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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCRJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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52
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Sipka G, Magyar M, Mezzetti A, Akhtar P, Zhu Q, Xiao Y, Han G, Santabarbara S, Shen JR, Lambrev PH, Garab G. Light-adapted charge-separated state of photosystem II: structural and functional dynamics of the closed reaction center. THE PLANT CELL 2021; 33:1286-1302. [PMID: 33793891 PMCID: PMC8225241 DOI: 10.1093/plcell/koab008] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/13/2020] [Indexed: 05/04/2023]
Abstract
Photosystem II (PSII) uses solar energy to oxidize water and delivers electrons for life on Earth. The photochemical reaction center of PSII is known to possess two stationary states. In the open state (PSIIO), the absorption of a single photon triggers electron-transfer steps, which convert PSII into the charge-separated closed state (PSIIC). Here, by using steady-state and time-resolved spectroscopic techniques on Spinacia oleracea and Thermosynechococcus vulcanus preparations, we show that additional illumination gradually transforms PSIIC into a light-adapted charge-separated state (PSIIL). The PSIIC-to-PSIIL transition, observed at all temperatures between 80 and 308 K, is responsible for a large part of the variable chlorophyll-a fluorescence (Fv) and is associated with subtle, dark-reversible reorganizations in the core complexes, protein conformational changes at noncryogenic temperatures, and marked variations in the rates of photochemical and photophysical reactions. The build-up of PSIIL requires a series of light-induced events generating rapidly recombining primary radical pairs, spaced by sufficient waiting times between these events-pointing to the roles of local electric-field transients and dielectric relaxation processes. We show that the maximum fluorescence level, Fm, is associated with PSIIL rather than with PSIIC, and thus the Fv/Fm parameter cannot be equated with the quantum efficiency of PSII photochemistry. Our findings resolve the controversies and explain the peculiar features of chlorophyll-a fluorescence kinetics, a tool to monitor the functional activity and the structural-functional plasticity of PSII in different wild-types and mutant organisms and under stress conditions.
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Affiliation(s)
- G�bor Sipka
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Melinda Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Alberto Mezzetti
- Universit� Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91191 Gif-sur-Yvette, France
- Laboratoire de R�activit� de Surface UMR 7197, Sorbonne University, Paris, France
| | - Parveen Akhtar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- ELI-ALPS, ELI-HU Nonprofit Ltd., Szeged, Hungary
| | - Qingjun Zhu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yanan Xiao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guangye Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Stefano Santabarbara
- Photosynthetic Research Unit, Institute of Biophysics, National Research Council of Italy, Milano, Italy
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Petar H Lambrev
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Author for correspondence: (G.G.), (P.H.L.)
| | - Győző Garab
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Author for correspondence: (G.G.), (P.H.L.)
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53
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Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future. CRYSTALS 2021. [DOI: 10.3390/cryst11050521] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources.
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54
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Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021; 296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of their evolutionary selection in carrying out their biological functions. Although the dynamics are more difficult to observe than a static, average structure, we are beginning to observe these dynamics and form sound mechanistic connections between structure, dynamics, and function. This progress is highlighted in case studies from myoglobin and adenylate kinase to the ribosome and molecular motors where these molecules are being probed with a multitude of techniques across many timescales. New approaches to time-resolved crystallography are allowing simple “movies” to be taken of proteins in action, and new methods of mapping the variations in cryo-electron microscopy are emerging to reveal a more complete description of life’s machines. The results of these new methods are aided in their dissemination by continual improvements in curation and distribution by the Protein Data Bank and their partners around the world.
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Affiliation(s)
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA; Department of Chemistry, Rice University, Houston, Texas, USA.
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55
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Li H, Nakajima Y, Nomura T, Sugahara M, Yonekura S, Chan SK, Nakane T, Yamane T, Umena Y, Suzuki M, Masuda T, Motomura T, Naitow H, Matsuura Y, Kimura T, Tono K, Owada S, Joti Y, Tanaka R, Nango E, Akita F, Kubo M, Iwata S, Shen JR, Suga M. Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography. IUCRJ 2021; 8:431-443. [PMID: 33953929 PMCID: PMC8086164 DOI: 10.1107/s2052252521002177] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.
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Affiliation(s)
- Hongjie Li
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shinichiro Yonekura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Siu Kit Chan
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Takanori Nakane
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Yamane
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Yasufumi Umena
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Taiki Motomura
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, -1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kitaku, Okayama, Okayama 700-8530, Japan
- Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan
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56
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Ramakrishnan S, Stagno JR, Magidson V, Heinz WF, Wang YX. Dependence of phase transition uniformity on crystal sizes characterized using birefringence. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:034301. [PMID: 34235229 PMCID: PMC8248999 DOI: 10.1063/4.0000098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 μm2) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.
