1
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Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Author Correction: Structural evidence for intermediates during O 2 formation in photosystem II. Nature 2024; 626:E12. [PMID: 38291188 PMCID: PMC10866699 DOI: 10.1038/s41586-024-07099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corey J Kaminsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julia Gätcke
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Stephanie Haupt
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabela I Nangca
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Holger Dobbek
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Zouni
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Nguyen RC, Davis I, Dasgupta M, Wang Y, Simon PS, Butryn A, Makita H, Bogacz I, Dornevil K, Aller P, Bhowmick A, Chatterjee R, Kim IS, Zhou T, Mendez D, Paley D, Fuller F, Alonso-Mori R, Batyuk A, Sauter NK, Brewster AS, Orville AM, Yachandra VK, Yano J, Kern JF, Liu A. In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. J Am Chem Soc 2023; 145:25120-25133. [PMID: 37939223 PMCID: PMC10799213 DOI: 10.1021/jacs.3c04991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.
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Affiliation(s)
- Romie C. Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Daniel Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Franklin Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, United States
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jan F. Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX 78249, United States
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3
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Bhowmick A, Simon PS, Bogacz I, Hussein R, Zhang M, Makita H, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Chernev P, Fuller FD, Fransson T, Alonso-Mori R, Brewster AS, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography. IUCrJ 2023; 10:642-655. [PMID: 37870936 PMCID: PMC10619448 DOI: 10.1107/s2052252523008928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn4Ca complex (Mn4CaO5) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of OX from a new water molecule, which disappears on completion of the reaction, implicating it in the O-O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn4Ca cluster.
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Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rana Hussein
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Margaret D. Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas Fransson
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm SE-10691, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Holger Dobbek
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Athina Zouni
- Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström, Uppsala University, Uppsala SE 75120, Sweden
- Department of Chemistry, Umeå University, Umeå SE 90187, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Bogacz I, Doyle MD, Dobbek H, Zouni A, Messinger J, Yachandra VK, Kern JF, Yano J. Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function. Photosynth Res 2023; 158:91-107. [PMID: 37266800 PMCID: PMC10684718 DOI: 10.1007/s11120-023-01018-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/29/2023] [Indexed: 06/03/2023]
Abstract
One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. This process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn4CaO5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the 'water wheel' to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn4CaO5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S0 → S1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421-425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624-12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831-15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).
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Affiliation(s)
- Rana Hussein
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany.
| | - Mohamed Ibrahim
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Holger Dobbek
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Athina Zouni
- Department of Biology, Humboldt-Universität Zu Berlin, 10099, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry-Ångström, Uppsala University, SE 75120, Uppsala, Sweden
- Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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5
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Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M. Structure of a ribonucleotide reductase R2 protein radical. Science 2023; 382:109-113. [PMID: 37797025 PMCID: PMC7615503 DOI: 10.1126/science.adh8160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.
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Affiliation(s)
- Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, CNRS, Université Toulouse III, Toulouse, France
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - Rohit Kumar
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Abhishek Sirohiwal
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agata Butryn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | | | | | | | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katarina Roos
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
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6
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Bogacz I, Makita H, Simon PS, Zhang M, Doyle MD, Chatterjee R, Fransson T, Weninger C, Fuller F, Gee L, Sato T, Seaberg M, Alonso-Mori R, Bergmann U, Yachandra VK, Kern J, Yano J. Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs. PURE APPL CHEM 2023; 95:891-897. [PMID: 38013689 PMCID: PMC10505480 DOI: 10.1515/pac-2023-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
X-ray crystallography and X-ray spectroscopy using X-ray free electron lasers plays an important role in understanding the interplay of structural changes in the protein and the chemical changes at the metal active site of metalloenzymes through their catalytic cycles. As a part of such an effort, we report here our recent development of methods for X-ray absorption spectroscopy (XAS) at XFELs to study dilute biological samples, available in limited volumes. Our prime target is Photosystem II (PS II), a multi subunit membrane protein complex, that catalyzes the light-driven water oxidation reaction at the Mn4CaO5 cluster. This is an ideal system to investigate how to control multi-electron/proton chemistry, using the flexibility of metal redox states, in coordination with the protein and the water network. We describe the method that we have developed to collect XAS data using PS II samples with a Mn concentration of <1 mM, using a drop-on-demand sample delivery method.
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Affiliation(s)
- Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Margaret D. Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Thomas Fransson
- Department of Theoretical chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Franklin Fuller
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Leland Gee
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Takahiro Sato
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | - Matthew Seaberg
- LCLS, SLAC National Accelerator Laboratory, 94025, Menlo Park, CA, USA
| | | | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, 53706, Madison, WI, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 94720, Berkeley, CA, USA
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7
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Doyle M, Bhowmick A, Wych DC, Lassalle L, Simon PS, Holton J, Sauter NK, Yachandra VK, Kern JF, Yano J, Wall ME. Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography. J Am Chem Soc 2023; 145:14621-14635. [PMID: 37369071 PMCID: PMC10347547 DOI: 10.1021/jacs.3c01412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 06/29/2023]
Abstract
Structural dynamics of water and its hydrogen-bonding networks play an important role in enzyme function via the transport of protons, ions, and substrates. To gain insights into these mechanisms in the water oxidation reaction in Photosystem II (PS II), we have performed crystalline molecular dynamics (MD) simulations of the dark-stable S1 state. Our MD model consists of a full unit cell with 8 PS II monomers in explicit solvent (861 894 atoms), enabling us to compute the simulated crystalline electron density and to compare it directly with the experimental density from serial femtosecond X-ray crystallography under physiological temperature collected at X-ray free electron lasers (XFELs). The MD density reproduced the experimental density and water positions with high fidelity. The detailed dynamics in the simulations provided insights into the mobility of water molecules in the channels beyond what can be interpreted from experimental B-factors and electron densities alone. In particular, the simulations revealed fast, coordinated exchange of waters at sites where the density is strong, and water transport across the bottleneck region of the channels where the density is weak. By computing MD hydrogen and oxygen maps separately, we developed a novel Map-based Acceptor-Donor Identification (MADI) technique that yields information which helps to infer hydrogen-bond directionality and strength. The MADI analysis revealed a series of hydrogen-bond wires emanating from the Mn cluster through the Cl1 and O4 channels; such wires might provide pathways for proton transfer during the reaction cycle of PS II. Our simulations provide an atomistic picture of the dynamics of water and hydrogen-bonding networks in PS II, with implications for the specific role of each channel in the water oxidation reaction.
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Affiliation(s)
- Margaret
D. Doyle
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Asmit Bhowmick
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David C. Wych
- Computer,
Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center
for Non-linear Studies, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United States
| | - Louise Lassalle
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Philipp S. Simon
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - James Holton
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Biochemistry and Biophysics, University
of California, San Francisco, San
Francisco, California 94158, United States
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nicholas K. Sauter
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Vittal K. Yachandra
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan F. Kern
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Michael E. Wall
- Computer,
Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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8
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Makita H, Simon PS, Kern J, Yano J, Yachandra VK. Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography. Curr Opin Struct Biol 2023; 80:102604. [PMID: 37148654 PMCID: PMC10793627 DOI: 10.1016/j.sbi.2023.102604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 05/08/2023]
Abstract
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
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Affiliation(s)
- Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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9
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Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Structural evidence for intermediates during O 2 formation in photosystem II. Nature 2023; 617:629-636. [PMID: 37138085 PMCID: PMC10191843 DOI: 10.1038/s41586-023-06038-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.
