1
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Bury G, Pushkar Y. Insights from Ca 2+→Sr 2+ substitution on the mechanism of O-O bond formation in photosystem II. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01117-2. [PMID: 39186214 DOI: 10.1007/s11120-024-01117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024]
Abstract
In recent years, there has been a steady interest in unraveling the intricate mechanistic details of water oxidation mechanism in photosynthesis. Despite the substantial progress made over several decades, a comprehensive understanding of the precise kinetics underlying O-O bond formation and subsequent evolution remains elusive. However, it is well-established that the oxygen evolving complex (OEC), specifically the CaMn4O5 cluster, plays a crucial role in O-O bond formation, undergoing a series of four oxidative events as it progresses through the S-states of the Kok cycle. To gain further insights into the OEC, researchers have explored the substitution of the Ca2+ cofactor with strontium (Sr), the sole atomic replacement capable of retaining oxygen-evolving activity. Empirical investigations utilizing spectroscopic techniques such as XAS, XRD, EPR, FTIR, and XANES have been conducted to probe the structural consequences of Ca2+→Sr2+ substitution. In parallel, the development of DFT and QM/MM computational models has explored different oxidation and protonation states, as well as variations in ligand coordination at the catalytic center involving amino acid residues. In this review, we critically evaluate and integrate these computational and spectroscopic approaches, focusing on the structural and mechanistic implications of Ca2+→Sr2+ substitution in PS II. We contribute DFT modelling and simulate EXAFS Fourier transforms of Sr-substituted OEC, analyzing promising structures of the S3 state. Through the combination of computational modeling and spectroscopic investigations, valuable insights have been gained, developing a deeper understanding of the photosynthetic process.
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Affiliation(s)
- Gabriel Bury
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, 47907, USA.
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2
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Rogers C, Hardwick O, Corry TA, Rummel F, Collison D, Bowen AM, O’Malley PJ. Magnetic and Electronic Structural Properties of the S 3 State of Nature's Water Oxidizing Complex: A Combined Study in ELDOR-Detected Nuclear Magnetic Resonance Spectral Simulation and Broken-Symmetry Density Functional Theory. ACS OMEGA 2022; 7:41783-41788. [PMID: 36406523 PMCID: PMC9670293 DOI: 10.1021/acsomega.2c06151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
ELDOR-detected nuclear magnetic resonance (EDNMR) spectral simulations combined with broken-symmetry density functional theory (BS-DFT) calculations are used to obtain and to assign the 55Mn hyperfine coupling constants (hfcs) for modified forms of the water oxidizing complex in the penultimate S3 state of the water oxidation cycle. The study shows that an open cubane form of the core Mn4CaO6 cluster explains the magnetic properties of the dominant S = 3 species in all cases studied experimentally with no need to invoke a closed cubane intermediate possessing a distorted pentacoordinate Mn4 ion as recently suggested. EDNMR simulations found that both the experimental bandwidth and multinuclear transitions may alter relative EDNMR peak intensities, potentially leading to incorrect assignment of hfcs. The implications of these findings for the water oxidation mechanism are discussed.
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3
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Rummel F, O’Malley PJ. How Nature Makes O 2: an Electronic Level Mechanism for Water Oxidation in Photosynthesis. J Phys Chem B 2022; 126:8214-8221. [PMID: 36206029 PMCID: PMC9589598 DOI: 10.1021/acs.jpcb.2c06374] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this paper, we combine broken symmetry density functional calculations and electron paramagnetic resonance analysis to obtain the electronic structure of the penultimate S3 state of nature's water-oxidizing complex and determine the electronic pathway of O-O bond formation. Analysis of the electronic structure changes along the reaction path shows that two spin crossovers, facilitated by the geometry and magnetism of the water-oxidizing complex, are used to provide a unique low-energy pathway. The pathway is facilitated via the formation and stabilization of the [O2]3- ion. This ion is formed between ligated deprotonated substrate waters, O5 and O6, and is stabilized by antiferromagnetic interaction with the Mn ions of the complex. Combining the computational, crystallographic, and spectroscopic data, we show that an equilibrium exists between the O5 oxo and O6 hydroxo forms with an S = 3 spin state and a deprotonated O6 form containing a two-center one-electron bond in [O5O6]3- which we identify as the form detected using crystallography. This form corresponds to an S = 6 spin state which we demonstrate gives rise to a low-intensity EPR spectrum compared with the accompanying S = 3 state, making its detection via EPR difficult and overshadowed by the S = 3 form. Simulations using 70% of the S = 6 component give rise to a superior fit to the experimental W-band EPR spectral envelope compared with an S = 3 only form. Analyses of the most recent X-ray emission spectroscopy first moment changes for solution and time-resolved crystal data are also shown to support the model. The computational, crystallographic, and spectroscopic data are shown to coalesce to the same picture of a predominant S = 6 species containing the first one-electron oxidation product of two water molecules, that is, [O5O6]3-. Progression of this form to the two-electron-oxidized peroxo and three-electron-oxidized superoxo forms, leading eventually to the evolution of triplet O2, is proposed to be the pathway nature adopts to oxidize water. The study reveals the key electronic, magnetic, and structural design features of nature's catalyst which facilitates water oxidation to O2 under ambient conditions.