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Affiliation(s)
- Saminathan Ramakrishnan
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Jason R. Stagno
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
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57
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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58
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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. NATURE REVIEWS. PHYSICS 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] [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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59
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Zabret J, Bohn S, Schuller SK, Arnolds O, Möller M, Meier-Credo J, Liauw P, Chan A, Tajkhorshid E, Langer JD, Stoll R, Krieger-Liszkay A, Engel BD, Rudack T, Schuller JM, Nowaczyk MM. Structural insights into photosystem II assembly. NATURE PLANTS 2021; 7:524-538. [PMID: 33846594 PMCID: PMC8094115 DOI: 10.1038/s41477-021-00895-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 05/07/2023]
Abstract
Biogenesis of photosystem II (PSII), nature's water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate from Thermosynechococcus elongatus at 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28 and Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (QB) and replace the bicarbonate ligand of non-haem iron with glutamate, a structural motif found in reaction centres of non-oxygenic photosynthetic bacteria. These results reveal mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the Mn4CaO5 cluster, which performs the unique water-splitting reaction.
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Affiliation(s)
- Jure Zabret
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Stefan Bohn
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sandra K Schuller
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- CryoEM of Molecular Machines, SYNMIKRO Research Center and Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Oliver Arnolds
- Biomolecular Spectroscopy and RUBiospek|NMR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Madeline Möller
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Pasqual Liauw
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Aaron Chan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Raphael Stoll
- Biomolecular Spectroscopy and RUBiospek|NMR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, Bochum, Germany.
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
| | - Jan M Schuller
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
- CryoEM of Molecular Machines, SYNMIKRO Research Center and Department of Chemistry, Philipps University of Marburg, Marburg, Germany.
| | - Marc M Nowaczyk
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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60
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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61
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Beyond X-rays: an overview of emerging structural biology methods. Emerg Top Life Sci 2021; 5:221-230. [DOI: 10.1042/etls20200272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/27/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.
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62
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Stohrer C, Horrell S, Meier S, Sans M, von Stetten D, Hough M, Goldman A, Monteiro DCF, Pearson AR. Homogeneous batch micro-crystallization of proteins from ammonium sulfate. Acta Crystallogr D Struct Biol 2021; 77:194-204. [PMID: 33559608 PMCID: PMC7869895 DOI: 10.1107/s2059798320015454] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/21/2020] [Indexed: 01/19/2023] Open
Abstract
The emergence of X-ray free-electron lasers has led to the development of serial macromolecular crystallography techniques, making it possible to study smaller and more challenging crystal systems and to perform time-resolved studies on fast time scales. For most of these studies the desired crystal size is limited to a few micrometres, and the generation of large amounts of nanocrystals or microcrystals of defined size has become a bottleneck for the wider implementation of these techniques. Despite this, methods to reliably generate microcrystals and fine-tune their size have been poorly explored. Working with three different enzymes, L-aspartate α-decarboxylase, copper nitrite reductase and copper amine oxidase, the precipitating properties of ammonium sulfate were exploited to quickly transition from known vapour-diffusion conditions to reproducible, large-scale batch crystallization, circumventing the tedious determination of phase diagrams. Furthermore, the specific ammonium sulfate concentration was used to fine-tune the crystal size and size distribution. Ammonium sulfate is a common precipitant in protein crystallography, making these findings applicable to many crystallization systems to facilitate the production of large amounts of microcrystals for serial macromolecular crystallography experiments.
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Affiliation(s)
- Claudia Stohrer
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sam Horrell
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Adrian Goldman
- Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
- Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, FIN-00014 Helsinki, Finland
| | - Diana C. F. Monteiro
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
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63
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Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Methods Mol Biol 2021; 2305:203-228. [PMID: 33950392 DOI: 10.1007/978-1-0716-1406-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.
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64
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Mäusle SM, Abzaliyeva A, Greife P, Simon PS, Perez R, Zilliges Y, Dau H. Activation energies for two steps in the S 2→ S 3 transition of photosynthetic water oxidation from time-resolved single-frequency infrared spectroscopy. J Chem Phys 2020; 153:215101. [PMID: 33291916 DOI: 10.1063/5.0027995] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The mechanism of water oxidation by the Photosystem II (PSII) protein-cofactor complex is of high interest, but specifically, the crucial coupling of protonation dynamics to electron transfer (ET) and dioxygen chemistry remains insufficiently understood. We drove spinach-PSII membranes by nanosecond-laser flashes synchronously through the water-oxidation cycle and traced the PSII processes by time-resolved single-frequency infrared (IR) spectroscopy in the spectral range of symmetric carboxylate vibrations of protein side chains. After the collection of IR-transients from 100 ns to 1 s, we analyzed the proton-removal step in the S2 ⇒ S3 transition, which precedes the ET that oxidizes the Mn4CaOx-cluster. Around 1400 cm-1, pronounced changes in the IR-transients reflect this pre-ET process (∼40 µs at 20 °C) and the ET step (∼300 µs at 20 °C). For transients collected at various temperatures, unconstrained multi-exponential simulations did not provide a coherent set of time constants, but constraining the ET time constants to previously determined values solved the parameter correlation problem and resulted in an exceptionally high activation energy of 540 ± 30 meV for the pre-ET step. We assign the pre-ET step to deprotonation of a group that is re-protonated by accepting a proton from the substrate-water, which binds concurrently with the ET step. The analyzed IR-transients disfavor carboxylic-acid deprotonation in the pre-ET step. Temperature-dependent amplitudes suggest thermal equilibria that determine how strongly the proton-removal step is reflected in the IR-transients. Unexpectedly, the proton-removal step is only weakly reflected in the 1400 cm-1 transients of PSII core complexes of a thermophilic cyanobacterium (T. elongatus).