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Affiliation(s)
- Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corey J Kaminsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julia Gätcke
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Stephanie Haupt
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isabela I Nangca
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Holger Dobbek
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Athina Zouni
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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10
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Doyle MD, Halavanau A, Zhang Y, Michine Y, Everts J, Fuller F, Alonso-Mori R, Yabashi M, Inoue IC, Osaka T, Yamada J, Inubushi Y, Hara T, Kern J, Yano J, Yachandra VK, Rohringer N, Yoneda H, Kroll T, Pellegrini C, Bergmann U. Seeded stimulated X-ray emission at 5.9 keV. Optica 2023; 10:513-519. [PMID: 38239819 PMCID: PMC10795508 DOI: 10.1364/optica.485989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 01/22/2024]
Abstract
X-ray free-electron lasers (XFELs) provide intense pulses that can generate stimulated X-ray emission, a phenomenon that has been observed and studied in materials ranging from neon to copper. Two schemes have been employed: amplified spontaneous emission (ASE) and seeded stimulated emission (SSE), where a second color XFEL pulse provides the seed. Both phenomena are currently explored for coherent X-ray laser sources and spectroscopy. Here, we report measurements of ASE and SSE of the 5.9 keV Mn Kα1 fluorescence line from a 3.9 molar NaMnO4 solution, pumped with 7 femtosecond FWHM XFEL pulses at 6.6 keV. We observed ASE at a pump pulse intensity of 1.7 × 1019 W/cm2, consistent with earlier findings. We observed SSE at dramatically reduced pump pulse intensities down to 1.1 × 1017 W/cm2. These intensities are well within the range of many existing XFEL instruments, which supports the experimental feasibility of SSE as a tool to generate coherent X-ray pulses, spectroscopic studies of transition metal complexes, and other applications.
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Affiliation(s)
- Margaret D. Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aliaksei Halavanau
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Yurina Michine
- Institute for Laser Science, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan
| | - Joshua Everts
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 9402, USA
- Department of Physics, University of Chicago, Chicago, Illinois 60637, USA
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Makina Yabashi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - IChiro Inoue
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jumpei Yamada
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Toru Hara
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nina Rohringer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, Universität Hamburg, Hamburg 20355, Germany
| | - Hitoki Yoneda
- Institute for Laser Science, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 9402, USA
| | - Claudio Pellegrini
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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11
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Simon PS, Makita H, Bogacz I, Fuller F, Bhowmick A, Hussein R, Ibrahim M, Zhang M, Chatterjee R, Cheah MH, Chernev P, Doyle MD, Brewster AS, Alonso-Mori R, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs. FEBS Lett 2023; 597:30-37. [PMID: 36310373 PMCID: PMC9839502 DOI: 10.1002/1873-3468.14527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/17/2023]
Abstract
Ever since the discovery that Mn was required for oxygen evolution in plants by Pirson in 1937 and the period-four oscillation in flash-induced oxygen evolution by Joliot and Kok in the 1970s, understanding of this process has advanced enormously using state-of-the-art methods. The most recent in this series of innovative techniques was the introduction of X-ray free-electron lasers (XFELs) a decade ago, which led to another quantum leap in the understanding in this field, by enabling operando X-ray structural and X-ray spectroscopy studies at room temperature. This review summarizes the current understanding of the structure of Photosystem II (PS II) and its catalytic centre, the Mn4 CaO5 complex, in the intermediate Si (i = 0-4)-states of the Kok cycle, obtained using XFELs.
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Affiliation(s)
- Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Franklin Fuller
- Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miao Zhang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mun Hon Cheah
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Margaret D Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roberto Alonso-Mori
- LINAC Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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12
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John J, Aurelius O, Srinivas V, Saura P, Kim IS, Bhowmick A, Simon PS, Dasgupta M, Pham C, Gul S, Sutherlin KD, Aller P, Butryn A, Orville AM, Cheah MH, Owada S, Tono K, Fuller FD, Batyuk A, Brewster AS, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Kern J, Lebrette H, Högbom M. Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography. eLife 2022; 11:79226. [PMID: 36083619 PMCID: PMC9462851 DOI: 10.7554/elife.79226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b-NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b-NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
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Affiliation(s)
- Juliane John
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.,MAX IV Laboratory, Lund University, Lund, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Cindy Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Agata Butryn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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13
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Zhang Y, Kroll T, Weninger C, Michine Y, Fuller FD, Zhu D, Alonso-Mori R, Sokaras D, Lutman AA, Halavanau A, Pellegrini C, Benediktovitch A, Yabashi M, Inoue I, Inubushi Y, Osaka T, Yamada J, Babu G, Salpekar D, Sayed FN, Ajayan PM, Kern J, Yano J, Yachandra VK, Yoneda H, Rohringer N, Bergmann U. Generation of intense phase-stable femtosecond hard X-ray pulse pairs. Proc Natl Acad Sci U S A 2022; 119:e2119616119. [PMID: 35290124 PMCID: PMC8944280 DOI: 10.1073/pnas.2119616119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/02/2022] [Indexed: 11/18/2022] Open
Abstract
Coherent nonlinear spectroscopies and imaging in the X-ray domain provide direct insight into the coupled motions of electrons and nuclei with resolution on the electronic length scale and timescale. The experimental realization of such techniques will strongly benefit from access to intense, coherent pairs of femtosecond X-ray pulses. We have observed phase-stable X-ray pulse pairs containing more than 3 × 107 photons at 5.9 keV (2.1 Å) with ∼1 fs duration and 2 to 5 fs separation. The highly directional pulse pairs are manifested by interference fringes in the superfluorescent and seeded stimulated manganese Kα emission induced by an X-ray free-electron laser. The fringes constitute the time-frequency X-ray analog of Young’s double-slit interference, allowing for frequency domain X-ray measurements with attosecond time resolution.
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Affiliation(s)
- Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Clemens Weninger
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- MAX IV Laboratory, Lund University, Lund 224 84, Sweden
| | - Yurina Michine
- Institute for Laser Science, The University of Electro-Communications, Chofu,Tokyo 182-8585, Japan
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Alberto A. Lutman
- Linac & FEL Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Aliaksei Halavanau
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Claudio Pellegrini
- Accelerator Research Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andrei Benediktovitch
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
| | - Makina Yabashi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Ichiro Inoue
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jumpei Yamada
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ganguli Babu
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Devashish Salpekar
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Farheen N. Sayed
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Pulickel M. Ajayan
- Department of Materials Science and NanoEngineering, Rice University, Houston, TX 77005
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Hitoki Yoneda
- Institute for Laser Science, The University of Electro-Communications, Chofu,Tokyo 182-8585, Japan
| | - Nina Rohringer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, Universität Hamburg, Hamburg 20355, Germany
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Physics, University of Wisconsin–Madison, Madison, WI 53706
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14
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Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J. Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition. Nat Commun 2021; 12:6531. [PMID: 34764256 PMCID: PMC8585918 DOI: 10.1038/s41467-021-26781-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.
