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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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Capone M, Parisse G, Narzi D, Guidoni L. Unravelling Mn 4Ca cluster vibrations in the S 1, S 2 and S 3 states of the Kok-Joliot cycle of photosystem II. Phys Chem Chem Phys 2024; 26:20598-20609. [PMID: 39037338 PMCID: PMC11290063 DOI: 10.1039/d4cp01307g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Vibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok-Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To better analyze the computational data and assign spectral peaks, we introduce an approach based on dipole-dipole correlation function of cluster moieties of the reaction center. Our analysis reveals variation in the infrared signature of the Mn4Ca cluster along the Kok-Joliot cycle, attributed to its increasing symmetry and rigidity resulting from the rising oxidation state of the Mn ions. Furthermore, we successfully assign the debated contributions in the frequency range around 600 cm-1. This computational methodology provides valuable insights for deciphering experimental infrared spectra and understanding the water oxidation process in both biological and artificial systems.
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Affiliation(s)
- Matteo Capone
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Gianluca Parisse
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Daniele Narzi
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
| | - Leonardo Guidoni
- Università degli studi dell'Aquila, Dipartimento di Scienze Fisiche e Chimiche, L'Aquila, Italy.
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3
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Mandal M, Saito K, Ishikita H. Substitution of Ca 2+ and changes in the H-bond network near the oxygen-evolving complex of photosystem II. Phys Chem Chem Phys 2023; 25:6473-6480. [PMID: 36785919 DOI: 10.1039/d2cp05036f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Ca2+, which provides binding sites for ligand water molecules W3 and W4 in the Mn4CaO5 cluster, is a prerequisite for O2 evolution in photosystem II (PSII). We report structural changes in the H-bond network and the catalytic cluster itself upon the replacement of Ca2+ with other alkaline earth metals, using a quantum mechanical/molecular mechanical approach. The small radius of Mg2+ makes W3 donate an H-bond to D1-Glu189 in Mg2+-PSII. If an additional water molecule binds at the large surface of Ba2+, it donates H-bonds to D1-Glu189 and the ligand water molecule at the dangling Mn, altering the H-bond network. The potential energy profiles of the H-bond between D1-Tyr161 (TyrZ) and D1-His190 and the interconversion between the open- and closed-cubane S2 conformations remain substantially unaltered upon the replacement of Ca2+. Remarkably, the O5⋯Ca2+ distance is shortest among all O5⋯metal distances irrespective of the radius being larger than that of Mg2+. Furthermore, Ca2+ is the only alkaline earth metal that equalizes the O5⋯metal and O2⋯metal distances and facilitates the formation of the symmetric cubane structure.
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Affiliation(s)
- Manoj Mandal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India.
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. .,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. .,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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4
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Saito K, Nakagawa M, Mandal M, Ishikita H. Role of redox-inactive metals in controlling the redox potential of heterometallic manganese-oxido clusters. PHOTOSYNTHESIS RESEARCH 2021; 148:153-159. [PMID: 34047897 PMCID: PMC8292285 DOI: 10.1007/s11120-021-00846-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/11/2021] [Indexed: 05/13/2023]
Abstract
Photosystem II (PSII) contains Ca2+, which is essential to the oxygen-evolving activity of the catalytic Mn4CaO5 complex. Replacement of Ca2+ with other redox-inactive metals results in a loss/decrease of oxygen-evolving activity. To investigate the role of Ca2+ in this catalytic reaction, we investigate artificial Mn3[M]O2 clusters redox-inactive metals [M] ([M] = Mg2+, Ca2+, Zn2+, Sr2+, and Y3+), which were synthesized by Tsui et al. (Nat Chem 5:293, 2013). The experimentally measured redox potentials (Em) of these clusters are best described by the energy of their highest occupied molecular orbitals. Quantum chemical calculations showed that the valence of metals predominantly affects Em(MnIII/IV), whereas the ionic radius of metals affects Em(MnIII/IV) only slightly.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
| | - Minesato Nakagawa
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Manoj Mandal
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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5
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de Lichtenberg C, Messinger J. Substrate water exchange in the S2 state of photosystem II is dependent on the conformation of the Mn4Ca cluster. Phys Chem Chem Phys 2020; 22:12894-12908. [DOI: 10.1039/d0cp01380c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural flexibility of the Mn4Ca cluster in photosystem II supports the exchange of the central O5 bridge.