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Affiliation(s)
- Sarah M Mäusle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Aiganym Abzaliyeva
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Paul Greife
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Philipp S Simon
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Rebeca Perez
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Yvonne Zilliges
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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65
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Zhu L, Chen X, Abola EE, Jing L, Liu W. Serial Crystallography for Structure-Based Drug Discovery. Trends Pharmacol Sci 2020; 41:830-839. [PMID: 32950259 PMCID: PMC7572805 DOI: 10.1016/j.tips.2020.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/17/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
Rational drug discovery has greatly accelerated the development of safer and more efficacious therapeutics, assisted significantly by insights from experimentally determined 3D structures of ligands in complex with their targets. Serial crystallography (SX) with X-ray free-electron lasers has enabled structural determination using micrometer- or nanometer-size crystals. This technology, applied in the past decade to solve structures of notoriously difficult-to-study drug targets at room temperature, has now been adapted for use in synchrotron radiation facilities. Ultrashort time scales allow time-resolved characterization of dynamic structural changes and pave the road to study the molecular mechanisms by 'molecular movie.' This article summarizes the latest progress in SX technology and deliberates its demanding applications in future structure-based drug discovery.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaoyu Chen
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Enrique E Abola
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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66
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Ren Z, Wang C, Shin H, Bandara S, Kumarapperuma I, Ren MY, Kang W, Yang X. An automated platform for in situ serial crystallography at room temperature. IUCRJ 2020; 7:1009-1018. [PMID: 33209315 PMCID: PMC7642789 DOI: 10.1107/s2052252520011288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Direct observation of functional motions in protein structures is highly desirable for understanding how these nanomachineries of life operate at the molecular level. Because cryogenic temperatures are non-physiological and may prohibit or even alter protein structural dynamics, it is necessary to develop robust X-ray diffraction methods that enable routine data collection at room temperature. We recently reported a crystal-on-crystal device to facilitate in situ diffraction of protein crystals at room temperature devoid of any sample manipulation. Here an automated serial crystallography platform based on this crystal-on-crystal technology is presented. A hardware and software prototype has been implemented, and protocols have been established that allow users to image, recognize and rank hundreds to thousands of protein crystals grown on a chip in optical scanning mode prior to serial introduction of these crystals to an X-ray beam in a programmable and high-throughput manner. This platform has been tested extensively using fragile protein crystals. We demonstrate that with affordable sample consumption, this in situ serial crystallography technology could give rise to room-temperature protein structures of higher resolution and superior map quality for those protein crystals that encounter difficulties during freezing. This serial data collection platform is compatible with both monochromatic oscillation and Laue methods for X-ray diffraction and presents a widely applicable approach for static and dynamic crystallographic studies at room temperature.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Sepalika Bandara
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Michael Y. Ren
- A. James Clark School of Engineering, University of Maryland, College Park, MD 20742, USA
| | - Weijia Kang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL 60607, USA
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67
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Abstract
![]()
Due
to the recent advances in X-ray free electron laser techniques,
bilin-containing cyanobacteriochrome photoreceptors have become prime
targets for the ever-expanding field of time-resolved structural biology.
However, to facilitate these challenging studies, it is essential
that the time scales of any structural changes during the photocycles
of cyanobacteriochromes be established. Here, we have used visible
and infrared transient absorption spectroscopy to probe the photocycle
of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple
orders of magnitude from picoseconds to seconds. Localized changes
in the bilin binding pocket occur in picoseconds to nanoseconds, followed
by more large-scale changes in protein structure, including formation
and breakage of a second thioether linkage, in microseconds to milliseconds.
The characterization of the entire photocycle will provide a vital
frame of reference for future time-resolved structural studies of
this model photoreceptor.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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68
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Vakili M, Vasireddi R, Gwozdz PV, Monteiro DCF, Heymann M, Blick RH, Trebbin M. Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:085108. [PMID: 32872940 DOI: 10.1063/5.0012806] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Free liquid jets are a common sample delivery method in serial femtosecond x-ray (SFX) crystallography. Gas dynamic virtual nozzles (GDVNs) use an outer gas stream to focus a liquid jet down to a few micrometers in diameter. Such nozzles can be fabricated through various methods (capillary grinding, soft lithography, digital light processing, and two-photon polymerization) and materials, such as glass, polydimethylsiloxane, and photosensitive polyacrylates. Here, we present a broadly accessible, rapid prototyping laser ablation approach to micromachine solvent-resistant and inert Kapton polyimide foils with highly reproducible geometric features that result in 3D flow-focused GDVNs suitable for crystallography experiments at synchrotrons and free-electron laser facilities.