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Affiliation(s)
- Rana Hussein
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mohamed Ibrahim
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Asmit Bhowmick
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Philipp S. Simon
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Ruchira Chatterjee
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Louise Lassalle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Margaret Doyle
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Isabel Bogacz
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - In-Sik Kim
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Mun Hon Cheah
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Sheraz Gul
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Casper de Lichtenberg
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden ,grid.12650.300000 0001 1034 3451Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Petko Chernev
- grid.8993.b0000 0004 1936 9457Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Cindy C. Pham
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Iris D. Young
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sergio Carbajo
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Franklin D. Fuller
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Roberto Alonso-Mori
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Alex Batyuk
- grid.512023.70000 0004 6047 9447Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Kyle D. Sutherlin
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aaron S. Brewster
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Robert Bolotovsky
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Derek Mendez
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - James M. Holton
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Nigel W. Moriarty
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Uwe Bergmann
- grid.14003.360000 0001 2167 3675Department of Physics, University of Wisconsin–Madison, Madison, WI 53706 USA
| | - Nicholas K. Sauter
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Holger Dobbek
- grid.7468.d0000 0001 2248 7639Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120, Uppsala, Sweden. .,Department of Chemistry, Umeå University, SE 90187, Umeå, Sweden.
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Vittal K. Yachandra
- grid.184769.50000 0001 2231 4551Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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15
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Keable SM, Kölsch A, Simon PS, Dasgupta M, Chatterjee R, Subramanian SK, Hussein R, Ibrahim M, Kim IS, Bogacz I, Makita H, Pham CC, Fuller FD, Gul S, Paley D, Lassalle L, Sutherlin KD, Bhowmick A, Moriarty NW, Young ID, Blaschke JP, de Lichtenberg C, Chernev P, Cheah MH, Park S, Park G, Kim J, Lee SJ, Park J, Tono K, Owada S, Hunter MS, Batyuk A, Oggenfuss R, Sander M, Zerdane S, Ozerov D, Nass K, Lemke H, Mankowsky R, Brewster AS, Messinger J, Sauter NK, Yachandra VK, Yano J, Zouni A, Kern J. Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I. Sci Rep 2021; 11:21787. [PMID: 34750381 PMCID: PMC8575901 DOI: 10.1038/s41598-021-00236-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/02/2021] [Indexed: 11/09/2022] Open
Abstract
Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.
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Affiliation(s)
- Stephen M Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adrian Kölsch
- Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Rana Hussein
- Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA
| | - Johannes P Blaschke
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden.,Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), 90187, Umeå, Sweden
| | - Petko Chernev
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
| | - Jangwoo Kim
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | | | | | | | | | - Karol Nass
- Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Henrik Lemke
- Paul Scherrer Institut, 5232, Villigen, Switzerland
| | | | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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16
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. Struct Dyn 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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17
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Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton I, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O'Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ. X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis. Sci Adv 2021; 7:eabh0250. [PMID: 34417180 PMCID: PMC8378823 DOI: 10.1126/sciadv.abh0250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/29/2021] [Indexed: 05/23/2023]
Abstract
Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
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Affiliation(s)
- Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jos J A G Kamps
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - James D S Linyard
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Pierre Aller
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ian Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Denis Shutin
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Agata Butryn
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 751 20 Uppsala, Sweden
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Lee O'Riordan
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, WI 53706, USA
| | - Robin L Owen
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Allen M Orville
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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18
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Butryn A, Simon PS, Aller P, Hinchliffe P, Massad RN, Leen G, Tooke CL, Bogacz I, Kim IS, Bhowmick A, Brewster AS, Devenish NE, Brem J, Kamps JJAG, Lang PA, Rabe P, Axford D, Beale JH, Davy B, Ebrahim A, Orlans J, Storm SLS, Zhou T, Owada S, Tanaka R, Tono K, Evans G, Owen RL, Houle FA, Sauter NK, Schofield CJ, Spencer J, Yachandra VK, Yano J, Kern JF, Orville AM. An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography. Nat Commun 2021; 12:4461. [PMID: 34294694 PMCID: PMC8298390 DOI: 10.1038/s41467-021-24757-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 11/08/2022] Open
Abstract
Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.
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Affiliation(s)
- Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, UK
| | - Ramzi N Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gabriel Leen
- PolyPico Technologies Ltd, Unit 10, Airways Technology Park, Rathmacullig West, Cork, Ireland
- Department of Electronic and Computer Engineering, University of Limerick, Limerick, Ireland
| | - Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, UK
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Jos J A G Kamps
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Pauline A Lang
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Patrick Rabe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - John H Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Bradley Davy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- School of Computing, University of Leeds, Leeds, UK
| | - Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Julien Orlans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- UMR0203, Biologie Fonctionnelle, Insectes et Interactions, Institut National des Sciences Appliquées de Lyon, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, University of Lyon, Villeurbanne, France
| | - Selina L S Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Hamburg, Germany
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Frances A Houle
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, UK
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Allen M Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, UK.
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19
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Fuller FD, Loukianov A, Takanashi T, You D, Li Y, Ueda K, Fransson T, Yabashi M, Katayama T, Weng TC, Alonso-Mori R, Bergmann U, Jan Kern, Yachandra VK, Wernet P, Yano J. Resonant X-ray emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser. Commun Chem 2021; 4:84. [PMID: 35291552 PMCID: PMC8920481 DOI: 10.1038/s42004-021-00512-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/21/2021] [Indexed: 01/27/2023] Open
Abstract
Hard X-ray spectroscopy is an element specific probe of electronic state, but signals are weak and require intense light to study low concentration samples. Free electron laser facilities offer the highest intensity X-rays of any available light source. The light produced at such facilities is stochastic, with spikey, broadband spectra that change drastically from shot to shot. Here, using aqueous ferrocyanide, we show that the resonant X-ray emission (RXES) spectrum can be inferred by correlating for each shot the fluorescence intensity from the sample with spectra of the fluctuating, self-amplified spontaneous emission (SASE) source. We obtain resolved narrow and chemically rich information in core-to-valence transitions of the pre-edge region at the Fe K-edge. Our approach avoids monochromatization, provides higher photon flux to the sample, and allows non-resonant signals like elastic scattering to be simultaneously recorded. The spectra obtained match well with spectra measured using a monochromator. We also show that inaccurate measurements of the stochastic light spectra reduce the measurement efficiency of our approach.
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Affiliation(s)
| | | | | | | | - Yiwen Li
- Tohoku University, Sendai, Miyagi Japan
| | | | | | | | - Tetsuo Katayama
- RIKEN SPring-8 Center, Sayo, Hyogo Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo Japan
| | - Tsu-Chien Weng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | | | | | - Jan Kern
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Junko Yano
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
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20
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Bergmann U, Kern J, Schoenlein RW, Wernet P, Yachandra VK, Yano J. Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes. Nat Rev Phys 2021; 3:264-282. [PMID: 34212130 PMCID: PMC8245202 DOI: 10.1038/s42254-021-00289-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 05/14/2023]
Abstract
The metal centres in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.
