plant seedlings in vivo, as a decay of the maximum quantum yield of PSII for primary photochemistry, were in the range of 75-101 ± 18 kDa, 2 to 3 times lower than those determined in vitro. Two abiotic stresses, heat and drought, imposed individually on Pisum sativum, increased the content of the dimeric core in SGU and the minimum functional size determined by RTA in vivo. These data suggest that PSII can also function as a monomer in vivo, while under heat and drought stress conditions, the dimeric PSII structure is predominant.

Structural and dynamic insights into Mn4Ca cluster-depleted Photosystem II

In the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn₄Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Understanding the molecular details of such a process has important implications in different fields, in particular inspiring synthesis and repair strategies for artificial photosynthesis devices. In this regard, a detailed structural and dynamic characterization of Photosystem II lacking a Mn₄Ca cluster, namely apo PSII, is a prerequisite for the full comprehension of the photoactivation. Recently, the structure of the apo PSII was resolved at 2.55 Å resolution [Zhang et al., eLife, 2017, 6, e26933], suggesting a pre-organized structure of the protein cavity hosting the cluster. Anyway, the question of whether these findings are a feature of the method used remains open. Here, by means of classical Molecular Dynamics simulations, we characterized the structural and dynamic features of the apo PSII for different protonation states of the cluster cavity. Albeit an overall conformational stability common to all investigated systems, we found significant deviations in the conformation of the side chains of the active site with respect to the X-ray positions. Our findings suggest that not all residues acting as Mn ligands are pre-organized prior to the Mn₄Ca formation and previous local conformational changes are required in order to bind the first Mn ion in the high-affinity binding site.

Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S₂ to S₃ transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

In situ cryo-ET structure of phycobilisome-photosystem II supercomplex from red alga

Phycobilisome (PBS) is the main light-harvesting antenna in cyanobacteria and red algae. How PBS transfers the light energy to photosystem II (PSII) remains to be elucidated. Here we report the in situ structure of the PBS-PSII supercomplex from Porphyridium purpureum UTEX 2757 using cryo-electron tomography and subtomogram averaging. Our work reveals the organized network of hemiellipsoidal PBS with PSII on the thylakoid membrane in the native cellular environment. In the PBS-PSII supercomplex, each PBS interacts with six PSII monomers, of which four directly bind to the PBS, and two bind indirectly. Additional three 'connector' proteins also contribute to the connections between PBS and PSIIs. Two PsbO subunits from adjacent PSII dimers bind with each other, which may promote stabilization of the PBS-PSII supercomplex. By analyzing the interaction interface between PBS and PSII, we reveal that αLCM and ApcD connect with CP43 of PSII monomer and that αLCM also interacts with CP47' of the neighboring PSII monomer, suggesting the multiple light energy delivery pathways. The in situ structures illustrate the coupling pattern of PBS and PSII and the arrangement of the PBS-PSII supercomplex on the thylakoid, providing the near-native 3D structural information of the various energy transfer from PBS to PSII.

Integrating on-grid immunogold labeling and cryo-electron tomography to reveal photosystem II structure and spatial distribution in thylakoid membranes

A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native environment. Here, we describe a workflow that combines on-grid immunogold labeling, followed by cryo-electron tomography (cryoET) imaging and structural analyses to identify and characterize the structure of photosystem II (PSII) complexes. Using an antibody specific to a core subunit of PSII, the D1 protein (uniquely found in the water splitting complex in all oxygenic photoautotrophs), we identified PSII complexes in biophysically active thylakoid membranes isolated from a model marine diatom Phaeodactylum tricornutum. Subsequent cryoET analyses of these protein complexes resolved two PSII structures: supercomplexes and dimeric cores. Our integrative approach establishes the structural signature of multimeric membrane protein complexes in their native environment and provides a pathway to elucidate their high-resolution structures.