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Affiliation(s)
- Mohammad Vakili
- Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ramakrishna Vasireddi
- Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Paul V Gwozdz
- Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diana C F Monteiro
- Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Heymann
- Center for Free-Electron Laser Science (CFEL), DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Robert H Blick
- Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Martin Trebbin
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA
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69
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Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers. CRYSTALS 2020. [DOI: 10.3390/cryst10070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs.
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70
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EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm. CRYSTALS 2020. [DOI: 10.3390/cryst10070588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.
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71
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Cox N, Pantazis DA, Lubitz W. Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data. Annu Rev Biochem 2020; 89:795-820. [DOI: 10.1146/annurev-biochem-011520-104801] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOxcomplex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.
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Affiliation(s)
- Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra ACT 2601, Australia
| | | | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim an der Ruhr, Germany
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72
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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: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [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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73
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First Experiments in Structural Biology at the European X-ray Free-Electron Laser. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10103642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination from sub-micron crystals as well as radiation-sensitive proteins. The European X-Ray Free-Electron Laser (EuXFEL), with its first light in 2017, ushered in a new era for ultrabright X-ray sources by providing an unparalleled megahertz-pulse repetition rate, with orders of magnitude more pulses per second than previous XFEL sources. This rapid pulse frequency has significant implications for structure determination; not only will data collection be faster (resulting in more structures per unit time), but experiments requiring large quantities of data, such as time-resolved structures, become feasible in a reasonable amount of experimental time. Early experiments at the SPB/SFX instrument of the EuXFEL demonstrate how such closely-spaced pulses can be successfully implemented in otherwise challenging experiments, such as time-resolved studies.
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74
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Li X, Li C, Liu H. SPIND-TC: an indexing method for two-color X-ray diffraction data. Acta Crystallogr A Found Adv 2020; 76:369-375. [PMID: 32356787 PMCID: PMC7233013 DOI: 10.1107/s2053273320001916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/10/2020] [Indexed: 11/24/2022] Open
Abstract
Recent developments of two-color operation modes at X-ray free-electron laser facilities provide new research opportunities, such as X-ray pump/X-ray probe experiments and multiple-wavelength anomalous dispersion phasing methods. However, most existing indexing methods were developed for indexing diffraction data from monochromatic X-ray beams. Here, a new algorithm is presented for indexing two-color diffraction data, as an extension of the sparse-pattern indexing algorithm SPIND, which has been demonstrated to be capable of indexing diffraction patterns with as few as five peaks. The principle and implementation of the two-color indexing method, SPIND-TC, are reported in this paper. The algorithm was tested on both simulated and experimental data of protein crystals. The results show that the diffraction data can be accurately indexed in both cases. Source codes are publicly available at https://github.com/lixx11/SPIND-TC.
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Affiliation(s)
- Xuanxuan Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, China
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, China
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75
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Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213183] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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76
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Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
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77
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Petrie S, Terrett R, Stranger R, Pace RJ. Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S 3 State Crystal Structures of Photosystem II. Chemphyschem 2020; 21:785-801. [PMID: 32133758 DOI: 10.1002/cphc.201901106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Indexed: 11/06/2022]
Abstract
Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S3 structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S1 structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5-O6 separation of ∼1.5 Å. In the latest S3 variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S3 , closely ligating one Mn, with O5-Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018) this oxidation state assumption predicted two energetically close S3 structural forms, one with the metal centres and O5 (as OH- ) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H2 O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S3 structure is also a likely superposition of forms, but with O5 (as OH- ) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural 'lability' of the WOC centre in the S3 state, which is likely catalytically relevant to its water splitting function.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Richard Terrett
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
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78
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Niozu A, Kumagai Y, Nishiyama T, Fukuzawa H, Motomura K, Bucher M, Asa K, Sato Y, Ito Y, Takanashi T, You D, Ono T, Li Y, Kukk E, Miron C, Neagu L, Callegari C, Di Fraia M, Rossi G, Galli DE, Pincelli T, Colombo A, Owada S, Tono K, Kameshima T, Joti Y, Katayama T, Togashi T, Yabashi M, Matsuda K, Nagaya K, Bostedt C, Ueda K. Characterizing crystalline defects in single nanoparticles from angular correlations of single-shot diffracted X-rays. IUCRJ 2020; 7:276-286. [PMID: 32148855 PMCID: PMC7055387 DOI: 10.1107/s205225252000144x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Characterizing and controlling the uniformity of nanoparticles is crucial for their application in science and technology because crystalline defects in the nanoparticles strongly affect their unique properties. Recently, ultra-short and ultra-bright X-ray pulses provided by X-ray free-electron lasers (XFELs) opened up the possibility of structure determination of nanometre-scale matter with Å spatial resolution. However, it is often difficult to reconstruct the 3D structural information from single-shot X-ray diffraction patterns owing to the random orientation of the particles. This report proposes an analysis approach for characterizing defects in nanoparticles using wide-angle X-ray scattering (WAXS) data from free-flying single nanoparticles. The analysis method is based on the concept of correlated X-ray scattering, in which correlations of scattered X-ray are used to recover detailed structural information. WAXS experiments of xenon nanoparticles, or clusters, were conducted at an XFEL facility in Japan by using the SPring-8 Ångstrom compact free-electron laser (SACLA). Bragg spots in the recorded single-shot X-ray diffraction patterns showed clear angular correlations, which offered significant structural information on the nanoparticles. The experimental angular correlations were reproduced by numerical simulation in which kinematical theory of diffraction was combined with geometric calculations. We also explain the diffuse scattering intensity as being due to the stacking faults in the xenon clusters.
