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Russell BP, Vinyard DJ. Conformational changes in a Photosystem II hydrogen bond network stabilize the oxygen-evolving complex. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149020. [PMID: 37956939 DOI: 10.1016/j.bbabio.2023.149020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
The Mn4CaO5 oxygen-evolving complex (OEC) in Photosystem II (PSII) is assembled in situ and catalyzes water oxidation. After OEC assembly, the PsbO extrinsic subunit docks to the lumenal face of PSII and both stabilizes the OEC and facilitates efficient proton transfer to the lumen. D1 residue R334 is part of a hydrogen bond network involved in proton release during catalysis and interacts directly with PsbO. D1-R334 has recently been observed in different conformations in apo- and holo-OEC PSII structures. We generated a D1-R334G point mutant in Synechocystis sp. PCC 6803 to better understand this residue's function. D1-R334G PSII is active under continuous light, but the OEC is unstable in darkness. Isolated D1-R334G core complexes have little bound PsbO and less manganese as the wild type control. The S2 intermediate is stabilized in D1-R334G indicating that the local environment around the OEC has been altered. These results suggest that the hydrogen bond network that includes D1-R334 exists in a different functional conformation during PSII biogenesis in the absence of PsbO.
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Affiliation(s)
- Brandon P Russell
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States of America
| | - David J Vinyard
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States of America.
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2
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Shimada Y, Sugiyama A, Nagao R, Noguchi T. Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II. J Phys Chem B 2022; 126:8202-8213. [PMID: 36199221 DOI: 10.1021/acs.jpcb.2c05869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Photosynthetic water oxidation takes place at the Mn4CaO5 cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S0-S4). Although the PSII structures have shown the presence of several channels around the Mn4CaO5 cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S2 → S3 transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S3 → S0 transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S2 → S3 transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S3 → S0 transition.
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Affiliation(s)
- Yuichiro Shimada
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ayane Sugiyama
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ryo Nagao
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan.,Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Okayama700-8530, Japan
| | - Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
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Kuroda H, Kawashima K, Ueda K, Ikeda T, Saito K, Ninomiya R, Hida C, Takahashi Y, Ishikita H. Proton transfer pathway from the oxygen-evolving complex in photosystem II substantiated by extensive mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148329. [PMID: 33069681 DOI: 10.1016/j.bbabio.2020.148329] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
We report a structure-based biological approach to identify the proton-transfer pathway in photosystem II. First, molecular dynamics (MD) simulations were conducted to analyze the H-bond network that may serve as a Grotthuss-like proton conduit. MD simulations show that D1-Asp61, the H-bond acceptor of H2O at the Mn4CaO5 cluster (W1), forms an H-bond via one water molecule with D1-Glu65 but not with D2-Glu312. Then, D1-Asp61, D1-Glu65, D2-Glu312, and the adjacent residues, D1-Arg334, D2-Glu302, and D2-Glu323, were thoroughly mutated to the other 19 residues, i.e., 114 Chlamydomonas chloroplast mutant cells were generated. Mutation of D1-Asp61 was most crucial. Only the D61E and D61C cells grew photoautotrophically and exhibit O2-evolving activity. Mutations of D2-Glu312 were less crucial to photosynthetic growth than mutations of D1-Glu65. Quantum mechanical/molecular mechanical calculations indicated that in the PSII crystal structure, the proton is predominantly localized at D1-Glu65 along the H-bond with D2-Glu312, i.e., pKa(D1-Glu65) > pKa(D2-Glu312). The potential-energy profile shows that the release of the proton from D1-Glu65 leads to the formation of the two short H-bonds between D1-Asp61 and D1-Glu65, which facilitates downhill proton transfer along the Grotthuss-like proton conduit in the S2 to S3 transition. It seems possible that D1-Glu65 is involved in the dominant pathway that proceeds from W1 via D1-Asp61 toward the thylakoid lumen, whereas D2-Glu312 and D1-Arg334 may be involved in alternative pathways in some mutants.
