1
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Kang XW, Wang K, Zhang X, Zhong D, Ding B. Elementary Reactions in the Functional Triads of the Blue-Light Photoreceptor BLUF Domain. J Phys Chem B 2024; 128:2065-2075. [PMID: 38391132 DOI: 10.1021/acs.jpcb.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The blue light using the flavin (BLUF) domain is one of the smallest photoreceptors in nature, which consists of a unique bidirectional electron-coupled proton relay process in its photoactivation reaction cycle. This perspective summarizes our recent efforts in dissecting the photocycle into three elementary processes, including proton-coupled electron transfer (PCET), proton rocking, and proton relay. Using ultrafast spectroscopy, we have determined the temporal sequence, rates, kinetic isotope effects (KIEs), and concertedness of these elementary steps. Our findings provide important implications for illuminating the photoactivation mechanism of the BLUF domain and suggest an engineering platform to characterize intricate reactions involving proton motions that are ubiquitous in nonphotosensitive protein machines.
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Affiliation(s)
- Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofan Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Programs of Chemical Physics, and Programs of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Kang X, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Ding B, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiu‐Wen Kang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zijing Chen
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Siwei Tang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tianyi Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bei Ding
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Department of Physics Department of Chemistry and Biochemistry and Programs of Biophysics Chemical Physics, and Biochemistry The Ohio State University Columbus OH 43210 USA
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3
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Ding B, Kang XW, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2021; 61:e202114423. [PMID: 34927328 DOI: 10.1002/anie.202114423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 11/10/2022]
Abstract
We present direct observation of ultrafast proton rocking in the central motif of a BLUF domain protein scaffold. The mutant design has taken considerations of modulating the proton-coupled electron transfer (PCET) driving forces by replacing Tyr in the original motif with Trp, as well as of removing the interference of a competing electron transfer pathway. Using femtosecond pump-probe spectroscopy and detailed kinetics analysis, we resolved an electron-transfer-coupled Grotthuss-type forward and reversed proton rocking along the FMN-Gln-Trp proton relay chain. The rates of forward and reversed proton transfer are determined to be very close, namely 51 ps vs 52 ps. The kinetic isotope effect (KIE) constants associated with the forward and reversed proton transfer are 3.9 and 5.3, respectively. The observation of ultrafast proton rocking is not only a crucial step towards revealing the nature of proton relay in BLUF domain, but also provides a new paradigm of proton transfer in proteins for theoretical investigations.
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Affiliation(s)
- Bei Ding
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, 800 Dongchuan Road, 200240, Shanghai, CHINA
| | - Xiu-Wen Kang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zijing Chen
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zhongneng Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yalin Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Siwei Tang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yifei Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Tianyi Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Dongping Zhong
- The Ohio State University, Department of Chemical and Biomolecular Engineering, CHINA
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4
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Determining the Electronic Structure of Paramagnetic Intermediates in membrane proteins: A high-resolution 2D 1H hyperfine sublevel correlation study of the redox-active tyrosines of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183422. [DOI: 10.1016/j.bbamem.2020.183422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/19/2020] [Accepted: 07/15/2020] [Indexed: 01/26/2023]
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5
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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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6
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Resa S, Millán A, Fuentes N, Crovetto L, Luisa Marcos M, Lezama L, Choquesillo-Lazarte D, Blanco V, Campaña AG, Cárdenas DJ, Cuerva JM. O–H and (CO)N–H bond weakening by coordination to Fe(ii). Dalton Trans 2019; 48:2179-2189. [DOI: 10.1039/c8dt04689a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coordination of hydroxyl/amide groups to Fe(ii) diminishes BDFEs of O–H and (CO)N–H bonds down to 76.0 and 80.5 kcal mol−1 respectively.