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Affiliation(s)
- Akinobu Niozu
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Yoshiaki Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Toshiyuki Nishiyama
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Hironobu Fukuzawa
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Koji Motomura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Maximilian Bucher
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Kazuki Asa
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Yuhiro Sato
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Yuta Ito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Tsukasa Takanashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Taishi Ono
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Yiwen Li
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - Catalin Miron
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191, Gif-sur-Yvette, France
- Extreme Light Infrastructure – Nuclear Physics (ELI–NP), Horia Hulubei National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125 Magurele, Jud. Ilfov, Romania
| | - Liviu Neagu
- Extreme Light Infrastructure – Nuclear Physics (ELI–NP), Horia Hulubei National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125 Magurele, Jud. Ilfov, Romania
- National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor PO Box MG-36, 077125 Magurele, Jud. Ilfov, Romania
| | - Carlo Callegari
- Elettra – Sincrotrone Trieste S.C.p.A, 34149 Basovizza, Trieste, Italy
| | - Michele Di Fraia
- Elettra – Sincrotrone Trieste S.C.p.A, 34149 Basovizza, Trieste, Italy
| | - Giorgio Rossi
- Department of Physics, Università degli Studi di Milano, Via G. Celoria 16, I-20133 Milano, Italy
| | - Davide E. Galli
- Department of Physics, Università degli Studi di Milano, Via G. Celoria 16, I-20133 Milano, Italy
| | - Tommaso Pincelli
- Department of Physics, Università degli Studi di Milano, Via G. Celoria 16, I-20133 Milano, Italy
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4–6, 14195 Berlin, Germany
| | - Alessandro Colombo
- Department of Physics, ETH Zürich, Stefano-Franscini-Platz 5, 8049 Zürich, Switzerland
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | - Tadashi Togashi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | | | | | - Kiyonobu Nagaya
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
- Laboratory for Femtochemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
- LUXS Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kiyoshi Ueda
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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79
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Mehrabi P, Müller-Werkmeister HM, Leimkohl JP, Schikora H, Ninkovic J, Krivokuca S, Andriček L, Epp SW, Sherrell D, Owen RL, Pearson AR, Tellkamp F, Schulz EC, Miller RJD. The HARE chip for efficient time-resolved serial synchrotron crystallography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:360-370. [PMID: 32153274 PMCID: PMC7064102 DOI: 10.1107/s1600577520000685] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 05/02/2023]
Abstract
Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.
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Affiliation(s)
- Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henrike M. Müller-Werkmeister
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Jan-Philipp Leimkohl
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jelena Ninkovic
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Silvia Krivokuca
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Ladislav Andriček
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Sascha W. Epp
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Darren Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Arwen R. Pearson
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Friedjof Tellkamp
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
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80
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Kato Y, Haniu S, Nakajima Y, Akita F, Shen JR, Noguchi T. FTIR Microspectroscopic Analysis of the Water Oxidation Reaction in a Single Photosystem II Microcrystal. J Phys Chem B 2020; 124:121-127. [PMID: 31825617 DOI: 10.1021/acs.jpcb.9b10154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microcrystals of photosystem II (PSII) have recently been used to investigate the intermediate structures of the water oxidizing complex during water oxidation by serial femtosecond crystallography using X-ray free electron lasers. To clarify the water oxidation mechanism, it is crucial to know whether the reaction proceeds properly in the microcrystals. In this work, we monitored the water oxidation reaction in a single PSII microcrystal using Fourier transform infrared (FTIR) microspectroscopy with the transmission method. Flash-induced micro-FTIR difference spectra of S-state transitions in a PSII microcrystal showed features virtually identical to the corresponding spectra previously obtained using the attenuated total reflection method for multiple microcrystals, representing the reactions near the crystal surface, as well as the spectra in solution. This observation indicates that the reaction processes of water oxidation proceed with relatively high efficiencies retaining native intermediate structures in the entire inside of a PSII microcrystal.
