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Article ; Online: Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography.

Makita, Hiroki / Simon, Philipp S / Kern, Jan / Yano, Junko / Yachandra, Vittal K

2023 Volume 80, Page(s) 102604

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 ...

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.
MeSH term(s)	Synchrotrons ; Electrons ; Crystallography, X-Ray ; Spectrum Analysis ; Lasers
Language	English
Publishing date	2023-05-04
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2023.102604
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Article ; Online: Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes.

Bergmann, Uwe / Kern, Jan / Schoenlein, Robert W / Wernet, Philippe / Yachandra, Vittal K / Yano, Junko

Nature reviews. Physics

2021 Volume 3, Issue 4, Page(s) 264–282

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 ... ...

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.
Language	English
Publishing date	2021-03-19
Publishing country	England
Document type	Journal Article
ISSN	2522-5820
ISSN (online)	2522-5820
DOI	10.1038/s42254-021-00289-3
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Article ; Online: Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.

Doyle, Margaret D / Bhowmick, Asmit / Wych, David C / Lassalle, Louise / Simon, Philipp S / Holton, James / Sauter, Nicholas K / Yachandra, Vittal K / Kern, Jan F / Yano, Junko / Wall, Michael E

Journal of the American Chemical Society

2023 Volume 145, Issue 27, Page(s) 14621–14635

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), ...

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 S
Language	English
Publishing date	2023-06-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c01412
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Article ; Online: Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function.

Hussein, Rana / Ibrahim, Mohamed / Bhowmick, Asmit / Simon, Philipp S / Bogacz, Isabel / Doyle, Margaret D / Dobbek, Holger / Zouni, Athina / Messinger, Johannes / Yachandra, Vittal K / Kern, Jan F / Yano, Junko

Photosynthesis research

2023 Volume 158, Issue 2, Page(s) 91–107

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 ... ...

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 Mn
MeSH term(s)	Protons ; Photosystem II Protein Complex/metabolism ; Water/metabolism ; Cryoelectron Microscopy ; Oxidation-Reduction
Chemical Substances	Protons ; Photosystem II Protein Complex ; Water (059QF0KO0R)
Language	English
Publishing date	2023-06-02
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	1475688-2
ISSN	1573-5079 ; 0166-8595
ISSN (online)	1573-5079
ISSN	0166-8595
DOI	10.1007/s11120-023-01018-w
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Article: Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs.

Bogacz, Isabel / Makita, Hiroki / Simon, Philipp S / Zhang, Miao / Doyle, Margaret D / Chatterjee, Ruchira / Fransson, Thomas / Weninger, Clemens / Fuller, Franklin / Gee, Leland / Sato, Takahiro / Seaberg, Matthew / Alonso-Mori, Roberto / Bergmann, Uwe / Yachandra, Vittal K / Kern, Jan / Yano, Junko

Pure and applied chemistry. Chimie pure et appliquee

2023 Volume 95, Issue 8, Page(s) 891–897

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 ... ...

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 Mn
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article
ZDB-ID	1514-3
ISSN	0033-4545
ISSN	0033-4545
DOI	10.1515/pac-2023-0213
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Article ; Online: Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers.

Kern, Jan / Yachandra, Vittal K / Yano, Junko

Current opinion in structural biology

2015 Volume 34, Page(s) 87–98

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 ...

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.
MeSH term(s)	Binding Sites ; Crystallography, X-Ray ; Lasers ; Metalloproteins/chemistry ; Metals/chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation ; Spectrum Analysis ; Temperature
Chemical Substances	Metalloproteins ; Metals
Language	English
Publishing date	2015-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2015.07.014
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Article ; Online: Calcium in the oxygen-evolving complex: structural and mechanistic role determined by X-ray spectroscopy.

Yachandra, Vittal K / Yano, Junko

Journal of photochemistry and photobiology. B, Biology

2011 Volume 104, Issue 1-2, Page(s) 51–59

Abstract: This review describes the results from X-ray Absorption Spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water-oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy ... ...