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6
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Five-coordinate Mn IV intermediate in the activation of nature's water splitting cofactor. Proc Natl Acad Sci U S A 2019; 116:16841-16846. [PMID: 31391299 DOI: 10.1073/pnas.1817526116] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature's water splitting cofactor passes through a series of catalytic intermediates (S0-S4) before O-O bond formation and O2 release. In the second last transition (S2 to S3) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all MnIV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S4 How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S3') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (>50%) in (i) chemical-modified cofactors in which Ca2+ is exchanged with Sr2+; the Mn4O5Sr cofactor remains active, but the S2-S3 and S3-S0 transitions are slower than for the Mn4O5Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S3' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S3 signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S2 state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S3' cofactor is similar to the high spin form of the preceding S2 state, which contains a cuboidal Mn3O4Ca unit tethered to an external, 5-coordinate Mn ion (Mn4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn4. The interaction of ammonia with the cofactor is also discussed.
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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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8
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Capone M, Narzi D, Tychengulova A, Guidoni L. On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:33-43. [PMID: 30801735 DOI: 10.1111/ppl.12949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Understanding the structural modification experienced by the Mn4 CaO5 oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S-states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S2 /S1 infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra.
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Affiliation(s)
- Matteo Capone
- Department of Information Engineering, Computational Science and Mathematics, Università dell'Aquila, 67100, L'Aquila, Italy
| | - Daniele Narzi
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Aliya Tychengulova
- Department of Basic Sciences Applied for Engineering, "Sapienza" Università di Roma, 00185, Rome, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Science, Università dell'Aquila, 67100, L'Aquila, Italy
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9
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Shoji M, Isobe H, Miyagawa K, Yamaguchi K. Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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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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11
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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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12
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Narzi D, Capone M, Bovi D, Guidoni L. Evolution from S3
to S4
States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics. Chemistry 2018; 24:10820-10828. [DOI: 10.1002/chem.201801709] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Daniele Narzi
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Federale de Lausanne; Av. F.-A. Forel 2 1015 Lausanne Switzerland
| | - Matteo Capone
- Dipartimento di Ingegneria e Scienze dell'Informazione e Matematica; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Daniele Bovi
- Dipartimento di Scienze Fisiche e Chimiche; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche; Universita degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
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13
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The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:342-356. [DOI: 10.1016/j.bbabio.2018.02.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 11/17/2022]
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14
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Beal NJ, Corry TA, O'Malley PJ. A Comparison of Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters for Intermediates Involved in the S 2 to S 3 State Transition of Nature's Oxygen Evolving Complex. J Phys Chem B 2018; 122:1394-1407. [PMID: 29300480 DOI: 10.1021/acs.jpcb.7b10843] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A broken symmetry density functional theory (BS-DFT) magnetic analysis of the S2, S2YZ•, and S3 states of Nature's oxygen evolving complex is performed for both the native Ca and Sr substituted forms. Good agreement with experiment is observed between the tyrosyl calculated g-tensor and 1H hyperfine couplings for the native Ca form. Changes in the hydrogen bonding environment of the tyrosyl radical in S2YZ• caused by Sr substitution lead to notable changes in the calculated g-tensor of the tyrosyl radical. Comparison of calculated and experimental 55Mn hyperfine couplings for the S3 state presently favors an open cubane form of the complex with an additional OH ligand coordinating to MnD. In Ca models, this additional ligation can arise by closed-cubane form deprotonation of the Ca ligand W3 in the S2YZ• state accompanied by spontaneous movement to the vacant Mn coordination site or by addition of an external OH group. For the Sr form, no spontaneous movement of W3 to the vacant Mn coordination site is observed in contrast to the native Ca form, a difference which may lead to the reduced catalytic activity of the Sr substituted form. BS-DFT studies on peroxo models of S3 as indicated by a recent X-ray free electron laser (XFEL) crystallography study give rise to a structural model compatible with experimental data and an S = 3 ground state compatible with EPR studies.