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4
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Donnan PH, Mansoorabadi SO. Broken-Symmetry Density Functional Theory Analysis of the Ω Intermediate in Radical S-Adenosyl-l-methionine Enzymes: Evidence for a Near-Attack Conformer over an Organometallic Species. J Am Chem Soc 2022; 144:3381-3385. [PMID: 35170316 DOI: 10.1021/jacs.2c00678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are found in all domains of life and catalyze a wide range of biochemical reactions. Recently, an organometallic intermediate, Ω, has been experimentally implicated in the 5'-deoxyadenosyl radical generation mechanism of the radical SAM superfamily. In this work, we employ broken-symmetry density functional theory to evaluate several structural models of Ω. The results show that the calculated hyperfine coupling constants (HFCCs) for the proposed organometallic structure of Ω are inconsistent with the experiment. In contrast, a near-attack conformer of SAM bound to the catalytic [4Fe-4S] cluster, in which the distance between the unique iron and SAM sulfur is ∼3 Å, yields HFCCs that are all within 1 MHz of the experimental values. These results clarify the structure of the ubiquitous Ω intermediate and suggest a paradigm shift reversal regarding the mechanism of SAM cleavage by members of the radical SAM superfamily.
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Affiliation(s)
- Patrick H Donnan
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
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5
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Debus RJ. Alteration of the O 2-Producing Mn 4Ca Cluster in Photosystem II by the Mutation of a Metal Ligand. Biochemistry 2021; 60:3841-3855. [PMID: 34898175 DOI: 10.1021/acs.biochem.1c00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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6
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Corry TA, O'Malley PJ. S 3 State Models of Nature's Water Oxidizing Complex: Analysis of Bonding and Magnetic Exchange Pathways, Assessment of Experimental Electron Paramagnetic Resonance Data, and Implications for the Water Oxidation Mechanism. J Phys Chem B 2021; 125:10097-10107. [PMID: 34463499 DOI: 10.1021/acs.jpcb.1c04459] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr2+ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn1 and Mn2 ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated 55Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.
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Affiliation(s)
- Thomas A Corry
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
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7
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Okamoto Y, Shimada Y, Nagao R, Noguchi T. Proton and Water Transfer Pathways in the S 2 → S 3 Transition of the Water-Oxidizing Complex in Photosystem II: Time-Resolved Infrared Analysis of the Effects of D1-N298A Mutation and NO 3- Substitution. J Phys Chem B 2021; 125:6864-6873. [PMID: 34152151 DOI: 10.1021/acs.jpcb.1c03386] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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.
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Affiliation(s)
- Yasutada Okamoto
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yuichiro Shimada
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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8
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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9
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Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Kawakami T. Theory of chemical bonds in metalloenzymes XXIII fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem II. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1725168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K. Yamaguchi
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - T. Kawakami
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
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10
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Kim CJ, Debus RJ. Roles of D1-Glu189 and D1-Glu329 in O2 Formation by the Water-Splitting Mn4Ca Cluster in Photosystem II. Biochemistry 2020; 59:3902-3917. [DOI: 10.1021/acs.biochem.0c00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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11
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Corry TA, O'Malley PJ. Electronic-Level View of O-O Bond Formation in Nature's Water Oxidizing Complex. J Phys Chem Lett 2020; 11:4221-4225. [PMID: 32374174 DOI: 10.1021/acs.jpclett.0c00794] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The crucial O-O bond forming step in the water oxidizing complex (WOC) of photosystem II is modeled using density functional theory calculations and compared with structural X-ray free electron laser (XFEL) determinations for the penultimate S3 state. Concerted electron flow between the Mn4O5 and Mn1O6 bonds of the complex and the nascent O-O bond is monitored using intrinsic bond orbital analysis along the reaction path. Concerted transfer to Mn1 and Mn4 of two electrons from the reactant oxos, O5 and O6, resulting in an unoccupied antibonding σ2p* orbital is the key to low barrier O-O bond formation. The potential energy surface for O-O bond formation shows a rather broad energy minimum for the oxo-oxo form ranging from 2.4-2.0 Å which may explain the relatively short O5-O6 bond distance reported in experimental structure studies. Alternatively the short O5-O6 bond distance may reflect a dynamic equilibrium model across the whole O-O potential energy surface.