Abstract	This review describes the results from X-ray Absorption Spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water-oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy studies using Ca or Sr-substituted PS II samples that established the presence of a MnCa heteronuclear structure and its orientation, and the most recent Sr X-ray spectroscopy study using biosynthetically prepared Sr-containing PS II in the various S-states that provide important insights into the requirement for Ca in the mechanism of the Mn(4)Ca catalytic center.
MeSH term(s)	Calcium/chemistry ; Calcium/physiology ; Catalytic Domain ; Oxygen/chemistry ; Photosystem II Protein Complex/chemistry ; Photosystem II Protein Complex/metabolism ; X-Ray Absorption Spectroscopy
Chemical Substances	Photosystem II Protein Complex ; Oxygen (S88TT14065) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2011-03-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	623022-2
ISSN	1873-2682 ; 1011-1344
ISSN (online)	1873-2682
ISSN	1011-1344
DOI	10.1016/j.jphotobiol.2011.02.019
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Article ; Online: Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs

FEBS Letters. 2023 Jan., v. 597, no. 1 p.30-37

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 ... ...

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 Mn₄CaO₅ complex, in the intermediate Sᵢ (i = 0–4)‐states of the Kok cycle, obtained using XFELs.
Keywords	X-radiation ; ambient temperature ; oxidation ; oxygen production ; photosynthesis ; spectroscopy
Language	English
Dates of publication	2023-01
Size	p. 30-37.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14527
Database	NAL-Catalogue (AGRICOLA)

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Article: Structure of the manganese complex in photosystem II: insights from X-ray spectroscopy.

Yachandra, Vittal K

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2002 Volume 357, Issue 1426, Page(s) 1347–57; discussion 1357–8, 1367

Abstract: We have used Mn K-edge absorption and Kbeta emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X-ray scattering spectroscopy; this technique ...

Abstract	We have used Mn K-edge absorption and Kbeta emission spectroscopy to determine the oxidation states of the Mn complex in the various S states. We have started exploring the new technique of resonant inelastic X-ray scattering spectroscopy; this technique can be characterized as a Raman process that uses K-edge energies (1s to 4p, ca. 6550 eV) to obtain L-edge-like spectra (2p to 3d, ca. 650 eV). The relevance of these data to the oxidation states and structure of the Mn complex is presented. We have obtained extended X-ray absorption fine structure data from the S(0) and S(3) states and observed heterogeneity in the Mn-Mn distances leading us to conclude that there may be three rather than two di-mu-oxo-bridged units present per tetranuclear Mn cluster. In addition, we have obtained data using Ca and Sr X-ray spectroscopy that provide evidence for a heteronuclear Mn-Ca cluster. The possibility of three di-mu-oxo-bridged Mn-Mn moieties and the proximity of Ca is incorporated into developing structural models for the Mn cluster. The involvement of bridging and terminal O ligands of Mn in the mechanism of oxygen evolution is discussed in the context of our X-ray spectroscopy results.
MeSH term(s)	Binding Sites ; Calcium ; Fourier Analysis ; Manganese/chemistry ; Manganese/metabolism ; Molecular Structure ; Oxidation-Reduction ; Oxygen/metabolism ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Photosystem II Protein Complex ; Spectrometry, X-Ray Emission ; Strontium
Chemical Substances	Photosynthetic Reaction Center Complex Proteins ; Photosystem II Protein Complex ; Manganese (42Z2K6ZL8P) ; Oxygen (S88TT14065) ; Calcium (SY7Q814VUP) ; Strontium (YZS2RPE8LE)
Language	English
Publishing date	2002-10-29
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	208382-6
ISSN	1471-2970 ; 0962-8436 ; 0080-4622 ; 0264-3839
ISSN (online)	1471-2970
ISSN	0962-8436 ; 0080-4622 ; 0264-3839
DOI	10.1098/rstb.2002.1133
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Article ; Online: Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography.

IUCrJ

2023 Volume 10, Issue Pt 6, Page(s) 642–655

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 ... ...

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 CO
Language	English
Publishing date	2023-11-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2754953-7
ISSN	2052-2525 ; 2052-2525
ISSN (online)	2052-2525
ISSN	2052-2525
DOI	10.1107/S2052252523008928
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