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Affiliation(s)
- Yuki Kato
- Division of Material Science, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan
| | - Satoshi Haniu
- Division of Material Science, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology , Okayama University , 3-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology , Okayama University , 3-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan.,Japan Science and Technology Agency, PRESTO , 4-1-8 Honcho , Kawaguchi, Saitama 332-0012 , Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology , Okayama University , 3-1-1 Tsushima-naka , Kita-ku, Okayama 700-8530 , Japan
| | - Takumi Noguchi
- Division of Material Science, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan
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81
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Limongelli V. Ligand binding free energy and kinetics calculation in 2020. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1455] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science – Center for Computational Medicine in Cardiology Università della Svizzera italiana (USI) Lugano Switzerland
- Department of Pharmacy University of Naples “Federico II” Naples Italy
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82
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Leonarski F, Mozzanica A, Brückner M, Lopez-Cuenca C, Redford S, Sala L, Babic A, Billich H, Bunk O, Schmitt B, Wang M. JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014305. [PMID: 32128347 PMCID: PMC7044001 DOI: 10.1063/1.5143480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 05/08/2023]
Abstract
In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU with 10 Mpixel at 2.2 kHz in the future. In this context, we highlight the challenges for computer architecture and how these challenges can be addressed with innovative hardware including IBM POWER9 servers and field-programmable gate arrays. We discuss also data science challenges, showing the effect of rounding and lossy compression schemes on the MX JUNGFRAU detector images.
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Affiliation(s)
- Filip Leonarski
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Martin Brückner
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Carlos Lopez-Cuenca
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Sophie Redford
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Andrej Babic
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Oliver Bunk
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Bernd Schmitt
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Meitian Wang
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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83
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Zhao F, Zhang B, Yan E, Sun B, Wang Z, He J, Yin D. A guide to sample delivery systems for serial crystallography. FEBS J 2019; 286:4402-4417. [PMID: 31618529 DOI: 10.1111/febs.15099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Feng‐Zhu Zhao
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bin Zhang
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Er‐Kai Yan
- School of Life Sciences Northwestern Polytechnical University Xi'an China
| | - Bo Sun
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Zhi‐Jun Wang
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Jian‐Hua He
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
| | - Da‐Chuan Yin
- School of Life Sciences Northwestern Polytechnical University Xi'an China
- Shenzhen Research Institute Northwestern Polytechnical University Shenzhen China
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84
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Suga M, Shimada A, Akita F, Shen JR, Tosha T, Sugimoto H. Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 2019; 1864:129466. [PMID: 31678142 DOI: 10.1016/j.bbagen.2019.129466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
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Affiliation(s)
- Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan..
| | - Atsuhiro Shimada
- Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Takehiko Tosha
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan..
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85
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A novel chlorophyll protein complex in the repair cycle of photosystem II. Proc Natl Acad Sci U S A 2019; 116:21907-21913. [PMID: 31594847 DOI: 10.1073/pnas.1909644116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In oxygenic photosynthetic organisms, photosystem II (PSII) is a unique membrane protein complex that catalyzes light-driven oxidation of water. PSII undergoes frequent damage due to its demanding photochemistry. It must undergo a repair and reassembly process following photodamage, many facets of which remain unknown. We have discovered a PSII subcomplex that lacks 5 key PSII core reaction center polypeptides: D1, D2, PsbE, PsbF, and PsbI. This pigment-protein complex does contain the PSII core antenna proteins CP47 and CP43, as well as most of their associated low molecular mass subunits, and the assembly factor Psb27. Immunoblotting, mass spectrometry, and ultrafast spectroscopic results support the absence of a functional reaction center in this complex, which we call the "no reaction center" complex (NRC). Analytical ultracentrifugation and clear native PAGE analysis show that NRC is a stable pigment-protein complex and not a mixture of free CP47 and CP43 proteins. NRC appears in higher abundance in cells exposed to high light and impaired protein synthesis, and genetic deletion of PsbO on the PSII luminal side results in an increased NRC population, indicative that NRC forms in response to photodamage as part of the PSII repair process. Our finding challenges the current model of the PSII repair cycle and implies an alternative PSII repair strategy. Formation of this complex may maximize PSII repair economy by preserving intact PSII core antennas in a single complex available for PSII reassembly, minimizing the risk of randomly diluting multiple recycling components in the thylakoid membrane following a photodamage event.
