| 1. |
- Alonso-Mori, R., et al.
(författare)
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Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs
- 2016
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Ingår i: Faraday discussions. - : Royal Society of Chemistry (RSC). - 1359-6640 .- 1364-5498. ; 194, s. 621-638
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Tidskriftsartikel (refereegranskat)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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| 2. |
- Bergmann, U, et al.
(författare)
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High-resolution X-ray spectroscopy of rare events : a different look at local structure and chemistry
- 2001
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Ingår i: Journal of Synchrotron Radiation. - Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA. CALTECH, Jet Prop Lab, Pasadena, CA 91109 USA. : MUNKSGAARD INT PUBL LTD. - 0909-0495 .- 1600-5775. ; 8, s. 199-203
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Tidskriftsartikel (refereegranskat)abstract
- The combination of large-acceptance high-resolution X-ray optics with bright synchrotron sources permits quantitative analysis of rare events such as X-ray fluorescence from very dilute systems, weak fluorescence transitions or X-ray Raman scattering. Transition-metal K beta fluorescence contains information about spin and oxidation state; examples of the characterization of the Mn oxidation states in the oxygen-evolving complex of photosystem II and Mn-consuming spores from the marine bacillus SG-1 are presented. Weaker features of the K beta spectrum resulting from valence-level and 'interatomic' ligand to metal transitions contain detailed information on the ligand-atom type, distance and orientation. Applications of this spectral region to characterize the local structure of model compounds are presented. X-ray Raman scattering (XRS) is an extremely rare event, but also represents a unique technique to obtain bulk-sensitive low-energy (<600 eV) X-ray absorption fine structure (XAFS) spectra using hard ( 10 keV) X-rays. A photon is inelastically scattered, losing part of its energy to promote an electron into an unoccupied level. In many cases, the cross section is proportional to that of the corresponding absorption process yielding the same X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) features. XRS finds application for systems that defy XAFS analysis at low energies, e.g. liquids or highly concentrated complex systems, reactive compounds and samples under extreme conditions (pressure, temperature). Recent results are discussed.
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| 3. |
- Cinco, R M, et al.
(författare)
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Orientation of calcium in the Mn4Ca cluster of the oxygen-evolving complex determined using polarized strontium EXAFS of photosystem II membranes
- 2004
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Ingår i: Biochemistry. - Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Melvin Calvin Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. : AMER CHEMICAL SOC. - 0006-2960 .- 1520-4995. ; 43:42, s. 13271-13282
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Tidskriftsartikel (refereegranskat)abstract
- The oxygen-evolving complex of photosystem II (PS II) in green plants and algae contains a cluster of four Mn atoms in the active site, which catalyzes the photoinduced oxidation of water to dioxygen. Along with Mn, calcium and chloride ions are necessary cofactors for proper functioning of the complex. The current Study using polarized Sr EXAFS on oriented Sr-reactivated samples shows that Fourier peak II, which fits best to Mn at 3.5 Angstrom rather than lighter atoms (C, N, O, or Cl), is dichroic, with a larger magnitude at 10degrees (angle between the PS II membrane normal and the X-ray electric field vector) and a smaller magnitude at 80degrees. Analysis of the dichroism of the Sr EXAFS yields a lower and upper limit of 0degrees and 23degrees for the average angle between the Sr-Mn vectors and the membrane normal and an isotropic coordination number (number of Mn neighbors to Sr) of 1 or 2 for these layered PS II samples. The results confirm the contention that Ca (Sr) is proximal to the Mn cluster and lead to refined working models of the heteronuclear Mn4Ca cluster of the oxygen-evolving complex in PS II.
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| 4. |
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| 5. |
- Lassalle, L., et al.