High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction

In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn₄CaO₅-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

Characterizing the supercomplex association of photosynthetic complexes in cyanobacteria

The light reactions of photosynthesis occur in thylakoid membranes that are densely packed with a series of photosynthetic complexes. The lateral organization and close association of photosynthetic complexes in native thylakoid membranes are vital for efficient light harvesting and energy transduction. Recently, analysis of the interconnections between photosynthetic complexes to form supercomplexes has garnered great interest. In this work, we report a method integrating immunoprecipitation, mass spectrometry and atomic force microscopy to identify the inter-complex associations of photosynthetic complexes in thylakoid membranes from the cyanobacterium Synechococcus elongatus PCC 7942. We characterize the preferable associations between individual photosynthetic complexes and binding proteins involved in the complex-complex interfaces, permitting us to propose the structural models of photosynthetic complex associations that promote the formation of photosynthetic supercomplexes. We also identified other potential binding proteins with the photosynthetic complexes, suggesting the highly connecting networks associated with thylakoid membranes. This study provides mechanistic insight into the physical interconnections of photosynthetic complexes and potential partners, which are crucial for efficient energy transfer and physiological acclimatization of the photosynthetic apparatus. Advanced knowledge of the protein organization and interplay of the photosynthetic machinery will inform rational design and engineering of artificial photosynthetic systems to supercharge energy production.

Solution Structure of the Detergent-Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques

Albeit achieving the X-ray diffraction structure of dimeric photosystem II core complexes (dPSIIcc) at the atomic resolution, the nature of the detergent belt surrounding dPSIIcc remains ambiguous. Therefore, the solution structure of the whole detergent-protein complex of dPSIIcc of Thermosynechococcus elongatus (T. elongatus) solubilized in n-dodecyl-ß-d-maltoside (ßDM) was investigated by a combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) with contrast variation. First, the structure of dPSIIcc was studied separately in SANS experiments using a contrast of 5% D₂O. Guinier analysis reveals that the dPSIIcc solution is virtually free of aggregation in the studied concentration range of 2-10 mg/mL dPSIIcc, and characterized by a radius of gyration of 62 Å. A structure reconstitution shows that dPSIIcc in buffer solution widely retains the crystal structure reported by X-ray free electron laser studies at room temperature with a slight expansion of the entire protein. Additional SANS experiments on dPSIIcc samples in a buffer solution containing 75% D₂O provide information about the size and shape of the whole detergent-dPSIIcc. The maximum position of P(r) function increases to 68 Å, i.e., it is about 6 Å larger than that of dPSIIcc only, thus indicating the presence of an additional structure. Thus, it can be concluded that dPSIIcc is surrounded by a monomolecular belt of detergent molecules under appropriate solubilization conditions. The homogeneity of the ßDM-dPSIIcc solutions was also verified using dynamic light scattering. Complementary SAXS experiments indicate the presence of unbound detergent micelles by a separate peak consistent with a spherical shape possessing a radius of about 40 Å. The latter structure also contributes to the SANS data but rather broadens the SANS curve artificially. Without the simultaneous inspection of SANS and SAXS data, this effect may lead to an apparent underestimation of the size of the PS II-detergent complex. The formation of larger unbound detergent aggregates in solution prior to crystallization may have a significant effect on the crystal formation or quality of the ßDM-dPSIIcc.

Structural variability, coordination and adaptation of a native photosynthetic machinery

Cyanobacterial thylakoid membranes represent the active sites for both photosynthetic and respiratory electron transport. We used high-resolution atomic force microscopy to visualize the native organization and interactions of photosynthetic complexes within the thylakoid membranes from the model cyanobacterium Synechococcus elongatus PCC 7942. The thylakoid membranes are heterogeneous and assemble photosynthetic complexes into functional domains to enhance their coordination and regulation. Under high light, the chlorophyll-binding proteins IsiA are strongly expressed and associate with Photosystem I (PSI), forming highly variable IsiA-PSI supercomplexes to increase the absorption cross-section of PSI. There are also tight interactions of PSI with Photosystem II (PSII), cytochrome b₆f, ATP synthase and NAD(P)H dehydrogenase complexes. The organizational variability of these photosynthetic supercomplexes permits efficient linear and cyclic electron transport as well as bioenergetic regulation. Understanding the organizational landscape and environmental adaptation of cyanobacterial thylakoid membranes may help inform strategies for engineering efficient photosynthetic systems and photo-biofactories.

