Energetics of proton release on the first oxidation step in the water-oxidizing enzyme.
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ABSTRACT:
SUBMITTER: Saito K
PROVIDER: S-EPMC4617610 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:As the terminal step in photosystem II, and a potential half-reaction for artificial photosynthesis, water oxidation (2H(2)O --> O(2) + 4e(-) + 4H(+)) is key, but it imposes a significant mechanistic challenge with requirements for both 4e(-)/4H(+) loss and O-O bond formation. Significant progress in water oxidation catalysis has been achieved recently by use of single-site Ru metal complex catalysts such as [Ru(Mebimpy)(bpy)(OH(2))](2+) [Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine; bpy = 2,2'-bipyridine]. When oxidized from to Ru(V) = O(3+), these complexes undergo O-O bond formation by O-atom attack on a H(2)O molecule, which is often the rate-limiting step. Microscopic details of O-O bond formation have been explored by quantum mechanical/molecular mechanical (QM/MM) simulations the results of which provide detailed insight into mechanism and a strategy for enhancing catalytic rates. It utilizes added bases as proton acceptors and concerted atom-proton transfer (APT) with O-atom transfer to the O atom of a water molecule in concert with proton transfer to the base (B). Base catalyzed APT reactivity in water oxidation is observed both in solution and on the surfaces of oxide electrodes derivatized by attached phosphonated metal complex catalysts. These results have important implications for catalytic, electrocatalytic, and photoelectrocatalytic water oxidation.
| S-EPMC2867729 | biostudies-literature
Project description:Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel-production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese-calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S(2) ? S(3) transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (Y Z OX). The rate-determining elementary step (?, approximately 30 µs at 20?°C) in the long-distance proton relocation toward the protein-water interface is characterized by a high activation energy (E(a) = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S(0) ? S(1) transition are similar (?, approximately 100 µs; E(a) = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established.
| S-EPMC3479599 | biostudies-literature
Project description:In oxygenic photosynthesis, solar energy drives the oxidation of water catalyzed by a Mn(4)Ca complex bound to the proteins of Photosystem II. Four protons are released during one turnover of the water oxidation cycle (S-state cycle), implying thermodynamic limitations at low pH. For proton concentrations ranging from 1 nm (pH 9) to 1 mm (pH 3), we have characterized the low-pH limitations using a new experimental approach: a specific pH-jump protocol combined with time-resolved measurement of the delayed chlorophyll fluorescence after nanosecond flash excitation. Effective pK values were determined for low-pH inhibition of the light-induced S-state transitions: pK(1)=3.3 ± 0.3, pK(2)=3.5 ± 0.2, and pK(3)≈pK(4)=4.6 ± 0.2. Alkaline inhibition was not observed. An extension of the classical Kok model facilitated assignment of these four pK values to specific deprotonation steps in the reaction cycle. Our results provide important support to the extended S-state cycle model and criteria needed for assessment of quantum chemical calculations of the mechanism of water oxidation. They also imply that, in intact organisms, the pH in the lumen compartment can hardly drop below 5, thereby limiting the ΔpH contribution to the driving force of ATP synthesis.
| S-EPMC3093894 | biostudies-literature
Project description:In photosystem II, light-induced water oxidation occurs at the Mn4CaO5 cluster. Here we demonstrate proton releases, dioxygen formation, and substrate water incorporation in response to Mn4CaO5 oxidation in the protein environment, using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. In S2, H2O at the W1 site forms a low-barrier H-bond with D1-Asp61. In the S2-to-S3 transition, oxidation of OW1H- to OW1•-, concerted proton transfer from OW1H- to D1-Asp61, and binding of a water molecule Wn-W1 at OW1•- are observed. In S4, W n-W1 facilitates oxo-oxyl radical coupling between OW1•- and corner μ-oxo O4. Deprotonation via D1-Asp61 leads to formation of OW1=O4. As OW1=O4 moves away from Mn, H2O at W539 is incorporated into the vacant O4 site of the O2-evolved Mn4CaO4 cluster, forming a μ-oxo bridge (Mn3-OW539-Mn4) in an exergonic process. Simultaneously, Wn-W1 is incorporated as W1, recovering the Mn4CaO5 cluster.
| S-EPMC5871790 | biostudies-literature
Project description:Quinol oxidation by the bc(1) complex of Rhodobacter sphaeroides occurs from an enzyme-substrate complex formed between quinol bound at the Q(o) site and the iron-sulfur protein (ISP) docked at an interface on cytochrome b. From the structure of the stigmatellin-containing mitochondrial complex, we suggest that hydrogen bonds to the two quinol hydroxyl groups, from Glu-272 of cytochrome b and His-161 of the ISP, help to stabilize the enzyme-substrate complex and aid proton release. Reduction of the oxidized ISP involves H transfer from quinol. Release of the proton occurs when the acceptor chain reoxidizes the reduced ISP, after domain movement to an interface on cytochrome c(1). Effects of mutations to the ISP that change the redox potential and/or the pK on the oxidized form support this mechanism. Structures for the complex in the presence of inhibitors show two different orientations of Glu-272. In stigmatellin-containing crystals, the side chain points into the site, to hydrogen bond with a ring hydroxyl, while His-161 hydrogen bonds to the carbonyl group. In the native structure, or crystals containing myxothiazol or beta-methoxyacrylate-type inhibitors, the Glu-272 side chain is rotated to point out of the site, to the surface of an external aqueous channel. Effects of mutation at this residue suggest that this group is involved in ligation of stigmatellin and quinol, but not quinone, and that the carboxylate function is essential for rapid turnover. H(+) transfer from semiquinone to the carboxylate side chain and rotation to the position found in the myxothiazol structure provide a pathway for release of the second proton.