(författare)
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Structure of intermediates of the water oxidation reaction in photosystem II
- 2019
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Ingår i: Acta Crystallographica Section A. - : International Union of Crystallography. - 2053-2733. ; A75
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Photosystem II (PSII) catalyzes the light driven oxidation of water into dioxygen, protons and electrons. This reaction takes place at the oxygen evolving complex (OEC) a Mn4CaO5 cluster, through five intermediate S-states (S0 to S4), S1 being the dark-stable state and S3 the highest oxidized semi-stable state before O-O bond formation and O2 evolution. We have been using fs X-ray pulses from an X-ray free electron laser (XFEL) to study the geometric and electronic structure of the OEC over the reaction cycle and recently reported high-resolution (around 2 Å) structures of PSII at room temperature for the four stable states in the S-state cycle as well as for two time points in the S2-S3 transition. Our results reveal important structural changes including the binding of one additional ‘water’, Ox, during the S2→S3 state transition. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 suggests 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. We also explored the extended network of H-bonds between amino acid residues and waters connecting the OEC to the bulk solvent. We observed several significant changes in this network during the S-state cycle. Based on these data we will discuss the dynamics of the catalytic site and its environment over the reaction cycle.
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| 6. |
- Messinger, Johannes, 1963-, et al.
(författare)
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Absence of Mn-centered oxidation in the S2 → S3 Transition: : Implications for the mechanism of photosynthetic water oxidation
- 2001
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 123:32, s. 7804-7820
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Tidskriftsartikel (refereegranskat)abstract
- A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen-evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S-3 --> [S-4] --> So transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn K beta X-ray emission spectroscopy (K beta XES) to this problem for the first time. The K beta XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S-2 --> S3 transition, in contrast to the S-0 --> S-1 and S-1 --> S-2 transitions. does not involve a Mn-centered oxidation. On the basis of new structural data from the S-3-state, manganese mu -oxo bridge radical formation is proposed for the S-2 --> S-3 transition, and three possible mechanisms for the O-O bond formation are presented.
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| 7. |
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| 8. |
- Robblee, J H, et al.
(författare)
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The Mn cluster in the S0 state of the oxygen-evolving complex of photosystem II studied by EXAFS spectroscopy: : Are there three di-μ-oxo-bridged Mn2 moieties in the tetranuclear Mn complex?
- 2002
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Ingår i: Journal of the American Chemical Society. - Lawrence Berkeley Natl Lab, Phys Biosci Div, Melvin Calvin Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 124:25, s. 7459-7471
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Tidskriftsartikel (refereegranskat)abstract
- A key component required for an understanding of the mechanism of the evolution of molecular oxygen by the photosynthetic oxygen-evolving complex (OEC) in photosystem II (PS II) is the knowledge of the structures of the Mn cluster in the OEC in each of its intermediate redox states, or S-states. In this paper, we report the first detailed structural characterization using Mn extended X-ray absorption fine structure (EXAFS) spectroscopy of the Mn cluster of the OEC in the S-0 state, which exists immediately after the release of molecular oxygen. On the basis of the EXAFS spectroscopic results, the most likely interpretation is that one of the di-mu-oxo-bridged Mn-Mn moieties in the OEC has increased in distance from 2.7 Angstrom in the dark-stable S-1 state to 2.85 Angstrom in the S-0 state. Furthermore, curve fitting of the distance heterogeneity present in the EXAFS data from the S-0 state leads to the intriguing possibility that three di-mu-oxo-bridged Mn-Mn moieties may exist in the OEC instead of the two cli-y-oxo-bridged Mn-Mn moieties that are widely used in proposed structural models for the OEC. This possibility is developed using novel structural models for the Mn cluster in the OEC which are consistent with the structural information available from EXAFS and the recent X-ray crystallographic structure of PS II at 3.8 Angstrom resolution.
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| 9. |
- Yano, J, et al.