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86
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Lubitz W, Chrysina M, Cox N. Water oxidation in photosystem II. PHOTOSYNTHESIS RESEARCH 2019; 142:105-125. [PMID: 31187340 PMCID: PMC6763417 DOI: 10.1007/s11120-019-00648-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/20/2019] [Indexed: 05/18/2023]
Abstract
Biological water oxidation, performed by a single enzyme, photosystem II, is a central research topic not only in understanding the photosynthetic apparatus but also for the development of water splitting catalysts for technological applications. Great progress has been made in this endeavor following the report of a high-resolution X-ray crystallographic structure in 2011 resolving the cofactor site (Umena et al. in Nature 473:55-60, 2011), a tetra-manganese calcium complex. The electronic properties of the protein-bound water oxidizing Mn4OxCa complex are crucial to understand its catalytic activity. These properties include: its redox state(s) which are tuned by the protein matrix, the distribution of the manganese valence and spin states and the complex interactions that exist between the four manganese ions. In this short review we describe how magnetic resonance techniques, particularly EPR, complemented by quantum chemical calculations, have played an important role in understanding the electronic structure of the cofactor. Together with isotope labeling, these techniques have also been instrumental in deciphering the binding of the two substrate water molecules to the cluster. These results are briefly described in the context of the history of biological water oxidation with special emphasis on recent work using time resolved X-ray diffraction with free electron lasers. It is shown that these data are instrumental for developing a model of the biological water oxidation cycle.
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Affiliation(s)
- Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | - Maria Chrysina
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim/Ruhr, Germany
| | - Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra, Australia
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87
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Cho S, Baker RP, Ji M, Urban S. Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Nat Struct Mol Biol 2019; 26:910-918. [PMID: 31570873 PMCID: PMC6858540 DOI: 10.1038/s41594-019-0296-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/09/2019] [Indexed: 12/04/2022]
Abstract
Protein cleavage inside the cell membrane triggers various patho-physiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, around which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.
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Affiliation(s)
- Sangwoo Cho
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rosanna P Baker
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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88
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Khakurel KP, Angelov B, Andreasson J. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Molecules 2019; 24:E3490. [PMID: 31561479 PMCID: PMC6804143 DOI: 10.3390/molecules24193490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
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Affiliation(s)
- Krishna P Khakurel
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
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89
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90
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van Thor JJ. Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:050901. [PMID: 31559317 PMCID: PMC6759419 DOI: 10.1063/1.5110685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/29/2019] [Indexed: 05/02/2023]
Abstract
Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.
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Affiliation(s)
- Jasper J. van Thor
- Molecular Biophysics, Imperial College London, London SW7 2AZ, United Kingdom
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91
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Data-driven challenges and opportunities in crystallography. Emerg Top Life Sci 2019; 3:423-432. [PMID: 33523208 PMCID: PMC7289006 DOI: 10.1042/etls20180177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.
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92
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Baba S, Shimada A, Mizuno N, Baba J, Ago H, Yamamoto M, Kumasaka T. A temperature-controlled cold-gas humidifier and its application to protein crystals with the humid-air and glue-coating method. J Appl Crystallogr 2019; 52:699-705. [PMID: 31396025 PMCID: PMC6662993 DOI: 10.1107/s1600576719006435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/06/2019] [Indexed: 11/23/2022] Open
Abstract
The room-temperature experiment has been revisited for macromolecular crystallography. Despite being limited by radiation damage, such experiments reveal structural differences depending on temperature, and it is expected that they will be able to probe structures that are physiologically alive. For such experiments, the humid-air and glue-coating (HAG) method for humidity-controlled experiments is proposed. The HAG method improves the stability of most crystals in capillary-free experiments and is applicable at both cryogenic and ambient temperatures. To expand the thermal versatility of the HAG method, a new humidifier and a protein-crystal-handling workbench have been developed. The devices provide temperatures down to 4°C and successfully maintain growth at that temperature of bovine cytochrome c oxidase crystals, which are highly sensitive to temperature variation. Hence, the humidifier and protein-crystal-handling workbench have proved useful for temperature-sensitive samples and will help reveal temperature-dependent variations in protein structures.
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Affiliation(s)
- Seiki Baba
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Nobuhiro Mizuno
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Junpei Baba
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
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93
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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94
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Krewald V, Neese F, Pantazis DA. Implications of structural heterogeneity for the electronic structure of the final oxygen-evolving intermediate in photosystem II. J Inorg Biochem 2019; 199:110797. [PMID: 31404888 DOI: 10.1016/j.jinorgbio.2019.110797] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Heterogeneity in intermediate catalytic states of the oxygen-evolving complex (OEC) of Photosystem II is known from a wide range of experimental and theoretical data, but its potential implications for the mechanism of water oxidation remain unexplored. We delineate the consequences of structural heterogeneity for the final step of the catalytic cycle by tracing the evolution of three spectroscopically relevant and structurally distinct components of the last metastable S3 state to the transient O2-evolving S4 state of the OEC. Using quantum chemical calculations, we show that each S3 isomer leads to a different electronic structure formulation for the active S4 state. Crucially, in addition to previously hypothesized Mn(IV)-oxyl species, we establish for the first time, how a genuine Mn(V)-oxo can be obtained in the catalytically active S4 state: this takes the form of a five-coordinate and locally high-spin (SMn = 1) Mn(V) site. This formulation for the S4 state evolves naturally from a preceding S3-state structural intermediate that contains a quasi-trigonal-bipyramidal Mn(IV) ion. The results strongly suggest that water binding in the S3 state is not prerequisite for reaching the oxygen-evolving S4 state of the complex, supporting the notion that both substrates are preloaded at the beginning of the catalytic cycle. This scenario allows true four-electron metal-centered hole accumulation to precede OO bond formation and hence the latter can proceed via a genuine even-electron mechanism. This can occur as intramolecular nucleophilic coupling of two oxo units synchronously with the binding of a water substrate for the next catalytic cycle.