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7
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Ogawa R, Sunatsuki Y, Suzuki T. Schiff Base Ligands Derived from l
-Histidine Methyl Ester: Characterization, Racemization, and Dimerization of Their Transition-Metal Complexes. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rina Ogawa
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
| | - Yukinari Sunatsuki
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
| | - Takayoshi Suzuki
- Department of Chemistry; Graduate School of Natural Science and Technology; Okayama University; 700-8530 Okayama Japan
- Research Institute for Interdisciplinary Science; Okayama University; 700-8530 Okayama Japan
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8
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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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9
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Matsuoka H, Mizutani S, Watanabe C, Yamauchi S. High-Frequency EPR Studies on Polymer Chain Morphology in Dip-Coated Films of Poly(3-hexylthiophene)/Fullerene Bulk-Heterojunctions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hideto Matsuoka
- Institute for Physical and Theoretical Chemistry, University of Bonn
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
| | - Shinichi Mizutani
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
| | - Chika Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
| | - Seigo Yamauchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
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10
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Temperature dependence of the oxidation kinetics of TyrZ and TyrD in oxygen-evolving photosystem II complexes throughout the range from 320K to 5K. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1283-96. [DOI: 10.1016/j.bbabio.2015.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 11/21/2022]
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11
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Nakamura S, Noguchi T. Infrared Detection of a Proton Released from Tyrosine YD to the Bulk upon Its Photo-oxidation in Photosystem II. Biochemistry 2015; 54:5045-53. [PMID: 26241205 DOI: 10.1021/acs.biochem.5b00568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photosystem II (PSII) has two symmetrically located, redox-active tyrosine residues, YZ and YD. Whereas YZ mediates the electron transfer from the water-oxidizing center to P680 in the main electron transfer pathway, YD functions as a peripheral electron donor to P680. To understand the mechanism of this functional difference between YZ and YD, it is essential to know where the proton is transferred upon its oxidation in the proton-coupled electron transfer process. In this study, we used Fourier transform infrared (FTIR) spectroscopy to examine whether the proton from YD is released from the protein into the bulk. The proton detection method previously used for water oxidation in PSII [Suzuki et al. (2009) J. Am. Chem. Soc. 131, 7849-7857] was applied to YD; a proton released into the bulk upon YD oxidation was trapped by a high-concentration Mes buffer, and the protonation reaction of Mes was monitored by FTIR difference spectroscopy. It was shown that 0.84 ± 0.10 protons are released into the bulk by oxidation of YD in one PSII center. This result indicates that the proton of YD is not transferred to the neighboring D2-His198 but is released from the protein; this is in sharp contrast to the YZ reaction, in which a proton is transferred to D1-His190 through a strong hydrogen bond. This functional difference is caused by differences in the hydrogen-bonded structures of YD and YZ, which are determined by the hydrogen bond partners at the Nπ sites of these His residues, i.e., D2-Arg294 and D1-Asn298, which function as a hydrogen bond donor and acceptor, respectively. This FTIR spectroscopy result supports the recent theoretical prediction [Saito et al. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 7690-7695] based on the X-ray crystallographic structure of PSII and explains the different rates of the redox reactions of YD and YZ.
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Affiliation(s)
- Shin Nakamura
- 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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12
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Retegan M, Cox N, Lubitz W, Neese F, Pantazis DA. The first tyrosyl radical intermediate formed in the S2-S3 transition of photosystem II. Phys Chem Chem Phys 2015; 16:11901-10. [PMID: 24760184 DOI: 10.1039/c4cp00696h] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EPR "split signals" represent key intermediates of the S-state cycle where the redox active D1-Tyr161 (YZ) has been oxidized by the reaction center of the photosystem II enzyme to its tyrosyl radical form, but the successive oxidation of the Mn4CaO5 cluster has not yet occurred (SiYZ˙). Here we focus on the S2YZ˙ state, which is formed en route to the final metastable state of the catalyst, the S3 state, the state which immediately precedes O-O bond formation. Quantum chemical calculations demonstrate that both isomeric forms of the S2 state, the open and closed cubane isomers, can form states with an oxidized YZ˙ residue without prior deprotonation of the Mn4CaO5 cluster. The two forms are expected to lie close in energy and retain the electronic structure and magnetic topology of the corresponding S2 state of the inorganic core. As expected, tyrosine oxidation results in a proton shift towards His190. Analysis of the electronic rearrangements that occur upon formation of the tyrosyl radical suggests that a likely next step in the catalytic cycle is the deprotonation of a terminal water ligand (W1) of the Mn4CaO5 cluster. Diamagnetic metal ion substitution is used in our calculations to obtain the molecular g-tensor of YZ˙. It is known that the gx value is a sensitive probe not only of the extent of the proton shift between the tyrosine-histidine pair, but also of the polarization environment of the tyrosine, especially about the phenolic oxygen. It is shown for PSII that this environment is determined by the Ca(2+) ion, which locates two water molecules about the phenoxyl oxygen, indirectly modulating the oxidation potential of YZ.