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Affiliation(s)
- Thomas A Corry
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
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12
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Petrie S, Terrett R, Stranger R, Pace RJ. Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S 3 State Crystal Structures of Photosystem II. Chemphyschem 2020; 21:785-801. [PMID: 32133758 DOI: 10.1002/cphc.201901106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Indexed: 11/06/2022]
Abstract
Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S3 structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S1 structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5-O6 separation of ∼1.5 Å. In the latest S3 variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S3 , closely ligating one Mn, with O5-Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018) this oxidation state assumption predicted two energetically close S3 structural forms, one with the metal centres and O5 (as OH- ) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H2 O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S3 structure is also a likely superposition of forms, but with O5 (as OH- ) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural 'lability' of the WOC centre in the S3 state, which is likely catalytically relevant to its water splitting function.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Richard Terrett
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
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13
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Lee HB, Marchiori DA, Chatterjee R, Oyala PH, Yano J, Britt RD, Agapie T. S = 3 Ground State for a Tetranuclear Mn IV4O 4 Complex Mimicking the S 3 State of the Oxygen-Evolving Complex. J Am Chem Soc 2020; 142:3753-3761. [PMID: 32013412 DOI: 10.1021/jacs.9b10371] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The S3 state is currently the last observable intermediate prior to O-O bond formation at the oxygen-evolving complex (OEC) of Photosystem II, and its electronic structure has been assigned to a homovalent MnIV4 core with an S = 3 ground state. While structural interpretations based on the EPR spectroscopic features of the S3 state provide valuable mechanistic insight, corresponding synthetic and spectroscopic studies on tetranuclear complexes mirroring the Mn oxidation states of the S3 state remain rare. Herein, we report the synthesis and characterization by XAS and multifrequency EPR spectroscopy of a MnIV4O4 cuboidal complex as a spectroscopic model of the S3 state. Results show that this MnIV4O4 complex has an S = 3 ground state with isotropic 55Mn hyperfine coupling constants of -75, -88, -91, and 66 MHz. These parameters are consistent with an αααβ spin topology approaching the trimer-monomer magnetic coupling model of pseudo-octahedral MnIV centers. Importantly, the spin ground state changes from S = 1/2 to S = 3 as the OEC is oxidized from the S2 state to the S3 state. This same spin state change is observed following oxidation of the previously reported MnIIIMnIV3O4 cuboidal complex to the MnIV4O4 complex described here. This sets a synthetic precedent for the observed low-spin to high-spin conversion in the OEC.
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Affiliation(s)
- Heui Beom Lee
- Department of Chemistry and Chemical Engineering , California Institute of Technology , 1200 East California Boulevard MC 127-72 , Pasadena , California 91125 , United States
| | - David A Marchiori
- Department of Chemistry , University of California Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Paul H Oyala
- Department of Chemistry and Chemical Engineering , California Institute of Technology , 1200 East California Boulevard MC 127-72 , Pasadena , California 91125 , United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - R David Britt
- Department of Chemistry , University of California Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Theodor Agapie
- Department of Chemistry and Chemical Engineering , California Institute of Technology , 1200 East California Boulevard MC 127-72 , Pasadena , California 91125 , United States
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14
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Abstract
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.