pH-Dependent Protonation of Surface Carboxylate Groups in PsbO Enables Local Buffering and Triggers Structural Changes

Photosystem II (PSII) catalyzes the splitting of water, releasing protons and dioxygen. Its highly conserved subunit PsbO extends from the oxygen-evolving center (OEC) into the thylakoid lumen and stabilizes the catalytic Mn4 CaO5 cluster. The high degree of conservation of accessible negatively charged surface residues in PsbO suggests additional functions, as local pH buffer or by affecting the flow of protons. For this discussion, we provide an experimental basis, through the determination of pKa values of water-accessible aspartate and glutamate side-chain carboxylate groups by means of NMR. Their distribution is strikingly uneven, with high pKa values around 4.9 clustered on the luminal PsbO side and values below 3.5 on the side facing PSII. pH-dependent changes in backbone chemical shifts in the area of the lumen-exposed loops are observed, indicating conformational changes. In conclusion, we present a site-specific analysis of carboxylate group proton affinities in PsbO, providing a basis for further understanding of proton transport in photosynthesis.

Structural basis of light-harvesting in the photosystem II core complex

Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.

Mimicking the Catalytic Center for the Water-Splitting Reaction in Photosystem II

The oxygen-evolving center (OEC) in photosystem II (PSII) of plants, algae and cyanobacteria is a unique natural catalyst that splits water into electrons, protons and dioxygen. The crystallographic studies of PSII have revealed that the OEC is an asymmetric Mn4CaO5-cluster. The understanding of the structure-function relationship of this natural Mn4CaO5-cluster is impeded mainly due to the complexity of the protein environment and lack of a rational chemical model as a reference. Although it has been a great challenge for chemists to synthesize the OEC in the laboratory, significant advances have been achieved recently. Different artificial complexes have been reported, especially a series of artificial Mn4CaO4-clusters that closely mimic both the geometric and electronic structures of the OEC in PSII, which provides a structurally well-defined chemical model to investigate the structure-function relationship of the natural Mn4CaO5-cluster. The deep investigations on this artificial Mn4CaO4-cluster could provide new insights into the mechanism of the water-splitting reaction in natural photosynthesis and may help the development of efficient catalysts for the water-splitting reaction in artificial photosynthesis.

Rates and pathways of energy migration from the phycobilisome to the photosystem II and to the orange carotenoid protein in cyanobacteria

The phycobilisome (PBS) is the cyanobacterial antenna complex which transfers absorbed light energy to the photosystem II (PSII), while the excess energy is nonphotochemically quenched by interaction of the PBS with the orange carotenoid protein (OCP). Here, the molecular model of the PBS-PSII-OCP supercomplex was utilized to assess the resonance energy transfer from PBS to PSII and, using the excitonic theory, the transfer from PBS to OCP. Our estimates show that the effective energy migration from PBS to PSII is realized due to the existence of several transfer pathways from phycobilin chromophores of the PBS to the neighboring antennal chlorophyll molecules of the PSII. At the same time, the single binding site of photoactivated OCP and the PBS is sufficient to realize the quenching.

