Short Hydrogen Bond between Redox-Active Tyrosine Y_Z and D1-His190 in the Photosystem II Crystal Structure

The crystal structure of photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed a remarkably short H-bond between redox-active tyrosine Y_Z and D1-His190 (2.46 Å donor–acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [Y_ZO···<b>H</b>···N_ε-His-N_δ<b>H</b>···OAsn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y_Z and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y_Z and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved

Strong Coupling between the Hydrogen Bonding Environment and Redox Chemistry during the S₂ to S₃ Transition in the Oxygen-Evolving Complex of Photosystem II

We have studied the early phase of the S₂ → S₃ transition in the oxygen-evolving complex (OEC) of photosystem II using the hybrid density functional theory with a quantum mechanical model composed of 338–341 atoms. Special attention is given to the vital role of water molecules in the vicinity of the Mn₄CaO₅ core. Our results demonstrate how important the dynamic behavior of surrounding water molecules is in mediating critical chemical transformations such as binding and deprotonation of substrates and hydration of the catalytic site and identify a strong coupling of water-chain relocation near the redox-active tyrosine residue Tyr161 (Tyr_Z) with oxidation of the Mn₄CaO₅ cluster by Tyr_Z^•+. The oxidation reaction is further promoted when the catalytic site is more solvated by water. These results indicate the importance of surrounding water molecules in biological catalysts as they ultimately lead to effective catalytic function and/or favorable electron-transfer dynamics

Chemical Equilibrium Models for the S₃ State of the Oxygen-Evolving Complex of Photosystem II

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S₃ state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol^–1 that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn₄CaO₅ cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn–O and O–O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed

Water Oxidation Chemistry of a Synthetic Dinuclear Ruthenium Complex Containing Redox-Active Quinone Ligands

We investigated theoretically the catalytic mechanism of electrochemical water oxidation in aqueous solution by a dinuclear ruthenium complex containing redox-active quinone ligands, [Ru₂(X)­(Y)­(3,6-tBu₂Q)₂(btpyan)]^<i>m</i>+ [X, Y = H₂O, OH, O, O₂; 3,6-tBu₂Q = 3,6-di-<i>tert</i>-butyl-1,2-benzoquinone; btpyan =1,8-bis­(2,2′:6′,2″-terpyrid-4′-yl)­anthracene] (<i>m</i> = 2, 3, 4) (<b>1</b>). The reaction involves a series of electron and proton transfers to achieve redox leveling, with intervening chemical transformations in a mesh scheme, and the entire molecular structure and motion of the catalyst <b>1</b> work together to drive the catalytic cycle for water oxidation. Two substrate water molecules can bind to <b>1</b> with simultaneous loss of one or two proton(s), which allows pH-dependent variability in the proportion of substrate-bound structures and following pathways for oxidative activation of the aqua/hydroxo ligands at low thermodynamic and kinetic costs. The resulting bis-oxo intermediates then undergo endothermic O–O radical coupling between two Ru­(III)–O^• units in an anti-coplanar conformation leading to bridged μ-peroxo or μ-superoxo intermediates. The μ-superoxo species can liberate oxygen with the necessity for the preceding binding of a water molecule, which is possible only after four-electron oxidation is completed. The magnitude of catalytic current would be limited by the inherent sluggishness of the hinge-like bending motion of the bridged μ-superoxo complex that opens up the compact, hydrophobic active site of the catalyst and thereby allows water entry under dynamic conditions. On the basis of a newly proposed mechanism, we rationalize the experimentally observed behavior of electrode kinetics with respect to potential and discuss what causes a high overpotential for water oxidation by <b>1</b>

Photosystem II Does Not Possess a Simple Excitation Energy Funnel: Time-Resolved Fluorescence Spectroscopy Meets Theory