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15
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Witwicki M, Walencik PK, Jezierska J. How accurate is density functional theory in predicting spin density? An insight from the prediction of hyperfine coupling constants. J Mol Model 2019; 26:10. [PMID: 31834497 DOI: 10.1007/s00894-019-4268-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/25/2019] [Indexed: 01/30/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has been proven to be an important technique for studying paramagnetic systems. Probably, the most accessible EPR parameter and the one that provides a significant amount of information about molecular structure and spin density is the hyperfine coupling constant (HFCC). Hence, accurate quantum-chemical modeling of HFCCs is frequently essential to the adequate interpretation of EPR spectra. It requires the precise spin density, which is the difference between the densities of α- and β-electrons, and thus, its quality is expected to reflect the quality of the total electron density. The question of which approximate exchange-correlation density functional yields sufficiently accurate HFCCs, and thus, the spin density remains open. To assess the performance of well-established density functionals for calculating HFCCs, we used a series of 26 small paramagnetic species and compared the obtained results to the CCSD reference values. The performance of DFT was also tested on EPR-studied o-semiquinone radical interacting with water molecules and Mg2+ cation. The HFCCs were additionally calculated by the DLPNO-CCSD method, and this wave function-based technique was found superior to all functionals we tested. Although some functionals were found, on average, to be fairly efficient, we found that the most accurate functional is system-dependent, and therefore, the DLPNO-CCSD method should be preferred for theoretical investigations of the HFCCs and spin density.
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Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Paulina K Walencik
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Julia Jezierska
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland
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16
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Kim CJ, Debus RJ. One of the Substrate Waters for O2 Formation in Photosystem II Is Provided by the Water-Splitting Mn4CaO5 Cluster’s Ca2+ Ion. Biochemistry 2019; 58:3185-3192. [DOI: 10.1021/acs.biochem.9b00418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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17
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Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Nakajima T, Kawakami T, Okumura M. Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn 4 O X (X = 5, 6) cluster in the Kok cycle S i (i = 0-3) of oxygen evolving complex of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:44-59. [PMID: 30847925 DOI: 10.1111/ppl.12960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The optimized geometries of the CaMn4 OX (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the Si (i = 0-3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the Si intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S3 state are investigated in detail in relation to recent SFX and XES experiments for the S3 state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S3 state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.
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Affiliation(s)
- Kizashi Yamaguchi
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
- Riken Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Okayama 700-8530, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki 305-8577, Japan
| | - Kouichi Miyagawa
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
| | | | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
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18
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The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation. INORGANICS 2019. [DOI: 10.3390/inorganics7040055] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The catalytic cycle of the oxygen-evolving complex (OEC) of photosystem II (PSII) comprises five intermediate states Si (i = 0–4), from the most reduced S0 state to the most oxidized S4, which spontaneously evolves dioxygen. The precise geometric and electronic structure of the Si states, and hence the mechanism of O–O bond formation in the OEC, remain under investigation, particularly for the final steps of the catalytic cycle. Recent advances in protein crystallography based on X-ray free-electron lasers (XFELs) have produced new structural models for the S3 state, which indicate that two of the oxygen atoms of the inorganic Mn4CaO6 core of the OEC are in very close proximity. This has been interpreted as possible evidence for “early-onset” O–O bond formation in the S3 state, as opposed to the more widely accepted view that the O–O bond is formed in the final state of the cycle, S4. Peroxo or superoxo formation in S3 has received partial support from computational studies. Here, a brief overview is provided of spectroscopic information, recent crystallographic results, and computational models for the S3 state. Emphasis is placed on computational S3 models that involve O–O formation, which are discussed with respect to their agreement with structural information, experimental evidence from various spectroscopic studies, and substrate exchange kinetics. Despite seemingly better agreement with some of the available crystallographic interpretations for the S3 state, models that implicate early-onset O–O bond formation are hard to reconcile with the complete line of experimental evidence, especially with X-ray absorption, X-ray emission, and magnetic resonance spectroscopic observations. Specifically with respect to quantum chemical studies, the inconclusive energetics for the possible isoforms of S3 is an acute problem that is probably beyond the capabilities of standard density functional theory.
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19
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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Spin, Valence, and Structural Isomerism in the S 3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity. J Chem Theory Comput 2019; 15:2375-2391. [PMID: 30855953 DOI: 10.1021/acs.jctc.8b01055] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S3 state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn···Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state ( Stotal = 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short O5···O6 distances (<2.0 Å) and long MnA···O5 distances (>2.0 Å). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.
