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Sirohiwal A, Neese F, Pantazis DA. Microsolvation of the Redox-Active Tyrosine-D in Photosystem II: Correlation of Energetics with EPR Spectroscopy and Oxidation-Induced Proton Transfer. J Am Chem Soc 2019; 141:3217-3231. [PMID: 30666866 PMCID: PMC6728127 DOI: 10.1021/jacs.8b13123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
- Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
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Kondo T, Matsuoka M, Azai C, Kobayashi M, Itoh S, Oh-oka H. Light-Induced Electron Spin-Polarized (ESP) EPR Signal of the P800+ Menaquinone– Radical Pair State in Oriented Membranes of Heliobacterium modesticaldum: Role/Location of Menaquinone in the Homodimeric Type I Reaction Center. J Phys Chem B 2018; 122:2536-2543. [DOI: 10.1021/acs.jpcb.7b12171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toru Kondo
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Masahiro Matsuoka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Chihiro Azai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Masami Kobayashi
- Division of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Shigeru Itoh
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Hirozo Oh-oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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Kondo T, Matsuoka M, Azai C, Itoh S, Oh-oka H. Orientations of Iron–Sulfur Clusters FA and FB in the Homodimeric Type-I Photosynthetic Reaction Center of Heliobacterium modesticaldum. J Phys Chem B 2016; 120:4204-12. [DOI: 10.1021/acs.jpcb.6b01112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toru Kondo
- Division
of Material Science (Physics), Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Masahiro Matsuoka
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Chihiro Azai
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Shigeru Itoh
- Center
for Gene Research, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan
| | - Hirozo Oh-oka
- Department
of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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Ishikita H, Saito K. Proton transfer reactions and hydrogen-bond networks in protein environments. J R Soc Interface 2013; 11:20130518. [PMID: 24284891 DOI: 10.1098/rsif.2013.0518] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.
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Affiliation(s)
- Hiroshi Ishikita
- Department of Biological Sciences, Graduate School of Science, Osaka University, , Machikaneyama-cho 1-1, Toyonaka 560-0043, Japan
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Kamidaki C, Kondo T, Noji T, Itoh T, Yamaguchi A, Itoh S. Alumina Plate Containing Photosystem I Reaction Center Complex Oriented inside Plate-Penetrating Silica Nanopores. J Phys Chem B 2013; 117:9785-92. [DOI: 10.1021/jp406589u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chihiro Kamidaki
- Division of Material Science
(Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Ai-chi 464-8602, Japan
| | - Toru Kondo
- Division of Material Science
(Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Ai-chi 464-8602, Japan
| | - Tomoyasu Noji
- Division of Material Science
(Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Ai-chi 464-8602, Japan
| | - Tetsuji Itoh
- Research Center for Compact
Chemical System, National Institute of Advanced Industrial Science and Technology (AIST), Nigatake 4-2-1, Miyagino-ku,
Sendai 983-8551, Japan
| | - Akira Yamaguchi
- College
of Science and Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Shigeru Itoh
- Division of Material Science
(Physics), Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Ai-chi 464-8602, Japan
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Chatterjee R, Coates CS, Milikisiyants S, Lee CI, Wagner A, Poluektov OG, Lakshmi KV. High-Frequency Electron Nuclear Double-Resonance Spectroscopy Studies of the Mechanism of Proton-Coupled Electron Transfer at the Tyrosine-D Residue of Photosystem II. Biochemistry 2013; 52:4781-90. [DOI: 10.1021/bi3012093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruchira Chatterjee
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Christopher S. Coates
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sergey Milikisiyants
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Cheng-I Lee
- Department of Life Science, National Chung Cheng University, 168 University Road,
Min-Hsiung, Chia-Yi 621, Taiwan
| | - Arlene Wagner
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - K. V. Lakshmi
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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Abstract
Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II [Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473(7345):55-60], we investigated the H-bonding environment of the redox-active tyrosine D (TyrD) and obtained insights that help explain its slow redox kinetics and the stability of TyrD(•). The water molecule distal to TyrD, located ~4 Å away from the phenolic O of TyrD, corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to the phenolic O of TyrD, corresponds to the presence of the unoxidized tyrosine. The H(+) released on oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasiirreversible, explaining the great stability of the TyrD(•). A symmetry-related proton pathway associated with tyrosine Z is pointed out, and this is associated with one of the Cl(-) sites. This may represent a proton pathway functional in the water oxidation cycle.