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Affiliation(s)
- Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany.
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13
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Hirao Y, Saito T, Kurata H, Kubo T. Isolation of a hydrogen-bonded complex based on the anthranol/anthroxyl pair: formation of a hydrogen-atom self-exchange system. Angew Chem Int Ed Engl 2015; 54:2402-5. [PMID: 25565433 DOI: 10.1002/anie.201410796] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/08/2022]
Abstract
A hydrogen-bonded complex was successfully isolated as crystals from the anthranol/anthroxyl pair in the self-exchange proton-coupled electron transfer (PCET) reaction. The anthroxyl radical was stabilized by the introduction of a 9-anthryl group at the carbon atom at the 10-position. The hydrogen-bonded complex with anthranol self-assembled by π-π stacking to form a one-dimensional chain in the crystal. The conformation around the hydrogen bond was similar to that of the theoretically predicted PCET activated complex of the phenol/phenoxyl pair. X-ray crystal analyses revealed the self-exchange of a hydrogen atom via the hydrogen bond, indicating the activation of the self-exchange PCET reaction between anthranol and anthroxyl. Magnetic measurements revealed that magnetic ordering inside the one-dimensional chain caused the inactivation of the self-exchange reaction.
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Affiliation(s)
- Yasukazu Hirao
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan).
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14
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Hirao Y, Saito T, Kurata H, Kubo T. Isolation of a Hydrogen-Bonded Complex Based on the Anthranol/Anthroxyl Pair: Formation of a Hydrogen-Atom Self-Exchange System. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Bernini C, Arezzini E, Basosi R, Sinicropi A. In silico spectroscopy of tryptophan and tyrosine radicals involved in the long-range electron transfer of cytochrome c peroxidase. J Phys Chem B 2014; 118:9525-37. [PMID: 25084495 DOI: 10.1021/jp5025153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c peroxidase (CcP) is a heme-containing enzyme that catalyzes the oxidation of the ferrocytochrome c to ferricytochrome c with concomitant reduction of H2O2 to H2O. Its catalytic cycle involves the formation of a double oxidized species (compound I) consisting of an oxoferryl center (Fe(IV)═O) and an amino acid radical (R(•)). Here we use a quantum-mechanics/molecular-mechanics (QM/MM) computational protocol based on density functional theory (DFT) and multiconfigurational perturbation theory (CASPT2) methods to reproduce specific features of compound I EPR and UV-vis spectra. The results show that the employed QM/MM models can correctly predict the magnetic, electronic and vibrational properties of the observed amino acid radicals of compound I. Furthermore, we have been able to confirm that the principal radical species of compound I is a tryptophan cationic radical located on residue 191 (Trp191(•+)) and that three tyrosine residues (Tyr203, Tyr236, and Tyr251), located along two possible ET pathways involving Trp191(•+), are possible candidates to host the secondary radical species.