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Affiliation(s)
- Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Keisuke Kawashima
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan
| | - Kazuyo Ueda
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Takuya Ikeda
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8654, Japan
| | - 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
| | - Ryo Ninomiya
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Chisato Hida
- Department of Biology, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, 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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4
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Zhang Y, Zhang R, Bai J, Liu W, Yang J, Bian L. Human laminin α3 chain G1 domain is a receptor for plasminogen Kringle 5 on human endothelial cells by biological specificity technologies and molecular dynamic. J Chromatogr A 2020; 1620:460986. [DOI: 10.1016/j.chroma.2020.460986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/30/2022]
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Nagao R, Ueoka-Nakanishi H, Noguchi T. D1-Asn-298 in photosystem II is involved in a hydrogen-bond network near the redox-active tyrosine Y Z for proton exit during water oxidation. J Biol Chem 2017; 292:20046-20057. [PMID: 29046348 DOI: 10.1074/jbc.m117.815183] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/04/2017] [Indexed: 01/19/2023] Open
Abstract
In photosynthetic water oxidation, two water molecules are converted into one oxygen molecule and four protons at the Mn4CaO5 cluster in photosystem II (PSII) via the S-state cycle. Efficient proton exit from the catalytic site to the lumen is essential for this process. However, the exit pathways of individual protons through the PSII proteins remain to be identified. In this study, we examined the involvement of a hydrogen-bond network near the redox-active tyrosine YZ in proton transfer during the S-state cycle. We focused on spectroscopic analyses of a site-directed variant of D1-Asn-298, a residue involved in a hydrogen-bond network near YZ We found that the D1-N298A mutant of Synechocystis sp. PCC 6803 exhibits an O2 evolution activity of ∼10% of the wild-type. D1-N298A and the wild-type D1 had very similar features of thermoluminescence glow curves and of an FTIR difference spectrum upon YZ oxidation, suggesting that the hydrogen-bonded structure of YZ and electron transfer from the Mn4CaO5 cluster to YZ were little affected by substitution. In the D1-N298A mutant, however, the flash-number dependence of delayed luminescence showed a monotonic increase without oscillation, and FTIR difference spectra of the S-state cycle indicated partial and significant inhibition of the S2 → S3 and S3 → S0 transitions, respectively. These results suggest that the D1-N298A substitution inhibits the proton transfer processes in the S2 → S3 and S3 → S0 transitions. This in turn indicates that the hydrogen-bond network near YZ can be functional as a proton transfer pathway during photosynthetic water oxidation.
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Affiliation(s)
- Ryo Nagao
- Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
| | - Hanayo Ueoka-Nakanishi
- 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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Debus RJ. FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:19-34. [PMID: 25038513 DOI: 10.1016/j.bbabio.2014.07.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/26/2022]
Abstract
The photosynthetic conversion of water to molecular oxygen is catalyzed by the Mn₄CaO₅ cluster in Photosystem II and provides nearly our entire supply of atmospheric oxygen. The Mn₄CaO₅ cluster accumulates oxidizing equivalents in response to light-driven photochemical events within Photosystem II and then oxidizes two molecules of water to oxygen. The Mn₄CaO₅ cluster converts water to oxygen much more efficiently than any synthetic catalyst because its protein environment carefully controls the cluster's reactivity at each step in its catalytic cycle. This control is achieved by precise choreography of the proton and electron transfer reactions associated with water oxidation and by careful management of substrate (water) access and proton egress. This review describes the FTIR studies undertaken over the past two decades to identify the amino acid residues that are responsible for this control and to determine the role of each. In particular, this review describes the FTIR studies undertaken to characterize the influence of the cluster's metal ligands on its activity, to delineate the proton egress pathways that link the Mn₄CaO₅ cluster with the thylakoid lumen, and to characterize the influence of specific residues on the water molecules that serve as substrate or as participants in the networks of hydrogen bonds that make up the water access and proton egress pathways. This information will improve our understanding of water oxidation by the Mn₄CaO₅ catalyst in Photosystem II and will provide insight into the design of new generations of synthetic catalysts that convert sunlight into useful forms of storable energy. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Richard J Debus
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521-0129, USA.
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7
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Service RJ, Hillier W, Debus RJ. Network of Hydrogen Bonds near the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II Probed with FTIR Difference Spectroscopy. Biochemistry 2014; 53:1001-17. [DOI: 10.1021/bi401450y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rachel J. Service
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Warwick Hillier
- Research
School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
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The extrinsic proteins of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:121-42. [PMID: 21801710 DOI: 10.1016/j.bbabio.2011.07.006] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 02/08/2023]
Abstract
In this review we examine the structure and function of the extrinsic proteins of Photosystem II. These proteins include PsbO, present in all oxygenic organisms, the PsbP and PsbQ proteins, which are found in higher plants and eukaryotic algae, and the PsbU, PsbV, CyanoQ, and CyanoP proteins, which are found in the cyanobacteria. These proteins serve to optimize oxygen evolution at physiological calcium and chloride concentrations. They also shield the Mn(4)CaO(5) cluster from exogenous reductants. Numerous biochemical, genetic and structural studies have been used to probe the structure and function of these proteins within the photosystem. We will discuss the most recent proposed functional roles for these components, their structures (as deduced from biochemical and X-ray crystallographic studies) and the locations of their proposed binding domains within the Photosystem II complex. This article is part of a Special Issue entitled: Photosystem II.