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Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Mitsuo Shoji
- Center for Computational Science , University of Tsukuba , Tsukuba , Ibaraki 305-8577 , Japan
| | - Takayoshi Suzuki
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design , Osaka University , Toyonaka , Osaka 560-0043 , Japan
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20
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Amin M, Kaur D, Yang KR, Wang J, Mohamed Z, Brudvig GW, Gunner MR, Batista V. Thermodynamics of the S2-to-S3 state transition of the oxygen-evolving complex of photosystem II. Phys Chem Chem Phys 2019; 21:20840-20848. [DOI: 10.1039/c9cp02308a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The S2 to S3 transition in the OEC of PSII changes the structure of the Mn cluster. Monte Carlo sampling finds a Ca terminal water moves to form a bridge to Mn4 and the Mn1 ligand E189 can be replaced with a hydroxyl as a proton is lost.
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Affiliation(s)
- Muhamed Amin
- Center for Free-Electron Laser Science
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- Department of Sciences
| | - Divya Kaur
- Department of Physics
- City College of New York
- 160 Convent Avenue
- New York
- USA
| | - Ke R. Yang
- Department of Chemistry, Yale University
- New Haven
- USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry
- Yale University
- New Haven
- USA
| | - Zainab Mohamed
- Zewail City of Science and Technology
- Sheikh Zayed
- 12588 Giza
- Egypt
| | | | - M. R. Gunner
- Department of Physics
- City College of New York
- 160 Convent Avenue
- New York
- USA
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21
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Corry TA, O'Malley PJ. Evidence of O-O Bond Formation in the Final Metastable S 3 State of Nature's Water Oxidizing Complex Implying a Novel Mechanism of Water Oxidation. J Phys Chem Lett 2018; 9:6269-6274. [PMID: 30336040 DOI: 10.1021/acs.jpclett.8b02793] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A novel mechanism for the final stages of Nature's photosynthetic water oxidation to molecular oxygen is proposed. This is based on a comparison of experimental and broken symmetry density functional theory (BS-DFT) calculated geometries and magnetic resonance properties of water oxidizing complex models in the final metastable oxidation state, S3. We show that peroxo models of the S3 state are in vastly superior agreement with the current experimental structural determinations compared with oxo-hydroxo models. Comparison of experimental and BS-DFT calculated 55Mn hyperfine couplings for the electron paramagnetic resonance (EPR) visible form shows better agreement for the oxo-hydroxo model. An equilibrium between oxo-hydroxo and peroxo models is proposed for the S3 state and the major implications for the final steps in the water oxidation mechanism are analyzed and discussed.
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Affiliation(s)
- Thomas A Corry
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
| | - Patrick J O'Malley
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
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22
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Petrie S, Stranger R, Pace RJ. Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S 3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å. Chemphyschem 2018; 19:3296-3309. [PMID: 30290080 DOI: 10.1002/cphc.201800686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/10/2022]
Abstract
Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5-O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
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23
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Affiliation(s)
- Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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24
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Kim CJ, Bao H, Burnap RL, Debus RJ. Impact of D1-V185 on the Water Molecules That Facilitate O2 Formation by the Catalytic Mn4CaO5 Cluster in Photosystem II. Biochemistry 2018; 57:4299-4311. [DOI: 10.1021/acs.biochem.8b00630] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher J. Kim
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Han Bao
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Robert L. Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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25
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Pushkar Y, Davis KM, Palenik MC. Model of the Oxygen Evolving Complex Which Is Highly Predisposed to O-O Bond Formation. J Phys Chem Lett 2018; 9:3525-3531. [PMID: 29863871 DOI: 10.1021/acs.jpclett.8b00800] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Light-driven water oxidation is a fundamental reaction in the biosphere. The Mn4Ca cluster of photosystem II cycles through five redox states termed S0-S4, after which oxygen is evolved. Critically, the timing of O-O bond formation within the Kok cycle remains unknown. By combining recent crystallographic, spectroscopic, and DFT results, we demonstrate an atomistic S3 state model with the possibility of a low barrier to O-O bond formation prior to the final oxidation step. Furthermore, the associated one electron oxidized S4 state does not provide more advantages in terms of spin alignment or the energy of O-O bond formation. We propose that a high energy peroxide isoform of the S3 state can preferentially be oxidized by Tyr zox in the course of final electron transfer leading to O2 evolution. Such a mechanism may explain the peculiar kinetic behavior of O2 evolution as well as serve as an evolutionary adaptation to avoid release of the harmful peroxides.
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Affiliation(s)
- Yulia Pushkar
- Department of Physics and Astronomy , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Katherine M Davis
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Mark C Palenik
- Chemistry Division , Naval Research Laboratory , NRC Research Associate, Code 6189, 4555 Overlook Avenue SW , Washington, DC 20375 , United States
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