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Affiliation(s)
- Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , Via A. Moro 2, 53100 Siena, Italy
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16
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Nakamura S, Nagao R, Takahashi R, Noguchi T. Fourier transform infrared detection of a polarizable proton trapped between photooxidized tyrosine YZ and a coupled histidine in photosystem II: relevance to the proton transfer mechanism of water oxidation. Biochemistry 2014; 53:3131-44. [PMID: 24786306 DOI: 10.1021/bi500237y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The redox-active tyrosine YZ (D1-Tyr161) in photosystem II (PSII) functions as an immediate electron acceptor of the Mn4Ca cluster, which is the catalytic center of photosynthetic water oxidation. YZ is also located in the hydrogen bond network that connects the Mn4Ca cluster to the lumen and hence is possibly related to the proton transfer process during water oxidation. To understand the role of YZ in the water oxidation mechanism, we have studied the hydrogen bonding interactions of YZ and its photooxidized neutral radical YZ(•) together with the interaction of the coupled His residue, D1-His190, using light-induced Fourier transform infrared (FTIR) difference spectroscopy. The YZ(•)-minus-YZ FTIR difference spectrum of Mn-depleted PSII core complexes exhibited a broad positive feature around 2800 cm(-1), which was absent in the corresponding spectrum of another redox-active tyrosine YD (D2-Tyr160). Analyses by (15)N and H/D substitutions, examination of the pH dependence, and density functional theory and quantum mechanics/molecular mechanics (QM/MM) calculations showed that this band arises from the N-H stretching vibration of the protonated cation of D1-His190 forming a charge-assisted strong hydrogen bond with YZ(•). This result provides strong evidence that the proton released from YZ upon its oxidation is trapped in D1-His190 and a positive charge remains on this His. The broad feature of the ~2800 cm(-1) band reflects a large proton polarizability in the hydrogen bond between YZ(•) and HisH(+). QM/MM calculations further showed that upon YZ oxidation the hydrogen bond network is rearranged and one water molecule moves toward D1-His190. From these data, a novel proton transfer mechanism via YZ(•)-HisH(+) is proposed, in which hopping of the polarizable proton of HisH(+) to this water triggers the transfer of the proton from substrate water to the luminal side. This proton transfer mechanism could be functional in the S2 → S3 transition, which requires proton release before electron transfer because of an excess positive charge on the Mn4Ca cluster.
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Affiliation(s)
- Shin Nakamura
- Division of Material Science, Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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17
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Theoretical study on mechanism of dioxygen evolution in photosystem II. II. Molecular and electronic structures at the S3 and S4 states of oxygen-evolving complex. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Gunner MR, Amin M, Zhu X, Lu J. Molecular mechanisms for generating transmembrane proton gradients. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:892-913. [PMID: 23507617 PMCID: PMC3714358 DOI: 10.1016/j.bbabio.2013.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 03/01/2013] [Indexed: 01/02/2023]
Abstract
Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.
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Affiliation(s)
- M R Gunner
- Department of Physics, City College of New York, New York, NY 10031, USA.
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19
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Ichino T, Yoshioka Y. Theoretical Study on the Mechanism of Dioxygen Evolution in Photosystem II. I. Molecular and Electronic Structures at the S0, S1, and S2States of Oxygen-Evolving Complex. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoya Ichino
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
| | - Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
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Sugiura M, Ogami S, Kusumi M, Un S, Rappaport F, Boussac A. Environment of TyrZ in photosystem II from Thermosynechococcus elongatus in which PsbA2 is the D1 protein. J Biol Chem 2012; 287:13336-47. [PMID: 22362776 DOI: 10.1074/jbc.m112.340323] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The main cofactors that determine the photosystem II (PSII) oxygen evolution activity are borne by the D1 and D2 subunits. In the cyanobacterium Thermosynechococcus elongatus, there are three psbA genes coding for D1. Among the 344 residues constituting D1, there are 21 substitutions between PsbA1 and PsbA3, 31 between PsbA1 and PsbA2, and 27 between PsbA2 and PsbA3. Here, we present the first study of PsbA2-PSII. Using EPR and UV-visible time-resolved absorption spectroscopy, we show that: (i) the time-resolved EPR spectrum of Tyr(Z)(•) in the (S(3)Tyr(Z)(•))' is slightly modified; (ii) the split EPR signal arising from Tyr(Z)(•) in the (S(2)Tyr(Z)(•))' state induced by near-infrared illumination at 4.2 K of the S(3)Tyr(Z) state is significantly modified; and (iii) the slow phases of P(680)(+) reduction by Tyr(Z) are slowed down from the hundreds of μs time range to the ms time range, whereas both the S(1)Tyr(Z)(•) → S(2)Tyr(Z) and the S(3)Tyr(Z)(•) → S(0)Tyr(Z) + O(2) transition kinetics remained similar to those in PsbA(1/3)-PSII. These results show that the geometry of the Tyr(Z) phenol and its environment, likely the Tyr-O···H···Nε-His bonding, are modified in PsbA2-PSII when compared with PsbA(1/3)-PSII. They also point to the dynamics of the proton-coupled electron transfer processes associated with the oxidation of Tyr(Z) being affected. From sequence comparison, we propose that the C144P and P173M substitutions in PsbA2-PSII versus PsbA(1/3)-PSII, respectively located upstream of the α-helix bearing Tyr(Z) and between the two α-helices bearing Tyr(Z) and its hydrogen-bonded partner, His-190, are responsible for these changes.