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Affiliation(s)
- Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Physics, University of Wisconsin–Madison, Madison, WI, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert W. Schoenlein
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Philippe Wernet
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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21
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Srinivas V, Banerjee R, Lebrette H, Jones JC, Aurelius O, Kim IS, Pham CC, Gul S, Sutherlin KD, Bhowmick A, John J, Bozkurt E, Fransson T, Aller P, Butryn A, Bogacz I, Simon P, Keable S, Britz A, Tono K, Kim KS, Park SY, Lee SJ, Park J, Alonso-Mori R, Fuller FD, Batyuk A, Brewster AS, Bergmann U, Sauter NK, Orville AM, Yachandra VK, Yano J, Lipscomb JD, Kern J, Högbom M. High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. J Am Chem Soc 2020; 142:14249-14266. [PMID: 32683863 DOI: 10.1021/jacs.0c05613] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Esra Bozkurt
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Pierre Aller
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen Keable
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-gun 679 5198, Japan
| | - Kyung Sook Kim
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang-Youn Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, Gyeongsangbuk-do 37673, South Korea
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Allen M Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm 106 91, Sweden
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22
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Kroll T, Weninger C, Fuller FD, Guetg MW, Benediktovitch A, Zhang Y, Marinelli A, Alonso-Mori R, Aquila A, Liang M, Koglin JE, Koralek J, Sokaras D, Zhu D, Kern J, Yano J, Yachandra VK, Rohringer N, Lutman A, Bergmann U. Observation of Seeded Mn Kβ Stimulated X-Ray Emission Using Two-Color X-Ray Free-Electron Laser Pulses. Phys Rev Lett 2020; 125:037404. [PMID: 32745427 PMCID: PMC7808879 DOI: 10.1103/physrevlett.125.037404] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/25/2020] [Accepted: 06/23/2020] [Indexed: 05/03/2023]
Abstract
Kβ x-ray emission spectroscopy is a powerful probe for electronic structure analysis of 3d transition metal systems and their ultrafast dynamics. Selectively enhancing specific spectral regions would increase this sensitivity and provide fundamentally new insights. Recently we reported the observation and analysis of Kα amplified spontaneous x-ray emission from Mn solutions using an x-ray free-electron laser to create the 1s core-hole population inversion [Kroll et al., Phys. Rev. Lett. 120, 133203 (2018)PRLTAO0031-900710.1103/PhysRevLett.120.133203]. To apply this new approach to the chemically more sensitive but much weaker Kβ x-ray emission lines requires a mechanism to outcompete the dominant amplification of the Kα emission. Here we report the observation of seeded amplified Kβ x-ray emission from a NaMnO_{4} solution using two colors of x-ray free-electron laser pulses, one to create the 1s core-hole population inversion and the other to seed the amplified Kβ emission. Comparing the observed seeded amplified Kβ emission signal with that from conventional Kβ emission into the same solid angle, we obtain a signal enhancement of more than 10^{5}. Our findings are the first important step of enhancing and controlling the emission of selected final states of the Kβ spectrum with applications in chemical and materials science.
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Affiliation(s)
- Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Franklin D. Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marc W. Guetg
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Agostino Marinelli
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jake Koralek
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nina Rohringer
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, 20355 Hamburg, Germany
| | - Alberto Lutman
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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23
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Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A 2020; 117:12624-12635. [PMID: 32434915 PMCID: PMC7293653 DOI: 10.1073/pnas.2000529117] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Thomas Fransson
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Franklin D Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Petko Chernev
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cindy C Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, OX11 0FA Didcot, United Kingdom
| | - Nicholas Saichek
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Trent Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Sergio Carbajo
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Shigeki Owada
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, 679-5198 Hyogo, Japan
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bolotovsky
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Derek Mendez
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany;
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden;
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
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24
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Chatterjee R, Weninger C, Loukianov A, Gul S, Fuller FD, Cheah MH, Fransson T, Pham CC, Nelson S, Song S, Britz A, Messinger J, Bergmann U, Alonso-Mori R, Yachandra VK, Kern J, Yano J. XANES and EXAFS of dilute solutions of transition metals at XFELs. J Synchrotron Radiat 2019; 26:1716-1724. [PMID: 31490163 PMCID: PMC6730626 DOI: 10.1107/s1600577519007550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/23/2019] [Indexed: 05/27/2023]
Abstract
This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anton Loukianov
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Cindy C. Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Britz
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johannes Messinger
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94704, USA
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25
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Chatterjee R, Lassalle L, Gul S, Fuller FD, Young ID, Ibrahim M, de Lichtenberg C, Cheah MH, Zouni A, Messinger J, Yachandra VK, Kern J, Yano J. Structural isomers of the S 2 state in photosystem II: do they exist at room temperature and are they important for function? Physiol Plant 2019; 166:60-72. [PMID: 30793319 PMCID: PMC6478542 DOI: 10.1111/ppl.12947] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 05/21/2023]
Abstract
In nature, an oxo-bridged Mn4 CaO5 cluster embedded in photosystem II (PSII), a membrane-bound multi-subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light-induced charge separations in the reaction center of PSII. The Mn4 CaO5 cluster accumulates four oxidizing equivalents to enable the four-electron four-proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S-states, S0 - S4 in the Kok cycle. One important question related to the catalytic mechanism of the oxygen-evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S-states and if such equilibria are essential for the mechanism of the O-O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S2 state of PSII with structural data collected of the S1 , S2 and S3 states by serial crystallography at neutral pH (∼6.5) using an X-ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S2 state, the room temperature crystallography data can be well-described by just one S2 structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Casper de Lichtenberg
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 75237 Uppsala, Sweden
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
- Correspondence Corresponding authors, , , ,
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence Corresponding authors, , , ,
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence Corresponding authors, , , ,
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence Corresponding authors, , , ,
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26
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Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK. Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature 2018; 563:421-425. [PMID: 30405241 DOI: 10.1038/s41586-018-0681-2] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/22/2018] [Indexed: 12/18/2022]
Abstract
Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2→S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.
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Affiliation(s)
- Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lacey Douthit
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Mun Hon Cheah
- Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Dmitry Shevela
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Julia Wersig
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ina Seuffert
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Agata Butryn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sergio Carbajo
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden. .,Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden.
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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27
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Alonso-Mori R, Asa K, Bergmann U, Brewster AS, Chatterjee R, Cooper JK, Frei HM, Fuller FD, Goggins E, Gul S, Fukuzawa H, Iablonskyi D, Ibrahim M, Katayama T, Kroll T, Kumagai Y, McClure BA, Messinger J, Motomura K, Nagaya K, Nishiyama T, Saracini C, Sato Y, Sauter NK, Sokaras D, Takanashi T, Togashi T, Ueda K, Weare WW, Weng TC, Yabashi M, Yachandra VK, Young ID, Zouni A, Kern JF, Yano J. Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs. Faraday Discuss 2018; 194:621-638. [PMID: 27711803 DOI: 10.1039/c6fd00084c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.
