Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II

How chloride functions to enable proton conduction in photosynthetic water oxidation: Time-resolved kinetics of intermediates (S-states) in vivo and bromide substitution

Chloride (Cl-) is essential for O2 evolution during photosynthetic water oxidation. Two chlorides near the water-oxidizing complex (WOC) in Photosystem II (PSII) structures from Thermosynechococcus elongatus (and T. vulcanus) have been postulated to transfer protons generated from water oxidation. We monitored four criteria: primary charge separation flash yield (P* → P+QA-), rates of water oxidation steps (S-states), rate of proton evolution, and flash O2 yield oscillations by measuring chlorophyll variable fluorescence (P* quenching), pH-sensitive dye changes, and oximetry. Br-substitution slows and destabilizes cellular growth, resulting from lower light-saturated O2 evolution rate (-20 %) and proton release (-36 % ΔpH gradient). The latter implies less ATP production. In Br- cultures, protonogenic S-state transitions (S2 → S3 → S0') slow with increasing light intensity and during O2/water exchange (S0' → S0 → S1), while the non-protonogenic S1 → S2 transition is kinetically unaffected. As flash rate increases in Cl- cultures, both rate and extent of acidification of the lumen increase, while charge recombination is suppressed relative to Br-. The Cl- advantage in rapid proton escape from the WOC to lumen is attributed to correlated ion-pair movement of H3O+Cl- in dry water channels vs. separated Br- and H+ ion movement through different regions (>200-fold difference in Bronsted acidities). By contrast, at low flash rates a previously unreported reversal occurs that favors Br- cultures for both proton evolution and less PSII charge recombination. In Br- cultures, slower proton transfer rate is attributed to stronger ion-pairing of Br- with AA residues lining the water channels. Both anions charge-neutralize protons and shepherd them to the lumen using dry aqueous channels.

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.

Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II

Photosynthetic water oxidation takes place at the Mn₄CaO₅ cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S₀-S₄). Although the PSII structures have shown the presence of several channels around the Mn₄CaO₅ cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S₂ → S₃ transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S₃ → S₀ transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S₂ → S₃ transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S₃ → S₀ transition.

Binding and functions of the two chloride ions in the oxygen-evolving center of photosystem II

Light-driven water oxidation in photosynthesis occurs at the oxygen-evolving center (OEC) of photosystem II (PSII). Chloride ions (Cl^-) are essential for oxygen evolution by PSII, and two Cl^- ions have been found to specifically bind near the Mn₄CaO₅ cluster in the OEC. The retention of these Cl^- ions within the OEC is critically supported by some of the membrane-extrinsic subunits of PSII. The functions of these two Cl^- ions and the mechanisms of their retention both remain to be fully elucidated. However, intensive studies performed recently have advanced our understanding of the functions of these Cl^- ions, and PSII structures from various species have been reported, aiding the interpretation of previous findings regarding Cl^- retention by extrinsic subunits. In this review, we summarize the findings to date on the roles of the two Cl^- ions bound within the OEC. Additionally, together with a short summary of the functions of PSII membrane-extrinsic subunits, we discuss the mechanisms of Cl^- retention by these extrinsic subunits.

Alteration of the O2-Producing Mn4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand

The O₂-evolving Mn₄Ca cluster in photosystem II (PSII) is arranged as a distorted Mn₃Ca cube that is linked to a fourth Mn ion (denoted as Mn4) by two oxo bridges. The Mn4 and Ca ions are bridged by residue D1-D170. This is also the only residue known to participate in the high-affinity Mn(II) site that participates in the light-driven assembly of the Mn₄Ca cluster. In this study, we use Fourier transform infrared difference spectroscopy to characterize the impact of the D1-D170E mutation. On the basis of analyses of carboxylate and carbonyl stretching modes and the O-H stretching modes of hydrogen-bonded water molecules, we show that this mutation alters the extensive network of hydrogen bonds that surrounds the Mn₄Ca cluster in the same manner as that of many other mutations. It also alters the equilibrium between conformers of the Mn₄Ca cluster in the dark-stable S₁ state so that a high-spin form of the S₂ state is produced during the S₁-to-S₂ transition instead of the low-spin form that gives rise to the S₂ state multiline electron paramagnetic resonance signal. The mutation may also change the coordination mode of the carboxylate group at position 170 to unidentate ligation of Mn4. This is the first mutation of a metal ligand in PSII that substantially impacts the spectroscopic signatures of the Mn₄Ca cluster without substantially eliminating O₂ evolution. The results have significant implications for our understanding of the roles of alternate active/inactive conformers of the Mn₄Ca cluster in the mechanism of O₂ formation.

Emergence of Electric Fields at the Water-C12E6 Surfactant Interface

We study the properties of the interface of water and the surfactant hexaethylene glycol monododecyl ether (C12E6) with a combination of heterodyne-detected vibrational sum frequency generation (HD-VSFG), Kelvin-probe measurements, and molecular dynamics (MD) simulations. We observe that the addition of the hydrogen-bonding surfactant C12E6, close to the critical micelle concentration (CMC), induces a drastic enhancement in the hydrogen bond strength of the water molecules close to the interface, as well as a flip in their net orientation. The mutual orientation of the water and C12E6 molecules leads to the emergence of a broad (∼3 nm) interface with a large electric field of ∼1 V/nm, as evidenced by the Kelvin-probe measurements and MD simulations. Our findings may open the door for the design of novel electric-field-tuned catalytic and light-harvesting systems anchored at the water-surfactant-air interface.

