Oxygen-Evolving Complex

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Gary W. Brudvig - One of the best experts on this subject based on the ideXlab platform.

  • thermodynamics of the s2 to s3 state transition of the oxygen evolving Complex of photosystem ii
    Physical Chemistry Chemical Physics, 2019
    Co-Authors: Gary W. Brudvig, Jimin Wang, Divya Kaur, Muhamed Amin, Ke R Yang, Zainab Mohamed, M R Gunner
    Abstract:

    The room temperature pump-probe X-ray free electron laser (XFEL) measurements used for serial femtosecond crystallography provide remarkable information about the structures of the catalytic (S-state) intermediates of the oxygen-evolution reaction of photosystem II. However, mixed populations of these intermediates and moderate resolution limit the interpretation of the data from current experiments. The S3 XFEL structures show extra density near the OEC that may correspond to a water/hydroxide molecule. However, in the latest structure, this additional oxygen is 2.08 A from the Oe2 of D1-E189, which is closer than the sum of the van der Waals radii of the two oxygens. Here, we use Boltzmann statistics and Monte Carlo sampling to provide a model for the S2-to-S3 state transition, allowing structural changes and the insertion of an additional water/hydroxide. Based on our model, water/hydroxide addition to the Oxygen-Evolving Complex (OEC) is not thermodynamically favorable in the S2g = 2 state, but it is in the S2g = 4.1 redox isomer. Thus, formation of the S3 state starts by a transition from the S2g = 2 to the S2g = 4.1 structure. Then, electrostatic interactions support protonation of D1-H190 and deprotonation of the Ca2+-ligated water (W3) with proton loss to the lumen. The W3 hydroxide moves toward Mn4, completing the coordination shell of Mn4 and favoring its oxidation to Mn(iv) in the S3 state. In addition, binding an additional hydroxide to Mn1 leads to a conformational change of D1-E189 in the S2g = 4.1 and S3 structures. In the S3 state a fraction of D1-E189 release from Mn1 and bind a proton.

  • thermodynamics of the s2 to s3 state transition of the oxygen evolving Complex of photosystem ii
    arXiv: Biological Physics, 2019
    Co-Authors: Gary W. Brudvig, Jimin Wang, Divya Kaur, Muhamed Amin, Ke R Yang, Zainab Mohamed, M R Gunner
    Abstract:

    The room temperature pump-probe X-ray free electron laser (XFEL) measurements used for serial femtosecond crystallography provide remarkable information about the structures of the catalytic (S-state) intermediates of the oxygen-evolution reaction of photosystem II. However, mixed populations of these intermediates and moderate resolution limit the interpretation of the data from current experiments. The S3 XFEL structures show extra density near the OEC that may correspond to a water/hydroxide molecule. However, in the latest structure, this additional oxygen is 2.08 {\AA} from the Oe2 of D1-E189, which is closer than the sum of the van der Waals radii of the two oxygens. Here, we use Boltzmann statistics and Monte Carlo sampling to provide a model for the S2-to-S3 state transition, allowing structural changes and the insertion of an additional water/hydroxide. Based on our model, water/hydroxide addition to the Oxygen-Evolving Complex (OEC) is not thermodynamically favorable in the S2 g = 2 state, but it is in the S2 g = 4.1 redox isomer. Thus, formation of the S3 state starts by a transition from the S2 g = 2 to the S2 g = 4.1 structure. Then, electrostatic interactions support protonation of D1-H190 and deprotonation of the Ca2+-ligated water (W3) with proton loss to the lumen. The W3 hydroxide moves toward Mn4, completing the coordination shell of Mn4 and moving with its oxidation to Mn(IV) in the S3 state. In addition, binding additional hydroxide to Mn1 leads to a conformational change of D1-E189 in the S2 g = 4.1 and S3 structures. In the S3 state in the population of protonated D1-E189 increases.

  • Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps
    Biochemistry, 2018
    Co-Authors: Jimin Wang, Gary W. Brudvig, Krystle Reiss, Victor S. Batista
    Abstract:

    Computational simulations of electrostatic potentials (ESPs), based on atomistic models and independent atomic scattering factors, have remained challenging when applied to the Oxygen-Evolving Complex (OEC) of photosystem II (PSII). Here, we overcome that challenge by using an ESP function obtained with density functional theory and atomic coordinates for the OEC of PSII obtained by optimization of the dark-adapted S1 state. We find that the ESP is much higher for the OEC than for the nearby reference side chain of amino acid residue D1-H190. In contrast, experimental ESP maps recently published for two PSII-light-harvesting Complex II super-Complexes show that the ESP of the OEC is approximately half the value of the D1-H190 side chain. The apparent disparity is attributed to a reduced 31-38% occupancy of the OEC, likely associated with its reduction by electron scattering.