(författare)
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X-ray damage to the Mn4Ca complex in single crystals of photosystem II: : A case study for metalloprotein crystallography
- 2005
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - , Phys Biosci Div, Melvin Calvin Lab, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. Tech Univ Berlin, Max Volmer Lab Biophys Chem, D-10623 Berlin, Germany. Stanford Synchrotron Radiat Lab, Stanford, CA 94305 USA. European Synchrotron Radiat Facil, F-38043 Grenoble, France. Free Univ Berlin, Inst Kristallog, D-14195 Berlin, Germany. Max Planck Inst Bioanorgan Chem, D-45470 Mulheim, Germany. : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 102:34, s. 12047-12052
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Tidskriftsartikel (refereegranskat)abstract
- X-ray absorption spectroscopy was used to measure the damage caused by exposure to x-rays to the Mn4Ca active site in single crystals of photosystem II as a function of dose and energy of x-rays, temperature, and time. These studies reveal that the conditions used for structure determination by x-ray crystallography cause serious damage specifically to the metal-site structure. The x-ray absorption spectra show that the structure changes from one that is characteristic of a high-valent Mn-4(III2,IV2), oxo-bridged Mn4Ca cluster to that of Mn(II) in aqueous solution. This damage to the metal site occurs at a dose that is more than one order of magnitude lower than the dose that results in loss of diffractivity and is commonly considered safe for protein crystallography. These results establish quantitative x-ray dose parameters that are applicable to redox-active metalloproteins. This case study shows that a careful evaluation of the structural intactness of the active site(s) by spectroscopic techniques can validate structures derived from crystallography and that it can be a valuable complementary method before structure-function correlations of metalloproteins can be made on the basis of high-resolution x-ray crystal structures.
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| 10. |
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| 11. |
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| 12. |
- Rabe, Patrick, et al.
(författare)
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X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:34
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Tidskriftsartikel (refereegranskat)abstract
- Isopenicillin N synthase (IPNS) catalyzes the unique reaction of L-delta-(alpha-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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| 13. |
- Young, Iris D., et al.
(författare)
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Structure of photosystem II and substrate binding at room temperature
- 2016
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Ingår i: Nature. - : Macmillan Publishers Ltd.. - 0028-0836 .- 1476-4687. ; 540:7633, s. 453-457
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Tidskriftsartikel (refereegranskat)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)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2,3. 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 site4–6. 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 XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8,9, 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 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10–13. 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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| 14. |
- Smolentsev, Grigory, et al.
(författare)
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X-ray emission spectroscopy to study Ligand Valence Orbitals in Mn coordination complexes
- 2009
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Ingår i: Journal of the American Chemical Society. - : ACS Publications. - 0002-7863 .- 1520-5126. ; 131:36, s. 13161-13167
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Tidskriftsartikel (refereegranskat)abstract
- We discuss a spectroscopic method to determine the character of chemical bonding and for the identification of metal ligands in coordination and bioinorganic chemistry. It is based on the analysis of satellite lines in X-ray emission spectra that arise from transitions between valence orbitals and the metal ion 1s level (valence-to-core XES). The spectra, in connection with calculations based on density functional theory (DFT), provide information that is complementary to other spectroscopic techniques, in particular X-ray absorption (XANES and EXAFS). The spectral shape is sensitive to protonation of ligands and allows ligands, which differ only slightly in atomic number (e.g., C, N, O...), to be distinguished. A theoretical discussion of the main spectral features is presented in terms of molecular orbitals for a series of Mn model systems: [Mn(H2O)6]2+, [Mn(H2O)5OH]+, and [Mn(H2O)5NH3]2+. An application of the method, with comparison between theory and experiment, is presented for the solvated Mn2+ ion in water and three Mn coordination complexes, namely [LMn(acac)N3]BPh4, [LMn(B2O3Ph2)(ClO4)], and [LMn(acac)N]BPh4, where L represents 1,4,7-trimethyl-1,4,7-triazacyclononane, acac stands for the 2,4-pentanedionate anion, and B2O3Ph2 represents the 1,3-diphenyl-1,3-dibora-2-oxapropane-1,3-diolato dianion.
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| 15. |
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| 16. |
- Zein, Samir, et al.
(författare)
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Focusing the view on nature's water-splitting catalyst
- 2008
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : ROYAL SOC. - 0962-8436 .- 1471-2970. ; 363:1494, s. 1167-1177
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Tidskriftsartikel (refereegranskat)abstract
- Nature invented a catalyst about 3 Gyr ago, which splits water with high efficiency into molecular oxygen and hydrogen equivalents (protons and electrons). This reaction is energetically driven by sunlight and the active centre contains relatively cheap and abundant metals: manganese and calcium. This biological system therefore forms the paradigm for all man-made attempts for direct solar fuel production, and several studies are underway to determine the electronic and geometric structures of this catalyst. In this report we briefly summarize the problems and the current status of these efforts and propose a density functional theory-based strategy for obtaining a reliable high-resolution structure of this unique catalyst that includes both the inorganic core and the first ligand sphere.
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