Proton and Water Transfer Pathways in the S2 → S3 Transition of the Water-Oxidizing Complex in Photosystem II: Time-Resolved Infrared Analysis of the Effects of D1-N298A Mutation and NO3- Substitution

Photosynthetic water oxidation is performed through a light-driven cycle of five intermediates (S₀-S₄ states) in photosystem II (PSII). The S₂ → S₃ transition, which involves concerted water and proton transfer, is a key process for understanding the water oxidation mechanism. Here, to identify the water and proton transfer pathways during the S₂ → S₃ transition, we examined the effects of D1-N298A mutation and NO₃^- substitution for Cl^-, which perturbed the O1 and Cl channels, respectively, on the S₂ → S₃ kinetics using time-resolved infrared spectroscopy. The S₂ → S₃ transition was retarded both upon NO₃^- substitution and upon D1-N298A mutation, whereas it was unaffected by further NO₃^- substitution in N298A PSII. The H/D kinetic isotope effect in N298A PSII was relatively small, revealing that water transfer is a rate-limiting step in this mutant. From these results, it was suggested that during the S₂ → S₃ transition, water delivery and proton release occur through the O1 and Cl channels, respectively.

Proton exit pathways surrounding the oxygen evolving complex of photosystem II

Photosystem II allows water to be the primary electron source for the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn₄CaO₅ inorganic core embedded on the lumenal side of PSII. Water-filled channels surrounding the OEC must bring in substrate water molecules, remove the product protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, extend from the OEC towards the aqueous surface more than 15 Å away. However, the role of each pathway in the transport in and out of the OEC is yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths. Hydrogen bond network analysis shows that near the OEC the waters are highly interconnected with similar free energy for hydronium at all locations. The paths diverge as they move towards the lumen. The water chain in the broad channel is better connected than in the narrow and large channels, where disruptions in the network are observed approximately 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel. Thus, a proton released from any location on the OEC can access all paths, but the likely exit to the lumen passes through PsbO via the broad channel.

Chloride involvement in the synthesis, functioning and repair of the photosynthetic apparatus in vivo

Cl^- has long been known as a micronutrient for oxygenic photosynthetic resulting from its role an essential cofactor for photosystem II (PSII). Evidence on the in vivo Cl^- distribution in Spinacia oleracea leaves and chloroplasts shows that sufficient Cl^- is present for the involvement in PSII function, as indicated by in vitro studies on, among other organisms, S. oleracea PsII. There is also sufficient Cl^- to function, with K⁺ , in parsing the H⁺ electrochemical potential difference (proton motive force) across the illuminated thylakoid membrane into electrical potential difference and pH difference components. However, recent in vitro work on PSII from S. oleracea shows that oxygen evolving complex (OEC) synthesis, and resynthesis after photodamage, requires significantly higher Cl^- concentrations than would satisfy the function of assembled PSII O₂ evolution of the synthesised PSII with the OEC. The low Cl^- affinity of OEC (re-)assembly could be a component limiting the rate of OEC (re-)assembly.

Molecular dynamics simulations in photosynthesis

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.

The Biochemical Properties of Manganese in Plants

Manganese (Mn) is an essential micronutrient with many functional roles in plant metabolism. Manganese acts as an activator and co-factor of hundreds of metalloenzymes in plants. Because of its ability to readily change oxidation state in biological systems, Mn plays and important role in a broad range of enzyme-catalyzed reactions, including redox reactions, phosphorylation, decarboxylation, and hydrolysis. Manganese(II) is the prevalent oxidation state of Mn in plants and exhibits fast ligand exchange kinetics, which means that Mn can often be substituted by other metal ions, such as Mg(II), which has similar ion characteristics and requirements to the ligand environment of the metal binding sites. Knowledge of the molecular mechanisms catalyzed by Mn and regulation of Mn insertion into the active site of Mn-dependent enzymes, in the presence of other metals, is gradually evolving. This review presents an overview of the chemistry and biochemistry of Mn in plants, including an updated list of known Mn-dependent enzymes, together with enzymes where Mn has been shown to exchange with other metal ions. Furthermore, the current knowledge of the structure and functional role of the three most well characterized Mn-containing metalloenzymes in plants; the oxygen evolving complex of photosystem II, Mn superoxide dismutase, and oxalate oxidase is summarized.

Research on Invulnerability Technology of Node Attack in Space-Based Information Network Based on Complex Network

With the rapid development of communications technology, the space-based information network (SBIN) is increasingly threatened by the outside world. Dynamic changes in any part of its interior can cause the collapse of the entire network. Therefore, research on the invulnerability of SBIN has become an urgent need to promote the economic development of our country and improve the living standards of our people. To this end, this paper has carried out research on the node-attacked invulnerability of SBIN based on the complex network theory. First, based on the model of SBIN, the internal parameters of the network are analyzed theoretically based on complex networks. Second, the paper proposes an improved tree attack strategy to analyze the invulnerability of SBIN, which constitutes a problem where the traditional attack strategy has a low invulnerability and the connected edge cannot fully realize the network function. Then, based on the improved tree attack strategy algorithm, this paper optimizes the invulnerability of SBIN by constructing four different edge-increasing strategies. Through the research, the LDF edge-increasing strategy makes the entire network flatter and can effectively improve the network’s ability to resist destruction. The research of invulnerability based on the complex network has a certain technical support and theoretical guidance for the construction of a reasonable and stable SBIN.