  • Energetics of the S2 State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II
    The journal of physical chemistry. B, 2017
    Co-Authors: David J. Vinyard, Victor S. Batista, Sahr Khan, Mikhail Askerka, Gary W. Brudvig
    Abstract:

    The S2 redox intermediate of the Oxygen-Evolving Complex in photosystem II is present as two spin isomers. The S = 1/2 isomer gives rise to a multiline electron paramagnetic resonance (EPR) signal at g = 2.0, whereas the S = 5/2 isomer exhibits a broad EPR signal at g = 4.1. The electronic structures of these isomers are known, but their role in the catalytic cycle of water oxidation remains unclear. We show that formation of the S = 1/2 state from the S = 5/2 state is exergonic at temperatures above 160 K. However, the S = 1/2 isomer decays to S1 more slowly than the S = 5/2 isomer. These differences support the hypotheses that the S3 state is formed via the S2 state S = 5/2 isomer and that the stabilized S2 state S = 1/2 isomer plays a role in minimizing S2QA- decay under light-limiting conditions.

  • Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II
    Biochemistry, 2016
    Co-Authors: David J. Vinyard, Richard J. Debus, Victor S. Batista, Mikhail Askerka, Gary W. Brudvig
    Abstract:

    Ammonia binds to two sites in the Oxygen-Evolving Complex (OEC) of Photosystem II (PSII). The first is as a terminal ligand to Mn in the S2 state, and the second is at a site outside the OEC that is competitive with chloride. Binding of ammonia in this latter secondary site results in the S2 state S = 5/2 spin isomer being favored over the S = 1/2 spin isomer. Using electron paramagnetic resonance spectroscopy, we find that ammonia binds to the secondary site in wild-type Synechocystis sp. PCC 6803 PSII, but not in D2-K317A mutated PSII that does not bind chloride. By combining these results with quantum mechanics/molecular mechanics calculations, we propose that ammonia binds in the secondary site in competition with D1-D61 as a hydrogen bond acceptor to the OEC terminal water ligand, W1. Implications for the mechanism of ammonia binding via its primary site directly to Mn4 in the OEC are discussed.

Johannes Messinger - One of the best experts on this subject based on the ideXlab platform.

Per E. M. Siegbahn - One of the best experts on this subject based on the ideXlab platform.

  • Cluster size convergence for the energetics of the oxygen evolving Complex in PSII.
    Journal of computational chemistry, 2017
    Co-Authors: Per E. M. Siegbahn
    Abstract:

    Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving Complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated. However, recently results were published by Isobe et al., suggesting that very different results could be obtained if the model was extended from 200 to 340 atoms. The present study aims at understanding where this difference comes from. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  • Substrate Water Exchange for the Oxygen Evolving Complex in PSII in the S1, S2, and S3 States
    Journal of the American Chemical Society, 2013
    Co-Authors: Per E. M. Siegbahn
    Abstract:

    Detailed mechanisms for substrate water exchange in the oxygen evolving Complex in photosystem II have been determined with DFT methods for large models. Existing interpretations of the experimental water exchange results have been quite different. By many groups, these results have been the main argument against the water oxidation mechanism suggested by DFT, in which the oxygen molecule is formed between a bridging oxo and an oxyl radical ligand in the center of the OEC. That mechanism is otherwise in line with most experiments. The problem has been that the mechanism requires a rather fast exchange of a bridging oxo ligand, which is not a common finding for smaller Mn-containing model systems. However, other groups have actually favored a substrate derived oxo ligand partly based on the same experiments. In the present study, three S-states have been studied, and the rates have been well reproduced by the calculations. The surprising experimental finding that water exchange in S1 is slower than the one...