Oxygenic photosynthesis: history, status and perspective

Cyanobacteria and plants carry out oxygenic photosynthesis. They use water to generate the atmospheric oxygen we breathe and carbon dioxide to produce the biomass serving as food, feed, fibre and fuel. This paper scans the emergence of structural and mechanistic understanding of oxygen evolution over the past 50 years. It reviews speculative concepts and the stepped insight provided by novel experimental and theoretical techniques. Driven by sunlight photosystem II oxidizes the catalyst of water oxidation, a hetero-metallic Mn4CaO5(H2O)4 cluster. Mn3Ca are arranged in cubanoid and one Mn dangles out. By accumulation of four oxidizing equivalents before initiating dioxygen formation it matches the four-electron chemistry from water to dioxygen to the one-electron chemistry of the photo-sensitizer. Potentially harmful intermediates are thereby occluded in space and time. Kinetic signatures of the catalytic cluster and its partners in the photo-reaction centre have been resolved, in the frequency domain ranging from acoustic waves via infra-red to X-ray radiation, and in the time domain from nano- to milli-seconds. X-ray structures to a resolution of 1.9 Å are available. Even time resolved X-ray structures have been obtained by clocking the reaction cycle by flashes of light and diffraction with femtosecond X-ray pulses. The terminal reaction cascade from two molecules of water to dioxygen involves the transfer of four electrons, two protons, one dioxygen and one water. A rigorous mechanistic analysis is challenging because of the kinetic enslaving at millisecond duration of six partial reactions (4e−, 1H+, 1O2). For the time being a peroxide-intermediate in the reaction cascade to dioxygen has been in focus, both experimentally and by quantum chemistry. Homo sapiens has relied on burning the products of oxygenic photosynthesis, recent and fossil. Mankind's total energy consumption amounts to almost one-fourth of the global photosynthetic productivity. If the average power consumption equalled one of those nations with the highest consumption per capita it was four times greater and matched the total productivity. It is obvious that biomass should be harvested for food, feed, fibre and platform chemicals rather than for fuel.

Structures of the intermediates of Kok's photosynthetic water oxidation clock

Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle^1,2. The model comprises four (meta)stable intermediates (S₀, S₁, S₂ and S₃) and one transient S₄ state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn₄CaO₅) cluster in the oxygen-evolving complex^3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone Q_B at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional 'water', Ox, during the S₂→S₃ state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S₃ state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O₂ release. Thus, our results exclude peroxo-bond formation in the S₃ state, and the nucleophilic attack of W3 onto W2 is unlikely.

Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II

Photosystem II uses the energy of absorbed light to split water molecules, generating molecular oxygen, electrons, and protons. The four protons generated during each reaction cycle are released to the lumen via mechanisms that are poorly understood. Given the complexity of photosystem II, which consists of multiple protein subunits and cofactor molecules and hosts numerous waters, a fundamental issue is finding transient networks of hydrogen bonds that bridge potential proton donor and acceptor groups. Here, we address this issue by performing all-atom molecular dynamics simulations of wild-type and mutant photosystem II monomers, which we analyze using a new protocol designed to facilitate efficient analysis of hydrogen-bond networks. Our computations reveal that local protein/water hydrogen-bond networks can assemble transiently in photosystem II such that the reaction center connects to the lumen. The dynamics of the hydrogen-bond networks couple to the protonation state of specific carboxylate groups and are altered in a mutant with defective proton transfer. Simulations on photosystem II without its extrinsic PsbO subunit provide a molecular interpretation of the elusive functional role of this subunit.

Role of missing carotenoid in reducing the fluorescence of single monomeric photosystem II core complexes

The fluorescence of monomeric photosystem II core complexes (mPSIIcc) of the cyanobacterium Thermosynechococcus elongatus, originating from redissolved crystals, is investigated by using single-molecule spectroscopy (SMS) at 1.6 K. The emission spectra of individual mPSIIcc are dominated by sharp zero-phonon lines, showing the existence of different emitters compatible with the F685, F689, and F695 bands reported formerly. The intensity of F695 is reduced in single mPSIIcc as compared to single PSIIcc-dimers (dPSIIcc). Crystal structures show that one of the β-carotene (β-Car) cofactors located at the monomer-monomer interface in dPSIIcc is missing in mPSIIcc. This β-Car in dPSIIcc is in van der Waals distance to chlorophyll (Chl) 17 in the CP47 subunit. We suggest that this Chl contributes to the F695 emitter. A loss of β-Car cofactors in mPSIIcc preparations will lead to an increased lifetime of the triplet state of Chl 17, which can explain the reduced singlet emission of F695 as observed in SMS.

Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography

Photosystem II (PSII) catalyzes the photo-oxidation of water to molecular oxygen and protons. The water splitting reaction occurs inside the oxygen-evolving complex (OEC) via a Mn₄CaO₅ cluster. To elucidate the reaction mechanism, detailed structural information for each intermediate state of the OEC is required. Despite the current high-resolution crystal structure of PSII at 1.85 Å and other efforts to follow the structural changes of the Mn₄CaO₅ cluster using X-ray free electron laser (XFEL) crystallography in addition to spectroscopic methods, many details about the reaction mechanism and conformational changes in the catalytic site during water oxidation still remain elusive. In this study, we present a rarely found successful application of the conventional macroseeding method to a large membrane protein like the dimeric PSII core complex (dPSIIcc). Combining microseeding with macroseeding crystallization techniques allowed us to reproducibly grow large dPSIIcc crystals with a size of ~3 mm. These large crystals will help improve the data collected from spectroscopic methods like polarized extended X-ray absorption fine structure (EXAFS) and single crystal electron paramagnetic resonance (EPR) techniques and are a prerequisite for determining a three-dimensional structure using neutron diffraction.

Why we need to know the structure of phosphorylated chloroplast light-harvesting complex II

In oxygenic photosynthesis there are two 'light states' - adaptations of the photosynthetic apparatus to spectral composition that otherwise favours either photosystem I or photosystem II. In chloroplasts of green plants the transition to light state 2 depends on phosphorylation of apoproteins of a membrane-intrinsic antenna, the chlorophyll-a/b-binding, light-harvesting complex II (LHC II), and on the resulting redistribution of absorbed excitation energy from photosystem II to photosystem I. The transition to light state 1 reverses these events and requires a phospho-LHC II phosphatase. Current structures of LHC II reveal little about possible steric effects of phosphorylation. The surface-exposed N-terminal domain of an LHC II polypeptide contains its phosphorylation site and is disordered in its unphosphorylated form. A molecular recognition hypothesis proposes that state transitions are a consequence of movement of LHC II between binding sites on photosystems I and II. In state 1, LHC II forms part of the antenna of photosystem II. In state 2, a unique but as yet unidentified 3-D structure of phospho-LHC II may attach it instead to photosystem I. One possibility is that the LHC II N-terminus becomes ordered upon phosphorylation, adopting a local alpha-helical secondary structure that initiates changes in LHC II tertiary and quaternary structure that sever contact with photosystem II while securing contact with photosystem I. In order to understand redistribution of absorbed excitation energy in photosynthesis we need to know the structure of LHC II in its phosphorylated form, and in its complex with photosystem I.

Coupled rows of PBS cores and PSII dimers in cyanobacteria: symmetry and structure

Phycobilisome (PBS) is a giant water-soluble photosynthetic antenna transferring the energy of absorbed light mainly to the photosystem II (PSII) in cyanobacteria. Under the low light conditions, PBSs and PSII dimers form coupled rows where each PBS is attached to the cytoplasmic surface of PSII dimer, and PBSs come into contact with their face surfaces (state 1). The model structure of the PBS core that we have developed earlier by comparison and combination of different fine allophycocyanin crystals, as reported in Zlenko et al. (Photosynth Res 130(1):347-356, 2016b), provides a natural way of the PBS core face-to-face stacking. According to our model, the structure of the protein-protein contact between the neighboring PBS cores in the rows is the same as the contact between the APC hexamers inside the PBS core. As a result, the rates of energy transfer between the cores can occur, and the row of PBS cores acts as an integral PBS "supercore" providing energy transfer between the individual PBS cores. The PBS cores row pitch in our elaborated model (12.4 nm) is very close to the PSII dimers row pitch obtained by the electron microscopy (12.2 nm) that allowed to unite a model of the PBS cores row with a model of the PSII dimers row. Analyzing the resulting model, we have determined the most probable locations of ApcD and ApcE terminal emitter subunits inside the bottom PBS core cylinders and also revealed the chlorophyll molecules of PSII gathering energy from the PBS.