| S-EPMC17835 | biostudies-literature
Project description:Cyanobacteria, algae, and plants oxidize water to the O2 we breathe, and consume CO2 during the synthesis of biomass. Although these vital processes are functionally and structurally well separated in photosynthetic organisms, there is a long-debated role for CO2/ in water oxidation. Using membrane-inlet mass spectrometry we demonstrate that acts as a mobile proton acceptor that helps to transport the protons produced inside of photosystem II by water oxidation out into the chloroplast's lumen, resulting in a light-driven production of O2 and CO2. Depletion of from the media leads, in the absence of added buffers, to a reversible down-regulation of O2 production by about 20%. These findings add a previously unidentified component to the regulatory network of oxygenic photosynthesis and conclude the more than 50-y-long quest for the function of CO2/ in photosynthetic water oxidation.
| S-EPMC4035973 | biostudies-literature
Project description:The energetics for proton reduction in FeFe-hydrogenase has been reinvestigated by theoretical modeling, in light of recent experiments. Two different mechanisms have been considered. In the first one, the bridging hydride position was blocked by the enzyme, which is the mechanism that has been supported by a recent spectroscopic study by Cramer et al. A major difficulty in the present study to agree with experimental energetics was to find the right position for the added proton in the first reduction step. It was eventually found that the best position was as a terminal hydride on the distal iron, which has not been suggested in any of the recent, experimentally based mechanisms. The lowest transition state was surprisingly found to be a bond formation between a proton on a cysteine and the terminal hydride. This type of TS is similar to the one for heterolytic H2 cleavage in NiFe hydrogenase. The second mechanism investigated here is not supported by the present calculations or the recent experiments by Cramer et al., but was still studied as an interesting comparison. In that mechanism, the formation of the bridging hydride was allowed. The H-H formation barrier is only 3.6 kcal/mol higher than for the first mechanism, but there are severe problems concerning the motion of the protons.
| S-EPMC7750917 | biostudies-literature
Project description:The oxomanganese complex [H(2)O(terpy)Mn(III)(μ-O)(2)Mn(IV)(terpy)H(2)O](3+) (1, terpy = 2,2':6-2″-terpyridine) is a biomimetic model of the oxygen evolving complex of photosystem II with terminal water ligands. When bound to TiO(2) surfaces, 1 is activated by primary oxidants (e.g., Ce(4+)(aq), or oxone in acetate buffers) to catalyze the oxidation of water yielding O(2) evolution [G. Li et al. Energy Environ. Sci. 2, 230-238 (2009)]. The activation is thought to involve oxidation of the inorganic core [Mn(III)(μ-O)(2)Mn(IV)](3+) to generate the [Mn(IV)(μ-O)(2)Mn(IV)](4+) state 1(ox) first and then the highly reactive Mn oxyl species Mn(IV)O(•) through proton coupled electron transfer (PCET). Here, we investigate the step 1 → 1(ox) as compared to the analogous conversion in an oxomanganese complex without terminal water ligands, the [(bpy)(2) Mn (III) (μ-O)(2) Mn (IV) (bpy)(2)](3+) complex (2, bpy = 2,2'-bipyridyl). We characterize the oxidation in terms of free energy calculations of redox potentials and pKa's as directly compared to cyclic voltammogram measurements. We find that the pKa's of terminal water ligands depend strongly on the oxidation states of the Mn centers, changing by ~13 pH units (i.e., from 14 to 1) during the III, IV→IV, IV transition. Furthermore, we find that the oxidation potential of 1 is strongly dependent on pH (in contrast to the pH-independent redox potential of 2) as well as by coordination of Lewis base moieties (e.g., carboxylate groups) that competitively bind to Mn by exchange with terminal water ligands. The reported analysis of ligand binding free energies, pKa's and redox potentials indicates that the III, IV→IV, IV oxidation of 1 in the presence of acetate (AcO(-)) involves the following PCET: [H(2)O(terpy)Mn(III)(μ-O)(2)Mn(IV)(terpy)AcO](2+) → [HO(terpy)Mn(IV)(μ-O)(2)Mn(IV)(terpy)AcO](2+) + H(+) + e(-).
| S-EPMC2935188 | biostudies-literature
Project description:Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.
| S-EPMC6728127 | biostudies-literature
Project description:The membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from O2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. O2 reduction produces water at the bimetallic heme a3/CuB active site next to a hydrophobic cavity deep within the membrane. Water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism. Here, we show by molecular dynamics simulations that the conserved arginine/heme a3 delta-propionate ion pair provides a gate, which exhibits reversible thermal opening that is governed by the redox state and the water molecules in the cavity. An important role of this gate in the proton-pumping mechanism is supported by site-directed mutagenesis experiments. Transport of the product water out of the enzyme must be rigidly controlled to prevent water-mediated proton leaks that could compromise the proton-pumping function. Exit of product water is observed through the same arginine/propionate gate, which provides an explanation for the observed extraordinary spatial specificity of water expulsion from the enzyme.
| S-EPMC1180778 | biostudies-literature