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Affiliation(s)
- R Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - K Asa
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - U Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - A S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - R Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J K Cooper
- Joint Center for Artificial Photosynthesis (JCAP), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - H M Frei
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - F D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - E Goggins
- Dept. of Chemistry, North Carolina State University, 2620 Yarborough Rd., Raleigh, NC 27695-8204, USA
| | - S Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - H Fukuzawa
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - M Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - T Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - T Kroll
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Y Kumagai
- IMRAM, Tohoku U., Sendai 980-8577, Japan
| | - B A McClure
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - K Motomura
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - K Nagaya
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - T Nishiyama
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - C Saracini
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - Y Sato
- Department of Physics, Graduate School of Science, Kyoto U., Kyoto, 606-8502, Japan
| | - N K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - D Sokaras
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - T Togashi
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - K Ueda
- IMRAM, Tohoku U., Sendai 980-8577, Japan and RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - W W Weare
- Dept. of Chemistry, North Carolina State University, 2620 Yarborough Rd., Raleigh, NC 27695-8204, USA
| | - T-C Weng
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
| | - M Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8/SACLA, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - V K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - I D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - A Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - J F Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA.
| | - J Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA. and Joint Center for Artificial Photosynthesis (JCAP), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA and IMRAM, Tohoku U., Sendai 980-8577, Japan
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Kubin M, Guo M, Ekimova M, Källman E, Kern J, Yachandra VK, Yano J, Nibbering ETJ, Lundberg M, Wernet P. Cr L-Edge X-ray Absorption Spectroscopy of Cr III(acac) 3 in Solution with Measured and Calculated Absolute Absorption Cross Sections. J Phys Chem B 2018; 122:7375-7384. [PMID: 29957942 DOI: 10.1021/acs.jpcb.8b04190] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
X-ray absorption spectroscopy at the L-edge of 3d transition metals is widely used for probing the valence electronic structure at the metal site via 2p-3d transitions. Assessing the information contained in L-edge absorption spectra requires systematic comparison of experiment and theory. We here investigate the Cr L-edge absorption spectrum of high-spin chromium acetylacetonate CrIII(acac)3 in solution. Using a transmission flatjet enables determining absolute absorption cross sections and spectra free from X-ray-induced sample damage. We address the challenges of measuring Cr L absorption edges spectrally close to the O K absorption edge of the solvent. We critically assess how experimental absorption cross sections can be used to extract information on the electronic structure of the studied system by comparing our results of this CrIII (3d3) complex to our previous work on L-edge absorption cross sections of MnIII(acac)3 (3d4) and MnII(acac)2 (3d5). Considering our experimental uncertainties, the most insightful experimental observable for this d3(CrIII)-d4(MnIII)-d5(MnII) series is the L-edge branching ratio, and we discuss it in comparison to semiempirical multiplet theory and ab initio restricted active space calculations. We further discuss and analyze trends in integrated absorption cross sections and correlate the spectral shapes with the local electronic structure at the metal sites.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , 12489 Berlin , Germany
| | - Meiyuan Guo
- Department of Chemistry-Ångström Laboratory , Uppsala University , SE-75121 Uppsala , Sweden
| | - Maria Ekimova
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin , Germany
| | - Erik Källman
- Department of Chemistry-Ångström Laboratory , Uppsala University , SE-75121 Uppsala , Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Erik T J Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , 12489 Berlin , Germany
| | - Marcus Lundberg
- Department of Chemistry-Ångström Laboratory , Uppsala University , SE-75121 Uppsala , Sweden
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , 12489 Berlin , Germany
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29
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Fransson T, Chatterjee R, Fuller FD, Gul S, Weninger C, Sokaras D, Kroll T, Alonso-Mori R, Bergmann U, Kern J, Yachandra VK, Yano J. X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry 2018; 57:4629-4637. [PMID: 29906115 DOI: 10.1021/acs.biochem.8b00325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kβ1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.
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Affiliation(s)
- Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
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30
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Kubin M, Kern J, Guo M, Källman E, Mitzner R, Yachandra VK, Lundberg M, Yano J, Wernet P. X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution. Phys Chem Chem Phys 2018; 20:16817-16827. [PMID: 29888772 PMCID: PMC6011208 DOI: 10.1039/c8cp03094d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
X-ray induced sample damage can impede electronic and structural investigations of radiation-sensitive samples studied with X-rays. Here we quantify dose-dependent sample damage to the prototypical MnIII(acac)3 complex in solution and at room temperature for the soft X-ray range, using X-ray absorption spectroscopy at the Mn L-edge. We observe the appearance of a reduced MnII species as the X-ray dose is increased. We find a half-damage dose of 1.6 MGy and quantify a spectroscopically tolerable dose on the order of 0.3 MGy (1 Gy = 1 J kg-1), where 90% of MnIII(acac)3 are intact. Our dose-limit is around one order of magnitude lower than the Henderson limit (half-damage dose of 20 MGy) which is commonly employed for protein crystallography with hard X-rays. It is comparable, however, to the dose-limits obtained for collecting un-damaged Mn K-edge spectra of the photosystem II protein, using hard X-rays. The dose-dependent reduction of MnIII observed here for solution samples occurs at a dose limit that is two to four orders of magnitude smaller than the dose limits previously reported for soft X-ray spectroscopy of iron samples in the solid phase. We compare our measured to calculated spectra from ab initio restricted active space (RAS) theory and discuss possible mechanisms for the observed dose-dependent damage of MnIII(acac)3 in solution. On the basis of our results, we assess the influence of sample damage in other experimental studies with soft X-rays from storage-ring synchrotron radiation sources and X-ray free-electron lasers.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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31
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Kubin M, Guo M, Ekimova M, Baker ML, Kroll T, Källman E, Kern J, Yachandra VK, Yano J, Nibbering ETJ, Lundberg M, Wernet P. Direct Determination of Absolute Absorption Cross Sections at the L-Edge of Dilute Mn Complexes in Solution Using a Transmission Flatjet. Inorg Chem 2018; 57:5449-5462. [PMID: 29634280 PMCID: PMC5972834 DOI: 10.1021/acs.inorgchem.8b00419] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 3d transition metals play a pivotal role in many charge transfer processes in catalysis and biology. X-ray absorption spectroscopy at the L-edge of metal sites probes metal 2p-3d excitations, providing key access to their valence electronic structure, which is crucial for understanding these processes. We report L-edge absorption spectra of MnII(acac)2 and MnIII(acac)3 complexes in solution, utilizing a liquid flatjet for X-ray absorption spectroscopy in transmission mode. With this, we derive absolute absorption cross-sections for the L-edge transitions with peak magnitudes as large as 12 and 9 Mb for MnII(acac)2 and MnIII(acac)3, respectively. We provide insight into the electronic structure with ab initio restricted active space calculations of these L-edge transitions, reproducing the experimental spectra with excellent agreement in terms of shapes, relative energies, and relative intensities for the two complexes. Crystal field multiplet theory is used to assign spectral features in terms of the electronic structure. Comparison to charge transfer multiplet calculations reveals the importance of charge transfer in the core-excited final states. On the basis of our experimental observations, we extrapolate the feasibility of 3d transition metal L-edge absorption spectroscopy using the liquid flatjet approach in probing highly dilute biological solution samples and possible extensions to table-top soft X-ray sources.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Meiyuan Guo
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-75121 Uppsala, Sweden
| | - Maria Ekimova
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Michael L. Baker
- The School of Chemistry, The University of Manchester at Harwell, Didcot, OX11 OFA, U.K
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Källman
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-75121 Uppsala, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik T. J. Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-75121 Uppsala, Sweden
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
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Kroll T, Weninger C, Alonso-Mori R, Sokaras D, Zhu D, Mercadier L, Majety VP, Marinelli A, Lutman A, Guetg MW, Decker FJ, Boutet S, Aquila A, Koglin J, Koralek J, DePonte DP, Kern J, Fuller FD, Pastor E, Fransson T, Zhang Y, Yano J, Yachandra VK, Rohringer N, Bergmann U. Stimulated X-Ray Emission Spectroscopy in Transition Metal Complexes. Phys Rev Lett 2018; 120:133203. [PMID: 29694162 PMCID: PMC6007888 DOI: 10.1103/physrevlett.120.133203] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/16/2017] [Indexed: 05/07/2023]
Abstract
We report the observation and analysis of the gain curve of amplified Kα x-ray emission from solutions of Mn(II) and Mn(VII) complexes using an x-ray free electron laser to create the 1s core-hole population inversion. We find spectra at amplification levels extending over 4 orders of magnitude until saturation. We observe bandwidths below the Mn 1s core-hole lifetime broadening in the onset of the stimulated emission. In the exponential amplification regime the resolution corrected spectral width of ∼1.7 eV FWHM is constant over 3 orders of magnitude, pointing to the buildup of transform limited pulses of ∼1 fs duration. Driving the amplification into saturation leads to broadening and a shift of the line. Importantly, the chemical sensitivity of the stimulated x-ray emission to the Mn oxidation state is preserved at power densities of ∼10^{20} W/cm^{2} for the incoming x-ray pulses. Differences in signal sensitivity and spectral information compared to conventional (spontaneous) x-ray emission spectroscopy are discussed. Our findings build a baseline for nonlinear x-ray spectroscopy for a wide range of transition metal complexes in inorganic chemistry, catalysis, and materials science.