The experimentally obtained time-resolved fluorescence spectra of photosystem II (PS II) core complexes, purified from a thermophilic cyanobacterium Thermosynechococcus vulcanus, at 5–180 K are compared with simulations. Dynamic localization effects of excitons are treated implicitly by introducing exciton domains of strongly coupled pigments. Exciton relaxations within a domain and exciton transfers between domains are treated on the basis of Redfield theory and generalized Förster theory, respectively. The excitonic couplings between the pigments are calculated by a quantum chemical/electrostatic method (Poisson-TrEsp). Starting with previously published values, a refined set of site energies of the pigments is obtained through optimization cycles of the fits of stationary optical spectra of PS II. Satisfactorily agreement between the experimental and simulated spectra is obtained for the absorption spectrum including its temperature dependence and the linear dichroism spectrum of PS II core complexes (PS II-CC). Furthermore, the refined site energies well reproduce the temperature dependence of the time-resolved fluorescence spectrum of PS II-CC, which is characterized by the emergence of a 695 nm fluorescence peak upon cooling down to 77 K and the decrease of its relative intensity upon further cooling below 77 K. The blue shift of the fluorescence band upon cooling below 77 K is explained by the existence of two red-shifted chlorophyll pools emitting at around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43 in CP43 (Chl numbering according to the nomenclature of Loll et al. <i>Nature</i> <b>2005</b>, <i>438</i>, 1040) while the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll is suggested to attract excitations from the peripheral light-harvesting complexes and might also be involved in photoprotection

Deformation of Chlorin Rings in the Photosystem II Crystal Structure

The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the P_D1 chlorin ring can be described predominantly by a large “doming mode” arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P_D2 was caused by a “saddling mode” arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P_D1 and Chl_D1, but not in P_D2 and Chl_D2. Furthermore, as P_D1 possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P_L possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in “the local steric protein environment” rather than the redox potential value in PSII

Evidence for an Unprecedented Histidine Hydroxyl Modification on D2-His336 in Photosystem II of <i>Thermosynechoccocus vulcanus</i> and <i>Thermosynechoccocus elongatus</i>

The electron density map of the 3D crystal of Photosystem II from Thermosynechococcus vulcanus with a 1.9 Å resolution (PDB: 3ARC) exhibits, in the two monomers in the asymmetric unit cell, an, until now, unidentified and uninterpreted strong difference in electron density centered at a distance of around 1.5 Å from the nitrogen Nδ of the imidazole ring of D2-His336. By MALDI-TOF/MS upon tryptic digestion, it is shown that ∼20–30% of the fragments containing the D2-His336 residue of Photosystem II from both Thermosynechococcus vulcanus and Thermosynechococcus elongatus bear an extra mass of +16 Da. Such an extra mass likely corresponds to an unprecedented post-translational or chemical hydroxyl modification of histidine

Oxygen-Evolving Porous Glass Plates Containing the Photosynthetic Photosystem II Pigment–Protein Complex

The development of artificial photosynthesis has focused on the efficient coupling of reaction at photoanode and cathode, wherein the production of hydrogen (or energy carriers) is coupled to the electrons derived from water-splitting reactions. The natural photosystem II (PSII) complex splits water efficiently using light energy. The PSII complex is a large pigment–protein complex (20 nm in diameter) containing a manganese cluster. A new photoanodic device was constructed incorporating stable PSII purified from a cyanobacterium Thermosynechococcus vulcanus through immobilization within 20 or 50 nm nanopores contained in porous glass plates (PGPs). PSII in the nanopores retained its native structure and high photoinduced water splitting activity. The photocatalytic rate (turnover frequency) of PSII in PGP was enhanced 11-fold compared to that in solution, yielding a rate of 50–300 mol e^–/(mol PSII·s) with 2,6-dichloroindophenol (DCIP) as an electron acceptor. The PGP system realized high local concentrations of PSII and DCIP to enhance the collisional reactions in nanotubes with low disturbance of light penetration. The system allows direct visualization/determination of the reaction inside the nanotubes, which contributes to optimize the local reaction condition. The PSII/PGP device will substantively contribute to the construction of artificial photosynthesis using water as the ultimate electron source

Probing the Lysine Proximal Microenvironments within Membrane Protein Complexes by Active Dimethyl Labeling and Mass Spectrometry

Positively charged lysines are crucial to maintaining the native structures of proteins and protein complexes by forming hydrogen bonds and electrostatic interactions with their proximal amino acid residues. However, it is still a challenge to develop an efficient method for probing the active proximal microenvironments of lysines without changing their biochemical/physical properties. Herein, we developed an active covalent labeling strategy combined with mass spectrometry to systematically probe the lysine proximal microenvironments within membrane protein complexes (∼700 kDa) with high throughput. Our labeling strategy has the advantages of high labeling efficiency and stability, preservation of the active charge states, as well as biological activity of the labeled proteins. In total, 121 lysines with different labeling levels were obtained for the photosystem II complexes from cyanobacteria, red algae, and spinach and provided important insights for understanding the conserved and nonconserved local structures of PSII complexes among evolutionarily divergent species that perform photosynthesis