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Affiliation(s)
- Nathan J Beal
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - 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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15
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Singh S, Singh A, Srivastava PK, Prasad SM. Cadmium toxicity and its amelioration by kinetin in tomato seedlings vis-à-vis ascorbate-glutathione cycle. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:76-84. [DOI: 10.1016/j.jphotobiol.2017.10.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 09/02/2017] [Accepted: 10/26/2017] [Indexed: 01/12/2023]
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16
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Narzi D, Coccia E, Manzoli M, Guidoni L. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem 2017; 229:93-98. [DOI: 10.1016/j.bpc.2017.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023]
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17
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Kim CJ, Debus RJ. Evidence from FTIR Difference Spectroscopy That a Substrate H2O Molecule for O2 Formation in Photosystem II Is Provided by the Ca Ion of the Catalytic Mn4CaO5 Cluster. Biochemistry 2017; 56:2558-2570. [DOI: 10.1021/acs.biochem.6b01278] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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18
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Narzi D, Mattioli G, Bovi D, Guidoni L. A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem II. Chemistry 2017; 23:6969-6973. [DOI: 10.1002/chem.201700722] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Daniele Narzi
- Institute of Chemical Sciences and Engineering; École polytechnique fédérale de Lausanne; Av. F.-A. Forel 2 1015 Lausanne Switzerland
| | | | - Daniele Bovi
- Pangea Formazione s.r.l.; via Gaspare Gozzi, 55 00145 Rome Italy
- Dipartimento di Scienze Fisiche e Chimiche; Università degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche; Università degli studi dell'Aquila; Via Vetoio (Coppito) 67100 L'Aquila Italy
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19
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Nakamura S, Noguchi T. Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn 4CaO 5 cluster in photosystem II. Proc Natl Acad Sci U S A 2016; 113:12727-12732. [PMID: 27729534 PMCID: PMC5111704 DOI: 10.1073/pnas.1607897113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO2, in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn4CaO5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S1 to S2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III)2Mn(IV)2, satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.
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Affiliation(s)
- Shin Nakamura
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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20
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Bovi D, Capone M, Narzi D, Guidoni L. Vibrational fingerprints of the Mn 4 CaO 5 cluster in Photosystem II by mixed quantum-classical molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1669-77. [DOI: 10.1016/j.bbabio.2016.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/16/2016] [Accepted: 07/12/2016] [Indexed: 11/16/2022]
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21
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Capone M, Narzi D, Bovi D, Guidoni L. Mechanism of Water Delivery to the Active Site of Photosystem II along the S(2) to S(3) Transition. J Phys Chem Lett 2016; 7:592-6. [PMID: 26799278 DOI: 10.1021/acs.jpclett.5b02851] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the cluster during the transition between the S2 and S3 states, which has been recently revealed to have the Mn4CaO5 catalytic cluster arranged in an open cubane fashion. In this Letter, by means of ab initio calculations, we investigated the possible pathways for the binding of the upcoming water molecule. Upon the four different possibilities checked in our calculations, the binding of the crystallographic water molecule, originally located nearby the Cl(-) binding site, showed the lowest activation energy barrier. Our findings therefore support the view in which the W2 hydroxyl group and the O5 oxygen act as substrates for the oxygen evolution. Within this framework the role of the open and closed Mn4CaO5 conformers is clarified as well as the exact mechanistic events occurring along the S2 to S3 transition.