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Keßen S, Teutloff C, Kern J, Zouni A, Bittl R. High-Field 2H-Mims-ENDOR Spectroscopy on PSII Single Crystals: Hydrogen Bonding of YD. Chemphyschem 2010; 11:1275-82. [DOI: 10.1002/cphc.200901019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- R P Pesavento
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Yoshii T, Kawamori A, Tonaka M, Akabori K. Relative positions of electron transfer components in Photosystem II studied by ‘2+1’ pulsed electron paramagnetic resonance: YD and QA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1999. [DOI: 10.1016/s0005-2728(99)00082-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Berthomieu C, Hienerwadel R, Boussac A, Breton J, Diner BA. Hydrogen bonding of redox-active tyrosine Z of photosystem II probed by FTIR difference spectroscopy. Biochemistry 1998; 37:10547-54. [PMID: 9692943 DOI: 10.1021/bi980788m] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The TyrZ./TyrZ FTIR difference spectrum is reported for the first time in Mn-depleted photosystem II (PS II)-enriched membranes of spinach, in PS II core complexes of Synechocystis sp. PCC 6803 WT, and in the mutant lacking TyrD (D2-Tyr160Phe). In Synechocystis, the v7'a(CO) and delta(COH) infrared modes of TyrZ are proposed to account at 1279 and 1255 cm-1. The frequency of these modes indicate that TyrZ is protonated at pH 6 and involved in a strong hydrogen bond to the side chain of a histidine, probably D1-His190. A positive signal at 1512 cm-1 is assigned to the v(CO) mode of TyrZ. on the basis of the 27 cm-1 downshift observed upon 13C-Tyr labeling at the Tyr ring C4 carbon. A second IR signal, at 1532 cm-1, is tentatively assigned to the v8a(CC) mode of TyrZ.. The frequency of the v(CO) mode of TyrZ. at 1512 cm-1 is comparable to that observed at 1513 cm-1 for the Tyr. obtained by UV photochemistry of tyrosinate in solution, while it is higher than that of TyrD. in WT PS II at 1503 cm-1 and that of non-hydrogen-bonded TyrD. in the D2-His189Gln mutant at 1497 cm-1 [Hienerwadel, R., Boussac, A., Breton, J., Diner, B. A., and Berthomieu, C. (1997) Biochemistry 36, 14712-14723]. This latter work and the present FTIR study suggest that hydrogen bonding induces an upshift of the v(CO) IR mode of tyrosyl radicals and that TyrZ. forms (a) stronger hydrogen bond(s) than TyrD. in WT PS II. Alternatively, the frequency difference between TyrZ. and TyrD. v(CO) modes could be explained by a more localized positive charge near the tyrosyl radical oxygen of TyrD. than TyrZ.. The TyrZ./TyrZ spectrum obtained in Mn-depleted PS II membranes of spinach shows large similarities with the S3'/S2' spectrum characteristic of radical formation in Mn-containing but Ca(2+)-depleted PS II, in support of the assignment using ESEEM of TyrZ. as being responsible for the split EPR signal observed upon illumination in these conditions [Tang, X.-S., Randall, D. W., Force, D. A., Diner, B. A., and Britt, R. D. (1996) J. Am. Chem. Soc. 118, 7638-7639]. The peak at 1514 cm-1 is assigned to the v(CO) mode of TyrZ. in these preparations, which indicates that Mn depletion only very slightly perturbs the immediate environment of TyrZ. phenoxyl.
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Affiliation(s)
- C Berthomieu
- CEA-Saclay, Section de Bioénergétique, Gif-sur-Yvette, France.
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Astashkin AV, Hara H, Kawamori A. The pulsed electron–electron double resonance and “2+1” electron spin echo study of the oriented oxygen-evolving and Mn-depleted preparations of photosystem II. J Chem Phys 1998. [DOI: 10.1063/1.475770] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Haumann M, Drevenstedt W, Hundelt M, Junge W. Photosystem II of green plants. Oxidation and deprotonation of the same component (histidine?) on S1∗ ⇒ S2∗ in chloride-depleted centers as on S2 ⇒ S3 in controls. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1996. [DOI: 10.1016/0005-2728(95)00152-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Microenvironments of tyrosine D+ and tyrosine Z+ in Photosystem II studied by proton matrix ENDOR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1994. [DOI: 10.1016/0005-2728(94)90212-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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