Solution structure of monomeric and trimeric photosystem I of Thermosynechococcus elongatus investigated by small-angle X-ray scattering

The structure of monomeric and trimeric photosystem I (PS I) of Thermosynechococcus elongatus BP1 (T. elongatus) was investigated by small-angle X-ray scattering (SAXS). The scattering data reveal that the protein-detergent complexes possess radii of gyration of 58 and 78 Å in the cases of monomeric and trimeric PS I, respectively. The results also show that the samples are monodisperse, virtually free of aggregation, and contain empty detergent micelles. The shape of the protein-detergent complexes can be well approximated by elliptical cylinders with a height of 78 Å. Monomeric PS I in buffer solution exhibits minor and major radii of the elliptical cylinder of about 50 and 85 Å, respectively. In the case of trimeric PS I, both radii are equal to about 110 Å. The latter model can be shown to accommodate three elliptical cylinders equal to those describing monomeric PS I. A structure reconstitution also reveals that the protein-detergent complexes are larger than their respective crystal structures. The reconstituted structures are larger by about 20 Å mainly in the region of the hydrophobic surfaces of the monomeric and trimeric PS I complexes. This seeming contradiction can be resolved by the addition of a detergent belt constituted by a monolayer of dodecyl-β-D-maltoside molecules. Assuming a closest possible packing, a number of roughly 1024 and 1472 detergent molecules can be determined for monomeric and trimeric PS I, respectively. Taking the monolayer of detergent molecules into account, the solution structure can be almost perfectly modeled by the crystal structures of monomeric and trimeric PS I.

Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO

The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3 crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn₄CaO₅-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn₄CaO₅-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn₄CaO₅-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn₄CaO₅-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.

DOI:http://dx.doi.org/10.7554/eLife.26933.001

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

A single residue controls electron transfer gating in photosynthetic reaction centers

Interquinone Q_A⁻ → Q_B electron-transfer (ET) in isolated photosystem II reaction centers (PSII-RC) is protein-gated. The temperature-dependent gating frequency “k” is described by the Eyring equation till levelling off at T ≥ 240 °K. Although central to photosynthesis, the gating mechanism has not been resolved and due to experimental limitations, could not be explored in vivo. Here we mimic the temperature dependency of “k” by enlarging V_D1-208, the volume of a single residue at the crossing point of the D1 and D2 PSII-RC subunits in Synechocystis 6803 whole cells. By controlling the interactions of the D1/D2 subunits, V_D1-208 (or 1/T) determines the frequency of attaining an ET-active conformation. Decelerated ET, impaired photosynthesis, D1 repair rate and overall cell physiology upon increasing V_D1-208 to above 130 ų, rationalize the >99% conservation of small residues at D1-208 and its homologous motif in non-oxygenic bacteria. The experimental means and resolved mechanism are relevant for numerous transmembrane protein-gated reactions.

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein-protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the "mass tags" selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein-protein interactions in membrane protein complexes.

Electrostatic Asymmetry in the Reaction Center of Photosystem II

The exciton Hamiltonian of the chlorophyll (Chl) and pheophytin (Pheo) pigments in the reaction center (RC) of photosystem II is computed based on recent crystal structures by using the Poisson-Boltzmann/quantum-chemical method. Computed site energies largely confirm a previous model inferred from fits of optical spectra, in which Chl_D1 has the lowest site energy, while that of Pheo_D1 is higher than that of Pheo_D2. The latter assignment has been challenged recently under reference to mutagenesis experiments. We argue that these data are not in contradiction to our results. We conclude that Chl_D1 is the primary electron donor in both isolated RCs and intact core complexes at least at cryogenic temperatures. The main source of asymmetry in site energies is the charge distribution in the protein. Because many small contributions from various structural elements have to be taken into account, it can be assumed that this asymmetry was established in evolution by global optimization of the RC protein.