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Affiliation(s)
- Matteo Capone
- Dipartimento di Chimica, Sapienza Università di Roma , 00185 Roma, Italy
| | - Daniele Narzi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , 67100 L'Aquila, Italy
| | - Daniele Bovi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , 67100 L'Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila , 67100 L'Aquila, Italy
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22
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Redox-coupled substrate water reorganization in the active site of Photosystem II-The role of calcium in substrate water delivery. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:740-8. [PMID: 26826591 DOI: 10.1016/j.bbabio.2016.01.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/10/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water splitting in nature and is the key enzyme for energy input into the biosphere. Important details of its mechanism are not well understood. In order to understand the mechanism of water splitting, we perform here large-scale density functional theory (DFT) calculations on the active site of PSII in different oxidation, spin and ligand states. Prior to formation of the O-O bond, we find that all manganese atoms are oxidized to Mn(IV) in the S3 state, consistent with earlier studies. We find here, however, that the formation of the S3 state is coupled to the movement of a calcium-bound hydroxide (W3) from the Ca to a Mn (Mn1 or Mn4) in a process that is triggered by the formation of a tyrosyl radical (Tyr-161) and its protonated base, His-190. We find that subsequent oxidation and deprotonation of this hydroxide on Mn1 result in formation of an oxyl-radical that can exergonically couple with one of the oxo-bridges (O5), forming an O-O bond. When O(2) leaves the active site, a second Ca-bound water molecule reorients to bridge the gap between the manganese ions Mn1 and Mn4, forming a new oxo-bridge for the next reaction cycle. Our findings are consistent with experimental data, and suggest that the calcium ion may control substrate water access to the water oxidation sites.
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Krewald V, Neese F, Pantazis DA. Redox potential tuning by redox-inactive cations in nature's water oxidizing catalyst and synthetic analogues. Phys Chem Chem Phys 2016; 18:10739-50. [DOI: 10.1039/c5cp07213a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fundamental differences between synthetic manganese clusters and the biological water oxidizing catalyst are demonstrated in the modulation of their redox potential by redox-inactive cations.
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Affiliation(s)
- Vera Krewald
- Max Planck Institute for Chemical Energy Conversion
- 45470 Mülheim an der Ruhr
- Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion
- 45470 Mülheim an der Ruhr
- Germany
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Escriche-Tur L, Jover J, Font-Bardia M, Aullón G, Corbella M. Magnetic Behavior of Heterometallic Wheels Having a [Mn(IV)6M2O9](10+) Core with M = Ca(2+) and Sr(2+). Inorg Chem 2015; 54:11596-605. [PMID: 26645300 DOI: 10.1021/acs.inorgchem.5b02131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Two new heterometallic Mn(IV)-M(2+) compounds with formula [Mn6M2O9(4-(t)BuC6H4COO)10(4-(t)BuC6H4COOH)5] (M = Ca(2+) (1), Sr(2+) (2)) have been crystallized. The core of both compounds consists of a planar Mn6 ring, where the Mn(IV) ions are alternatively bridged by (μ3-O)2(μ-RCOO) and (μ4-O)(μ-RCOO)2 ligands, and the two alkaline earth ions are located to both sides of the wheel, linked to the oxo bridges, generating three fused [Mn2M2O4](4+) cuboids. These compounds show a net antiferromagnetic behavior, more important for 2 (Sr(2+)) than for 1 (Ca(2+)). The fitting of the experimental data was performed with the support of DFT calculations, considering four different exchange pathways: two between adjacent Mn(IV) ions (J1 and J2) and two between nonadjacent Mn(IV) ions (J3 and J4). The results of the analysis show that J1 and J2 are of the opposite sign, the ferromagnetic contribution corresponding to the [Mn2(μ4-O)(μ-RCOO)2](4+) unit (J2). The influence of the M(2+) ions in the magnetic behavior is analyzed for 1 and 2 and for three hypothetical models with the structural parameters of 1 containing Mg(2+), Sr(2+) or without the M(2+) ions. In spite of the diamagnetic character of the alkaline earth ions, their influence on the magnetic behavior has been evidenced and correlated with their polarizing effect. Moreover, the magnetic interactions between nonadjacent ions are non-negligible.
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Affiliation(s)
| | | | | | - Gabriel Aullón
- Institut de Química Teòrica i Computacional de la Universitat de Barcelona (IQTCUB) , Barcelona 08028, Spain
| | - Montserrat Corbella
- Institut de Nanociencia i Nanotecnologia de la Universitat de Barcelona (IN2UB) , Barcelona 08028, Spain
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