  • The effect of backbone constraints: the case of water oxidation by the Oxygen-Evolving Complex in PSII.
    Chemphyschem : a European journal of chemical physics and physical chemistry, 2011
    Co-Authors: Per E. M. Siegbahn
    Abstract:

    The procedure for fixing atoms of amino acid residues in cluster model calculations on enzymes is reviewed. Examples from recent calculations on photosystem II (PSII) and Mo,Cu-dependent CO dehydrogenase are given. In this context, the cluster model work on finding a mechanism for O?O bond formation and a structure of the Oxygen-Evolving Complex in PSII is also reviewed. In that work, fixing certain atoms played an important role. The main part of the present study concerns the mechanism in PSII using models based on the new high-resolution (1.9 angstrom) X-ray structure, which is compared to that using the old, theoretically suggested, structure. It is concluded that the mechanism remains the same, with a similar barrier height. Finally, a connection between the OEC structure and Mn,Ca-containing minerals is also briefly discussed.

  • An energetic comparison of different models for the oxygen evolving Complex of photosystem II.
    Journal of the American Chemical Society, 2009
    Co-Authors: Per E. M. Siegbahn
    Abstract:

    The computed total energy from a cluster model DFT calculation is used to discriminate between different suggested models for the oxygen evolving Complex of photosystem II. The comparison between different structures rules out several suggestions. Only one suggested structure remains.

  • Mechanism and Energy Diagram for O-O Bond Formation in the Oxygen Evolving Complex in Photosystem II
    2008
    Co-Authors: Per E. M. Siegbahn
    Abstract:

    Mechanism and Energy Diagram for O-O Bond Formation in the Oxygen Evolving Complex in Photosystem II

Victor S. Batista - One of the best experts on this subject based on the ideXlab platform.

  • Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II
    Inorganics, 2019
    Co-Authors: Krystle Reiss, Uriel N. Morzan, Alex T. Grigas, Victor S. Batista
    Abstract:

    The influence of the environment on the functionality of the Oxygen-Evolving Complex (OEC) of photosystem II has long been a subject of great interest. In particular, various water channels, which could serve as pathways for substrate water diffusion, or proton translocation, are thought to be critical to catalytic performance of the OEC. Here, we address the dynamical nature of hydrogen bonding along the water channels by performing molecular dynamics (MD) simulations of the OEC and its surrounding protein environment in the S1 and S2 states. Through the eigenvector centrality (EC) analysis, we are able to determine the characteristics of the water network and assign potential functions to the major channels, namely that the narrow and broad channels are likely candidates for proton/water transport, while the large channel may serve as a path for larger ions such as chloride and manganese thought to be essential during PSII assembly.

  • Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps
    Biochemistry, 2018
    Co-Authors: Jimin Wang, Gary W. Brudvig, Krystle Reiss, Victor S. Batista
    Abstract:

    Computational simulations of electrostatic potentials (ESPs), based on atomistic models and independent atomic scattering factors, have remained challenging when applied to the Oxygen-Evolving Complex (OEC) of photosystem II (PSII). Here, we overcome that challenge by using an ESP function obtained with density functional theory and atomic coordinates for the OEC of PSII obtained by optimization of the dark-adapted S1 state. We find that the ESP is much higher for the OEC than for the nearby reference side chain of amino acid residue D1-H190. In contrast, experimental ESP maps recently published for two PSII-light-harvesting Complex II super-Complexes show that the ESP of the OEC is approximately half the value of the D1-H190 side chain. The apparent disparity is attributed to a reduced 31-38% occupancy of the OEC, likely associated with its reduction by electron scattering.

  • Energetics of the S2 State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II
    The journal of physical chemistry. B, 2017
    Co-Authors: David J. Vinyard, Victor S. Batista, Sahr Khan, Mikhail Askerka, Gary W. Brudvig
    Abstract:

    The S2 redox intermediate of the Oxygen-Evolving Complex in photosystem II is present as two spin isomers. The S = 1/2 isomer gives rise to a multiline electron paramagnetic resonance (EPR) signal at g = 2.0, whereas the S = 5/2 isomer exhibits a broad EPR signal at g = 4.1. The electronic structures of these isomers are known, but their role in the catalytic cycle of water oxidation remains unclear. We show that formation of the S = 1/2 state from the S = 5/2 state is exergonic at temperatures above 160 K. However, the S = 1/2 isomer decays to S1 more slowly than the S = 5/2 isomer. These differences support the hypotheses that the S3 state is formed via the S2 state S = 5/2 isomer and that the stabilized S2 state S = 1/2 isomer plays a role in minimizing S2QA- decay under light-limiting conditions.

  • Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II
    Biochemistry, 2016
    Co-Authors: David J. Vinyard, Richard J. Debus, Victor S. Batista, Mikhail Askerka, Gary W. Brudvig
    Abstract:

    Ammonia binds to two sites in the Oxygen-Evolving Complex (OEC) of Photosystem II (PSII). The first is as a terminal ligand to Mn in the S2 state, and the second is at a site outside the OEC that is competitive with chloride. Binding of ammonia in this latter secondary site results in the S2 state S = 5/2 spin isomer being favored over the S = 1/2 spin isomer. Using electron paramagnetic resonance spectroscopy, we find that ammonia binds to the secondary site in wild-type Synechocystis sp. PCC 6803 PSII, but not in D2-K317A mutated PSII that does not bind chloride. By combining these results with quantum mechanics/molecular mechanics calculations, we propose that ammonia binds in the secondary site in competition with D1-D61 as a hydrogen bond acceptor to the OEC terminal water ligand, W1. Implications for the mechanism of ammonia binding via its primary site directly to Mn4 in the OEC are discussed.

  • S0-State model of the Oxygen-Evolving Complex of photosystem II.
    Biochemistry, 2013
    Co-Authors: Rhitankar Pal, Gary W. Brudvig, Christian F. A. Negre, Leslie Vogt, Ravi Pokhrel, Mehmed Z. Ertem, Victor S. Batista
    Abstract:

    The S0 → S1 transition of the Oxygen-Evolving Complex (OEC) of photosystem II is one of the least understood steps in the Kok cycle of water splitting. We introduce a quantum mechanics/molecular mechanics (QM/MM) model of the S0 state that is consistent with extended X-ray absorption fine structure spectroscopy and X-ray diffraction data. In conjunction with the QM/MM model of the S1 state, we address the proton-coupled electron-transfer (PCET) process that occurs during the S0 → S1 transition, where oxidation of a Mn center and deprotonation of a μ-oxo bridge lead to a significant rearrangement in the OEC. A hydrogen bonding network, linking the D1-D61 residue to a Mn-bound water molecule, is proposed to facilitate the PCET mechanism.

Kizashi Yamaguchi - One of the best experts on this subject based on the ideXlab platform.

  • Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.
    Inorganic chemistry, 2015
    Co-Authors: Hiroshi Isobe, Jian-ren Shen, Mitsuo Shoji, Kizashi Yamaguchi
    Abstract:

    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 tem...

  • Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving Complex of photosystem II
    Chemical Physics Letters, 2015
    Co-Authors: Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Kizashi Yamaguchi
    Abstract:

    Abstract Full geometry optimizations of ([CaMn4O4(CH3COO)8(py)(CH3COOH)2], (py: pyridine) (1)) were performed at the UB3LYP theoretical level. 1 is a theoretical model for the synthetic model ([CaMn4O4(ButCOO)8(py)(ButCOOH)2], (But: t-butyl) (2)) which closely mimicks the native oxygen evolving Complex (OEC) in photosystem II. It was shown that the X-ray structure of 2 was well reproduced by 1 in the (Mn1(III), Mn2(IV), Mn3(IV), Mn4(III)) valence state with the unprotonated O5 (O5 = O2−), and two different valence states were obtained in the one-electron oxidized state. Importance of the Jahn–Teller effect of the Mn(III) site for the structural deformations was presented.

  • QM/MM study of the S2 to S3 transition reaction in the Oxygen-Evolving Complex of photosystem II
    Chemical Physics Letters, 2015
    Co-Authors: Mitsuo Shoji, Hiroshi Isobe, Kizashi Yamaguchi
    Abstract:

    Abstract Catalytic reactions of the proton and electron transfers occurring at the Oxygen-Evolving Complex (OEC) of photosystem II during the S 2 –S 3 transition were investigated by the quantum mechanics/molecular mechanics (QM/MM) methodology. Two favorable reaction pathways were elucidated. Both reactions start by moving the Ca-bound water (W3) to the vacant Mn(III) coordination at the left-opened (L) or right-opened (R) form. The former reaction pathway, in which W3 coordinates to the Mn4 at the S 2 -L form, has lower activation barriers than the latter. Thus, easier proton transfers from W3 to the Tyr161 phenol anion can be performed.

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