Photocurrent Generation of Reconstituted Photosystem II on a Self-Assembled Gold Film

Photosystem II (PSII)-modified gold electrodes were prepared by the deposition of PSII reconstituted with platinum nanoparticles (PtNPs) on Au electrodes. PtNPs modified with 1-[15-(3,5,6-trimethyl-1,4-benzoquinone-2-yl)]pentadecyl disulfide ((TMQ(CH₂)₁₅S)₂) were incorporated into the Q_B site of PSII isolated from thermophilic cyanobacterium Thermosynechococcus elongatus. The reconstitution was confirmed by Q_A-reoxidation measurements. PSII reconstituted with PtNPs was deposited and integrated on a Au(111) surface modified with 4,4'-biphenyldithiol. The cross section of the reconstituted PSII film on the Au electrode was investigated by SEM. Absorption spectra showed that the surface coverage of the electrode was about 18 pmol PSII cm^-2. A photocurrent density of 15 nAcm^-2 at E = +0.10 V (vs Ag/AgCl) was observed under 680 nm irradiation. The photoresponse showed good reversibility under alternating light and dark conditions. Clear photoresponses were not observed in the absence of PSII and molecular wire. These results supported the photocurrent originated from PSII and moved to a gold electrode by light irradiation, which also confirmed conjugation with orientation through the molecular wire.

Structure of photosystem II and substrate binding at room temperature

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn₄CaO₅ cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S₀ to S₄), in which S₁ is the dark-stable state and S₃ is the last semi-stable state before O-O bond formation and O₂ evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S₁), two-flash illuminated (2F; S₃-enriched), and ammonia-bound two-flash illuminated (2F-NH₃; S₃-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S₁ state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn₄CaO₅ cluster in the S₂ and S₃ states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Challenges facing an understanding of the nature of low-energy excited states in photosynthesis

While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.

The lowest-energy chlorophyll of photosystem II is adjacent to the peripheral antenna: Emitting states of CP47 assigned via circularly polarized luminescence

The identification of low-energy chlorophyll pigments in photosystem II (PSII) is critical to our understanding of the kinetics and mechanism of this important enzyme. We report parallel circular dichroism (CD) and circularly polarized luminescence (CPL) measurements at liquid helium temperatures of the proximal antenna protein CP47. This assembly hosts the lowest-energy chlorophylls in PSII, responsible for the well-known "F695" fluorescence band of thylakoids and PSII core complexes. Our new spectra enable a clear identification of the lowest-energy exciton state of CP47. This state exhibits a small but measurable excitonic delocalization, as predicated by its CD and CPL. Using structure-based simulations incorporating the new spectra, we propose a revised set of site energies for the 16 chlorophylls of CP47. The significant difference from previous analyses is that the lowest-energy pigment is assigned as Chl 612 (alternately numbered Chl 11). The new assignment is readily reconciled with the large number of experimental observations in the literature, while the most common previous assignment for the lowest energy pigment, Chl 627(29), is shown to be inconsistent with CD and CPL results. Chl 612(11) is near the peripheral light-harvesting system in higher plants, in a lumen-exposed region of the thylakoid membrane. The low-energy pigment is also near a recently proposed binding site of the PsbS protein. This result consequently has significant implications for our understanding of the kinetics and regulation of energy transfer in PSII.

A generic protocol for protein crystal dehydration using the HC1b humidity controller

Dehydration may change the crystal lattice and affect the mosaicity, resolution and quality of X-ray diffraction data. A dehydrating environment can be generated around a crystal in several ways with various degrees of precision and complexity. This study uses a high-precision crystal humidifier/dehumidifier to provide an airstream of known relative humidity in which the crystals are mounted: a precise yet hassle-free approach to altering crystal hydration. A protocol is introduced to assess the impact of crystal dehydration systematically applied to nine experimental crystal systems. In one case, that of glucose isomerase, dehydration triggering a change of space group from I222 to P21212 was observed. This observation is supported by an extended study of the behaviour of the glucose isomerase crystal structure during crystal dehydration.