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Affiliation(s)
- Thomas Kroll
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Laurent Mercadier
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Vinay P Majety
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Agostino Marinelli
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alberto Lutman
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marc W Guetg
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Franz-Josef Decker
- Accelerator Directorate, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jake Koralek
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jan Kern
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Yu Zhang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence, Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nina Rohringer
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, 20355 Hamburg, Germany
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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Hussein R, Ibrahim M, Chatterjee R, Coates L, Müh F, Yachandra VK, Yano J, Kern J, Dobbek H, Zouni A. Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography. Cryst Growth Des 2018; 18:85-94. [PMID: 29962903 PMCID: PMC6020701 DOI: 10.1021/acs.cgd.7b00878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Photosystem II (PSII) catalyzes the photo-oxidation of water to molecular oxygen and protons. The water splitting reaction occurs inside the oxygen-evolving complex (OEC) via a Mn4CaO5 cluster. To elucidate the reaction mechanism, detailed structural information for each intermediate state of the OEC is required. Despite the current high-resolution crystal structure of PSII at 1.85 Å and other efforts to follow the structural changes of the Mn4CaO5 cluster using X-ray free electron laser (XFEL) crystallography in addition to spectroscopic methods, many details about the reaction mechanism and conformational changes in the catalytic site during water oxidation still remain elusive. In this study, we present a rarely found successful application of the conventional macroseeding method to a large membrane protein like the dimeric PSII core complex (dPSIIcc). Combining microseeding with macroseeding crystallization techniques allowed us to reproducibly grow large dPSIIcc crystals with a size of ~3 mm. These large crystals will help improve the data collected from spectroscopic methods like polarized extended X-ray absorption fine structure (EXAFS) and single crystal electron paramagnetic resonance (EPR) techniques and are a prerequisite for determining a three-dimensional structure using neutron diffraction.
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Affiliation(s)
- Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
- Corresponding Authors: (R.H.) Phone; +49 30 2093 47933; . (A.Z.) Phone: +49 30 2093 47930;
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leighton Coates
- Neutron Scattering Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Frank Müh
- Institute of Theoretical Physics, Johannes Kepler University Linz, Linz, Austria
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
- Corresponding Authors: (R.H.) Phone; +49 30 2093 47933; . (A.Z.) Phone: +49 30 2093 47930;
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34
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Lassalle-Kaiser B, Gul S, Kern J, Yachandra VK, Yano J. In situ/Operando studies of electrocatalysts using hard X-ray spectroscopy. J Electron Spectros Relat Phenomena 2017; 221:18-27. [PMID: 29515287 PMCID: PMC5836735 DOI: 10.1016/j.elspec.2017.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This review focuses on the use of X-ray absorption and emission spectroscopy techniques using hard X-rays to study electrocatalysts under in situ/operando conditions. We describe the importance and the versatility of methods in the study of electrodes in contact with the electrolytes, when being cycled through the catalytic potentials during the progress of the oxygen-evolution, oxygen reduction and hydrogen evolution reactions. The catalytic oxygen evolution reaction is illustrated with examples using Co, Ni and Mn oxides, and Mo and Co sulfides are used as an example for the hydrogen evolution reaction. A bimetallic, bifunctional oxygen evolving and oxygen reducing Ni/Mn oxide is also presented. The various advantages and constraints in the use of these techniques and the future outlook are discussed.
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Affiliation(s)
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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35
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Miner EM, Gul S, Ricke ND, Pastor E, Yano J, Yachandra VK, Van Voorhis T, Dincă M. Mechanistic Evidence for Ligand-Centered Electrocatalytic Oxygen Reduction with the Conductive MOF Ni3(hexaiminotriphenylene)2. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02647] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Elise M. Miner
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sheraz Gul
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nathan D. Ricke
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ernest Pastor
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Vittal K. Yachandra
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Troy Van Voorhis
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mircea Dincă
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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36
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Kubin M, Kern J, Gul S, Kroll T, Chatterjee R, Löchel H, Fuller FD, Sierra RG, Quevedo W, Weniger C, Rehanek J, Firsov A, Laksmono H, Weninger C, Alonso-Mori R, Nordlund DL, Lassalle-Kaiser B, Glownia JM, Krzywinski J, Moeller S, Turner JJ, Minitti MP, Dakovski GL, Koroidov S, Kawde A, Kanady JS, Tsui EY, Suseno S, Han Z, Hill E, Taguchi T, Borovik AS, Agapie T, Messinger J, Erko A, Föhlisch A, Bergmann U, Mitzner R, Yachandra VK, Yano J, Wernet P. Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers. Struct Dyn 2017; 4:054307. [PMID: 28944255 PMCID: PMC5586166 DOI: 10.1063/1.4986627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/15/2017] [Indexed: 05/19/2023]
Abstract
X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | | | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Heike Löchel
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Wilson Quevedo
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Christian Weniger
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Jens Rehanek
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Anatoly Firsov
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dennis L Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - James M Glownia
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Joshua J Turner
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Michael P Minitti
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Georgi L Dakovski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Anurag Kawde
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Jacob S Kanady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Emily Y Tsui
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sandy Suseno
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zhiji Han
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ethan Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Taketo Taguchi
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Andrew S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Alexei Erko
- Institute for Nanometre Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | | | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Rolf Mitzner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
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37
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christopher J Pollock
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philipp Bräuer
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christian G Roessler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Peter T Docker
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Amie K Boal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - J Martin Bollinger
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carsten Krebs
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Chemistry, Stanford University, Stanford, California, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Allen M Orville
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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38
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Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature 2016; 540:453-457. [PMID: 27871088 DOI: 10.1038/nature20161] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/14/2016] [Indexed: 12/16/2022]
Abstract
Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
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Affiliation(s)
- Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Franklin Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rosalie Tran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Thomas Kroll
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Lacey Douthit
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Pham Long Vo
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Håkan Nilsson
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Mun Hon Cheah
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Dmitriy Shevela
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Claudio Saracini
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mackenzie A Bean
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ina Seuffert
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Peter T Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marcin Sikorski
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas J Lane
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Joseph Robinson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | | | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David G Waterman
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK and CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Philippe Wernet
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305.,Department of Structural Biology, Stanford University, Stanford, CA 94305
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Petrus H Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.,Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE 75237 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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39
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Kroll T, Kern J, Kubin M, Ratner D, Gul S, Fuller FD, Löchel H, Krzywinski J, Lutman A, Ding Y, Dakovski GL, Moeller S, Turner JJ, Alonso-Mori R, Nordlund DL, Rehanek J, Weniger C, Firsov A, Brzhezinskaya M, Chatterjee R, Lassalle-Kaiser B, Sierra RG, Laksmono H, Hill E, Borovik A, Erko A, Föhlisch A, Mitzner R, Yachandra VK, Yano J, Wernet P, Bergmann U. X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser. Opt Express 2016; 24:22469-22480. [PMID: 27828320 PMCID: PMC5234502 DOI: 10.1364/oe.24.022469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/18/2016] [Accepted: 08/26/2016] [Indexed: 05/29/2023]
Abstract
X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.