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9
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Ho FM. Structural and mechanistic investigations of photosystem II through computational methods. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:106-20. [PMID: 21565158 DOI: 10.1016/j.bbabio.2011.04.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/22/2011] [Accepted: 04/02/2011] [Indexed: 11/17/2022]
Abstract
The advent of oxygenic photosynthesis through water oxidation by photosystem II (PSII) transformed the planet, ultimately allowing the evolution of aerobic respiration and an explosion of ecological diversity. The importance of this enzyme to life on Earth has ironically been paralleled by the elusiveness of a detailed understanding of its precise catalytic mechanism. Computational investigations have in recent years provided more and more insights into the structural and mechanistic details that underlie the workings of PSII. This review will present an overview of some of these studies, focusing on those that have aimed at elucidating the mechanism of water oxidation at the CaMn₄ cluster in PSII, and those exploring the features of the structure and dynamics of this enzyme that enable it to catalyse this energetically demanding reaction. This article is part of a Special Issue entitled: Photosystem II.
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Affiliation(s)
- Felix M Ho
- Deparment of Photochemistry and Molecular Sciences, Angström Laboratory, Uppsala University, Sweden.
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Krol M, Ivanov AG, Booij-James I, Mattoo AK, Sane PV, Hüner NP. Absence of the major light-harvesting antenna proteins alters the redox properties of photosystem II reaction centres in thechlorina F2mutant of barley. Biochem Cell Biol 2009; 87:557-66. [DOI: 10.1139/o09-013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although the chlorina F2 mutant of barley specifically exhibits reduced levels of the major light-harvesting polypeptides associated with photosystem II (PSII), thermoluminescence measurements of photosystem reaction centre photochemistry revealed that S2/S3QB–charge recombinations were shifted to lower temperatures, while the characteristic peak of S2QA–charge recombinations was shifted to higher temperatures compared with wild-type (WT) barley. Thus, we show that the absence of the major light-harvesting polypeptides affects the redox properties of PSII reaction centres. Radiolabeling studies in vivo and in vitro with [32P]orthophosphate or [γ-32P]ATP, respectively, demonstrated that the D1 PSII reaction centre polypeptide is phosphorylated in both the WT and the F2 mutant. In contrast with the radiolabeling results, phosphorylation of D1 and other PSII proteins, although detected in WT barley, was ambiguous in the F2 mutant when the phosphothreonine antibody method of detection was used. Thus, caution must be exercised in the use of commercially available phosphothreonine antibodies to estimate thylakoid polypeptide phosphorylation. Furthermore, in membrano, the D1 polypeptide of the F2 mutant was less susceptible to trypsin treatment than that of WT barley. The role of the light-harvesting complex in modulating the structure and function of the D1 polypeptide of PSII reaction centers is discussed.
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Affiliation(s)
- Marianna Krol
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Alexander G. Ivanov
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Isabelle Booij-James
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Autar K. Mattoo
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - P. V. Sane
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Norman P.A. Hüner
- Department of Biology and the Biotron Experimental Climate Change Research Centre, University of Western Ontario, 1151 Richmond Street N., London, ON N6A 5B7, Canada
- Henry A. Wallace Beltsville Agricultural Research Center, USDA/ARS, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
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Makarova VV, Kosourov S, Krendeleva TE, Semin BK, Kukarskikh GP, Rubin AB, Sayre RT, Ghirardi ML, Seibert M. Photoproduction of hydrogen by sulfur-deprived C. reinhardtii mutants with impaired photosystem II photochemical activity. PHOTOSYNTHESIS RESEARCH 2007; 94:79-89. [PMID: 17701084 DOI: 10.1007/s11120-007-9219-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 07/03/2007] [Indexed: 05/16/2023]
Abstract
Photoproduction of H2 was examined in a series of sulfur-deprived Chlamydomonas reinhardtii D1-R323 mutants with progressively impaired PSII photochemical activity. In the R323H, R323D, and R323E D1 mutants, replacement of arginine affects photosystem II (PSII) function, as demonstrated by progressive decreases in O2-evolving activity and loss of PSII photochemical activity. Significant changes in PSII activity were found when the arginine residue was replaced by negatively charged amino acid residues (R323D and R323E). However, the R323H (positively charged or neutral, depending on the ambient pH) mutant had minimal changes in PSII activity. The R323H, R323D, and R323E mutants and the pseudo-wild-type (pWt) with restored PSII function were used to study the effects of sulfur deprivation on H2-production activity. All of these mutants exhibited significant changes in the normal parameters associated with the H2-photoproduction process, such as a shorter aerobic phase, lower accumulation of starch, a prolonged anaerobic phase observed before the onset of H2-production, a shorter duration of H2-production, lower H2 yields compared to the pWt control, and slightly higher production of dark fermentation products such as acetate and formate. The more compromised the PSII photochemical activity, the more dramatic was the effect of sulfur deprivation on the H2-production process, which depends both on the presence of residual PSII activity and the amount of stored starch.
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Affiliation(s)
- Valeria V Makarova
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO 80401, USA
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