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Affiliation(s)
- Vera Krewald
- Theoretische Chemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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95
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Zhang B, Sun L. Across the Board: Licheng Sun on the Mechanism of O-O Bond Formation in Photosystem II. CHEMSUSCHEM 2019; 12:3401-3404. [PMID: 31240851 DOI: 10.1002/cssc.201901438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 06/09/2023]
Abstract
In this series of articles, the board members of ChemSusChem discuss recent research articles that they consider of exceptional quality and importance for sustainability. This entry features Prof. L. Sun, who proposes a special mechanism for O-O bond formation in photosystem II with involvement of an MnVII -oxo species induced by charge- and structural rearrangements. In this viewpoint, Proton transfer is involved in changes of the first coordination spheres around the MnVII -oxo site on the dangling Mn4 with de- and re-coordination of carboxylates (Glu333 and Asp170).
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Affiliation(s)
- BiaoBiao Zhang
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-10044, Sweden
| | - Licheng Sun
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-10044, Sweden
- State Key Laboratory of Fine Chemicals, Institute of Artificial Photosynthesis, DUT-KTH Joint Education and Research Centre on Molecular Devices, Dalian University of Technology, Dalian, 116024, P.R. China
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96
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Kim D, Echelmeier A, Cruz Villarreal J, Gandhi S, Quintana S, Egatz-Gomez A, Ros A. Electric Triggering for Enhanced Control of Droplet Generation. Anal Chem 2019; 91:9792-9799. [PMID: 31260621 DOI: 10.1021/acs.analchem.9b01449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that uses X-ray free-electron lasers (XFEL) to determine structures of biomolecular complexes. Specifically, it benefits the study of atomic resolution structures of large membrane protein complexes and time-resolved reactions with crystallography. One major drawback of SFX studies with XFELs is the consumption of large amounts of a protein crystal sample to collect a complete X-ray diffraction data set for high-resolution crystal structures. This increases the time and resources required for sample preparation and experimentation. The intrinsic pulsed nature of all current X-ray sources is a major reason why such large amounts of sample are required. Any crystal sample that is delivered in the path of the X-ray beam during its "off-time" is wasted. To address this large sample consumption issue, we developed a 3D printed microfluidic system with integrated metal electrodes for water-in-oil droplet generation to dynamically create and manipulate aqueous droplets. We demonstrate on-demand droplet generation using DC potentials and the ability to tune the frequency of droplet generation through the application of AC potentials. More importantly, to assist with the synchronization of droplets and XFEL pulses, we show that the device can induce a phase shift in the base droplet generation frequency. This novel approach to droplet generation has the potential to reduce sample waste by more than 95% for SFX experiments with XFELs performed with liquid jets and can operate under low- and high-pressure liquid injection systems.
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Affiliation(s)
- Daihyun Kim
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Austin Echelmeier
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sahir Gandhi
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sebastian Quintana
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Ana Egatz-Gomez
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Alexandra Ros
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
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97
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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98
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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99
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Li X, Li C, Liu H. ClickX: a visualization-based program for preprocessing of serial crystallography data. J Appl Crystallogr 2019; 52:674-682. [PMID: 31236097 PMCID: PMC6557179 DOI: 10.1107/s1600576719005363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Serial crystallography is a powerful technique in structure determination using many small crystals at X-ray free-electron laser or synchrotron radiation facilities. The large diffraction data volumes require high-throughput software to preprocess the raw images for subsequent analysis. ClickX is a program designated for serial crystallography data preprocessing, capable of rapid data sorting for online feedback and peak-finding refinement by parameter optimization. The graphical user interface (GUI) provides convenient access to various operations such as pattern visualization, statistics plotting and parameter tuning. A batch job module is implemented to facilitate large-data-volume processing. A two-step geometry calibration for single-panel detectors is also integrated into the GUI, where the beam center and detector tilting angles are optimized using an ellipse center shifting method first, then all six parameters, including the photon energy and detector distance, are refined together using a residual minimization method. Implemented in Python, ClickX has good portability and extensibility, so that it can be installed, configured and used on any computing platform that provides a Python interface or common data file format. ClickX has been tested in online analysis at the Pohang Accelerator Laboratory X-ray Free-Electron Laser, Korea, and the Linac Coherent Light Source, USA. It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.
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Affiliation(s)
- Xuanxuan Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, People’s Republic of China
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, People’s Republic of China
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, ZPark II, Haidian, Beijing 100193, People’s Republic of China
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100
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Hutchison CDM, van Thor JJ. Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20170474. [PMID: 30929625 PMCID: PMC6452057 DOI: 10.1098/rsta.2017.0474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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