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Affiliation(s)
- Thomas Kroll
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jan Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Daniel Ratner
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Heike Löchel
- Institute for Nanometer Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Jacek Krzywinski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alberto Lutman
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Yuantao Ding
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Georgi L. Dakovski
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Joshua J. Turner
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dennis L. Nordlund
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jens Rehanek
- Institute for Nanometer Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
- Paul-Scherrer-Institut, 5232 Villigen-PSI, Switzerland
| | - Christian Weniger
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Alexander Firsov
- Institute for Nanometer Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Maria Brzhezinskaya
- Institute for Nanometer Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Benedikt Lassalle-Kaiser
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 GIF-SUR-YVETTE Cedex, France
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ethan Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, USA
| | - Andrew Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, USA
| | - Alexei Erko
- Institute for Nanometer Optics and Technology, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Alexander Föhlisch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
- Institut für Physik und Astronomie, Universität Potsdam Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - Rolf Mitzner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 12489 Berlin, Germany
| | - Uwe Bergmann
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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40
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Chatterjee R, Han G, Kern J, Gul S, Fuller FD, Garachtchenko A, Young ID, Weng TC, Nordlund D, Alonso-Mori R, Bergmann U, Sokaras D, Hatakeyama M, Yachandra VK, Yano J. Structural Changes Correlated with Magnetic Spin State Isomorphism in the S 2 State of the Mn 4CaO 5 Cluster in the Oxygen-Evolving Complex of Photosystem II. Chem Sci 2016; 7:5236-5248. [PMID: 28044099 PMCID: PMC5201215 DOI: 10.1039/c6sc00512h] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022] Open
Abstract
The Mn4CaO5 cluster in Photosystem II catalyzes the four-electron redox reaction of water oxidation in natural photosynthesis. This catalytic reaction cycles through four intermediate states (Si, i = 0 to 4), involving changes in the redox state of the four Mn atoms in the cluster. Recent studies suggest the presence and importance of isomorphous structures within the same redox/intermediate S-state. It is highly likely that geometric and electronic structural flexibility play a role in the catalytic mechanism. Among the catalytic intermediates that have been identified experimentally thus far, there is clear evidence of such isomorphism in the S2 state, with a high-spin (5/2) (HS) and a low spin (1/2) (LS) form, identified and characterized by their distinct electron paramagnetic resonance (EPR spectroscopy) signals. We studied these two S2 isomers with Mn extended X-ray absorption fine structure (EXAFS) and absorption and emission spectroscopy (XANES/XES) to characterize the structural and electronic structural properties. The geometric and electronic structure of the HS and LS S2 states are different as determined using Mn EXAFS and XANES/XES, respectively. The Mn K-edge XANES and XES for the HS form are different from the LS and indicate a slightly lower positive charge on the Mn atoms compared to the LS form. Based on the EXAFS results which are clearly different, we propose possible structural differences between the two spin states. Such structural and magnetic redox-isomers if present at room temperature, will likely play a role in the mechanism for water-exchange/oxidation in photosynthesis.
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Affiliation(s)
- Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Guangye Han
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
- LCLS
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Anna Garachtchenko
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Tsu-Chien Weng
- Center for High Pressure Science &Technology Advanced Research
,
Shanghai
, China
| | - Dennis Nordlund
- SSRL
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | | | - Uwe Bergmann
- PULSE
, SLAC National Accelerator Laboratory
,
Menlo Park
, CA
, USA
| | | | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division
, Lawrence Berkeley National Laboratory
,
MS 66-0200, 1 Cyclotron Rd.
, Berkeley
, CA 94720-8099
, USA
.
;
; Tel: +1 510 486 4366
; Tel: +1 510 486 4963
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41
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Sauter NK, Echols N, Adams PD, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK. No observable conformational changes in PSII. Nature 2016; 533:E1-2. [PMID: 27193689 DOI: 10.1038/nature17983] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/21/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nathaniel Echols
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Petrus H Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, 90187 Umeå, Sweden
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, 90187 Umeå, Sweden
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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42
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Ibrahim M, Chatterjee R, Hellmich J, Tran R, Bommer M, Yachandra VK, Yano J, Kern J, Zouni A. Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures. Struct Dyn 2016; 2:041705. [PMID: 26726311 PMCID: PMC4697744 DOI: 10.1063/1.4919741] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/23/2015] [Indexed: 05/05/2023]
Abstract
In photosynthesis, photosystem II (PSII) is the multi-subunit membrane protein complex that catalyzes photo-oxidation of water into dioxygen through the oxygen evolving complex (OEC). To understand the water oxidation reaction, it is important to get structural information about the transient and intermediate states of the OEC in the dimeric PSII core complex (dPSIIcc). In recent times, femtosecond X-ray pulses from the free electron laser (XFEL) are being used to obtain X-ray diffraction (XRD) data of dPSIIcc microcrystals at room temperature that are free of radiation damage. In our experiments at the XFEL, we used an electrospun liquid microjet setup that requires microcrystals less than 40 μm in size. In this study, we explored various microseeding techniques to get a high yield of monodisperse uniform-sized microcrystals. Monodisperse microcrystals of dPSIIcc of uniform size were a key to improve the stability of the jet and the quality of XRD data obtained at the XFEL. This was evident by an improvement of the quality of the datasets obtained, from 6.5Å, using crystals grown without the micro seeding approach, to 4.5Å using crystals generated with the new method.
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Affiliation(s)
- Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
| | - Ruchira Chatterjee
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
| | - Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA ; LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany ; Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universitüt, D-10623 Berlin, Germany
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43
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Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat Methods 2016; 13:59-62. [PMID: 26619013 PMCID: PMC4890631 DOI: 10.1038/nmeth.3667] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/14/2015] [Indexed: 01/30/2023]
Abstract
We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).