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Affiliation(s)
- Miwa Sugiura
- Cell-Free Science and Technology Research Center, Ehime University, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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Stoll S, Shafaat HS, Krzystek J, Ozarowski A, Tauber MJ, Kim JE, Britt RD. Hydrogen bonding of tryptophan radicals revealed by EPR at 700 GHz. J Am Chem Soc 2011; 133:18098-101. [PMID: 22007694 PMCID: PMC3251908 DOI: 10.1021/ja208462t] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Redox-active tryptophans are important in biological electron transfer and redox biochemistry. Proteins can tune the electron transfer kinetics and redox potentials of tryptophan via control of the protonation state and the hydrogen-bond strength. We examine the local environment of two neutral tryptophan radicals (Trp108 on the solvent-exposed surface and Trp48 buried in the hydrophobic core) in two azurin variants. Ultrahigh-field EPR spectroscopy at 700 GHz and 25 T allowed complete resolution of all of the principal components of the g tensors of the two radicals and revealed significant differences in the g tensor anisotropies. The spectra together with (2)H ENDOR spectra and supporting DFT calculations show that the g tensor anisotropy is directly diagnostic of the presence or absence as well as the strength of a hydrogen bond to the indole nitrogen. The approach is a powerful one for identifying and characterizing hydrogen bonds that are critical in the regulation of tryptophan-assisted electron transfer and tryptophan-mediated redox chemistry in proteins.
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California Davis, Davis California 95616, United States
| | - Hannah S. Shafaat
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - J. Krzystek
- National High Magnetic Field Laboratory, Florida State University, Tallahassee Florida 32310, United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, Tallahassee Florida 32310, United States
| | - Michael J. Tauber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093, United States
| | - R. David Britt
- Department of Chemistry, University of California Davis, Davis California 95616, United States
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Sizeable Increase of Kinetic Isotope Effects and Tunnelling in Coupled Electron–Proton Transfers in Presence of the Quaternary Ions. PCET Processes and Hydrogen Tunnelling as a “Probe” for Structuring and Dynamical Phenomena in Water Solution. Z PHYS CHEM 2011. [DOI: 10.1524/zpch.2012.0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Keough JM, Jenson DL, Zuniga AN, Barry BA. Proton coupled electron transfer and redox-active tyrosine Z in the photosynthetic oxygen-evolving complex. J Am Chem Soc 2011; 133:11084-7. [PMID: 21714528 PMCID: PMC3246746 DOI: 10.1021/ja2041139] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton coupled electron transfer (PCET) reactions play an essential role in many enzymatic processes. In PCET, redox-active tyrosines may be involved as intermediates when the oxidized phenolic side chain deprotonates. Photosystem II (PSII) is an excellent framework for studying PCET reactions, because it contains two redox-active tyrosines, YD and YZ, with different roles in catalysis. One of the redox-active tyrosines, YZ, is essential for oxygen evolution and is rapidly reduced by the manganese-catalytic site. In this report, we investigate the mechanism of YZ PCET in oxygen-evolving PSII. To isolate YZ(•) reactions, but retain the manganese-calcium cluster, low temperatures were used to block the oxidation of the metal cluster, high microwave powers were used to saturate the YD(•) EPR signal, and YZ(•) decay kinetics were measured with EPR spectroscopy. Analysis of the pH and solvent isotope dependence was performed. The rate of YZ(•) decay exhibited a significant solvent isotope effect, and the rate of recombination and the solvent isotope effect were pH independent from pH 5.0 to 7.5. These results are consistent with a rate-limiting, coupled proton electron transfer (CPET) reaction and are contrasted to results obtained for YD(•) decay kinetics at low pH. This effect may be mediated by an extensive hydrogen-bond network around YZ. These experiments imply that PCET reactions distinguish the two PSII redox-active tyrosines.
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Affiliation(s)
- James M. Keough
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - David L. Jenson
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Ashley N. Zuniga
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Bridgette A. Barry
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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