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Affiliation(s)
- Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - E. Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sheraz Gul
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Jan Kern
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Mohamed Ibrahim
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | | | - Iris D. Young
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elia A. Junco
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elisabetta V. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Athina Zouni
- Institute für Biologie, Humboldt University of Berlin, Berlin, Germany
| | - Junko Yano
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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44
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Yamaguchi T, Yano J, Yachandra VK, Nihei Y, Togashi H, Szilagyi RK, Kohzuma T. The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin. BCSJ 2015. [DOI: 10.1246/bcsj.20150225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory
| | | | - Yuko Nihei
- Institute of Applied Beam Science, Ibaraki University
| | | | | | | |
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45
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Kern J, Yachandra VK, Yano J. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers. Curr Opin Struct Biol 2015; 34:87-98. [PMID: 26342144 DOI: 10.1016/j.sbi.2015.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK. Erratum: Corrigendum: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 2015. [DOI: 10.1038/nmeth0715-692d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lohmiller T, Shelby ML, Long X, Yachandra VK, Yano J. Removal of Ca(2+) from the Oxygen-Evolving Complex in Photosystem II Has Minimal Effect on the Mn4O5 Core Structure: A Polarized Mn X-ray Absorption Spectroscopy Study. J Phys Chem B 2015; 119:13742-54. [PMID: 25989608 DOI: 10.1021/acs.jpcb.5b03559] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ca(2+)-depleted and Ca(2+)-reconstituted spinach photosystem II was studied using polarized X-ray absorption spectroscopy of oriented PS II preparations to investigate the structural and functional role of the Ca(2+) ion in the Mn4O5Ca cluster of the oxygen-evolving complex (OEC). Samples were prepared by low pH/citrate treatment as one-dimensionally ordered membrane layers and poised in the Ca(2+)-depleted S1 (S1') and S2 (S2') states, the S2'YZ(•) state, at which point the catalytic cycle of water oxidation is inhibited, and the Ca(2+)-reconstituted S1 state. Polarized Mn K-edge XANES and EXAFS spectra exhibit pronounced dichroism. Polarized EXAFS data of all states of Ca(2+)-depleted PS II investigated show only minor changes in distances and orientations of the Mn-Mn vectors compared to the Ca(2+)-containing OEC, which may be attributed to some loss of rigidity of the core structure. Thus, removal of the Ca(2+) ion does not lead to fundamental distortion or rearrangement of the tetranuclear Mn cluster, which indicates that the Ca(2+) ion in the OEC is not critical for structural maintenance of the cluster, at least in the S1 and S2 states, but fulfills a crucial catalytic function in the mechanism of the water oxidation reaction. On the basis of this structural information, reasons for the inhibitory effect of Ca(2+) removal are discussed, attributing to the Ca(2+) ion a fundamental role in organizing the surrounding (substrate) water framework and in proton-coupled electron transfer to YZ(•) (D1-Tyr161).
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Affiliation(s)
- Thomas Lohmiller
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Megan L Shelby
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Xi Long
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-5230, United States
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Gul S, Ng JWD, Alonso-Mori R, Kern J, Sokaras D, Anzenberg E, Lassalle-Kaiser B, Gorlin Y, Weng TC, Zwart PH, Zhang JZ, Bergmann U, Yachandra VK, Jaramillo TF, Yano J. Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry. Phys Chem Chem Phys 2015; 17:8901-12. [PMID: 25747045 DOI: 10.1039/c5cp01023c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multielectron catalytic reactions, such as water oxidation, nitrogen reduction, or hydrogen production in enzymes and inorganic catalysts often involve multimetallic clusters. In these systems, the reaction takes place between metals or metals and ligands to facilitate charge transfer, bond formation/breaking, substrate binding, and release of products. In this study, we present a method to detect X-ray emission signals from multiple elements simultaneously, which allows for the study of charge transfer and the sequential chemistry occurring between elements. Kβ X-ray emission spectroscopy (XES) probes charge and spin states of metals as well as their ligand environment. A wavelength-dispersive spectrometer based on the von Hamos geometry was used to disperse Kβ signals of multiple elements onto a position detector, enabling an XES spectrum to be measured in a single-shot mode. This overcomes the scanning needs of the scanning spectrometers, providing data free from temporal and normalization errors and therefore ideal to follow sequential chemistry at multiple sites. We have applied this method to study MnOx-based bifunctional electrocatalysts for the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). In particular, we investigated the effects of adding a secondary element, Ni, to form MnNiOx and its impact on the chemical states and catalytic activity, by tracking the redox characteristics of each element upon sweeping the electrode potential. The detection scheme we describe here is general and can be applied to time-resolved studies of materials consisting of multiple elements, to follow the dynamics of catalytic and electron transfer reactions.
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Affiliation(s)
- Sheraz Gul
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra VK. The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130324. [PMID: 24914152 DOI: 10.1098/rstb.2013.0324] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.
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Affiliation(s)
- Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität Berlin, Berlin 10099, Germany
| | | | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität Berlin, Berlin 10099, Germany
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Abstract
Oxygen, that supports all aerobic life, is abundant in the atmosphere because of its constant regeneration by photosynthetic water oxidation, which is catalyzed by a Mn₄CaO₅ cluster in photosystem II (PS II), a multi subunit membrane protein complex. X-ray and other spectroscopy studies of the electronic and geometric structure of the Mn₄CaO₅ cluster as it advances through the intermediate states have been important for understanding the mechanism of water oxidation. The results and interpretations, especially from X-ray spectroscopy studies, regarding the geometric and electronic structure and the changes as the system proceeds through the catalytic cycle will be summarized in this review. This review will also include newer methodologies in time-resolved X-ray diffraction and spectroscopy that have become available since the commissioning of the X-ray free electron laser (XFEL) and are being applied to study the oxygen-evolving complex (OEC). The femtosecond X-ray pulses of the XFEL allows us to outrun X-ray damage at room temperature, and the time-evolution of the photo-induced reaction can be probed using a visible laser-pump followed by the X-ray-probe pulse. XFELs can be used to simultaneously determine the light-induced protein dynamics using crystallography and the local chemistry that occurs at the catalytic center using X-ray spectroscopy under functional conditions. Membrane inlet mass spectrometry has been important for providing direct information about the exchange of substrate water molecules, which has a direct bearing on the mechanism of water oxidation. Moreover, it has been indispensable for the time-resolved X-ray diffraction and spectroscopy studies and will be briefly reviewed in this chapter. Given the role of PS II in maintaining life in the biosphere and the future vision of a renewable energy economy, understanding the structure and mechanism of the photosynthetic water oxidation catalyst is an important goal for the future.
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Affiliation(s)
- Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K. Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Håkan Nilsson
- Department of Chemistry, Chemistry Biology Centre (KBC), Umeå University, S-90187 Umeå, Sweden
| | - Sergey Koroidov
- Department of Chemistry, Chemistry Biology Centre (KBC), Umeå University, S-90187 Umeå, Sweden
| | - Johannes Messinger
- Department of Chemistry, Chemistry Biology Centre (KBC), Umeå University, S-90187 Umeå, Sweden
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