251
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Beyerlein KR, Adriano L, Heymann M, Kirian R, Knoška J, Wilde F, Chapman HN, Bajt S. Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:125104. [PMID: 26724070 DOI: 10.1063/1.4936843] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.
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Affiliation(s)
- K R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
| | - L Adriano
- Photon Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
| | - M Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
| | - R Kirian
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
| | - J Knoška
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - F Wilde
- Helmholtz-Zentrum Geesthacht, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - H N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
| | - S Bajt
- Photon Science, Deutsches Elektronen-Synchrotron, Notkestraβe 85, 22607 Hamburg, Germany
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252
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Nakane T, Song C, Suzuki M, Nango E, Kobayashi J, Masuda T, Inoue S, Mizohata E, Nakatsu T, Tanaka T, Tanaka R, Shimamura T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Iwata S, Sugahara M. Native sulfur/chlorine SAD phasing for serial femtosecond crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2519-25. [PMID: 26627659 PMCID: PMC4667287 DOI: 10.1107/s139900471501857x] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/04/2015] [Indexed: 12/31/2022]
Abstract
Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.
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Affiliation(s)
- Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Changyong Song
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Jun Kobayashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsuya Masuda
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shigeyuki Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toru Nakatsu
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, 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
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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253
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Abstract
X-ray crystallography, the workhorse of structural biology, has been revolutionized by the advent of serial femtosecond crystallography using X-ray free electron lasers. Here, the fast pace and history of discoveries are discussed together with current challenges and the method’s great potential to make new structural discoveries, such as the ability to generate molecular movies of biomolecules at work.
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Affiliation(s)
- Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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254
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Heinz S, Liauw P, Nickelsen J, Nowaczyk M. Analysis of photosystem II biogenesis in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:274-87. [PMID: 26592144 DOI: 10.1016/j.bbabio.2015.11.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/13/2015] [Accepted: 11/15/2015] [Indexed: 11/25/2022]
Abstract
Photosystem II (PSII), a large multisubunit membrane protein complex found in the thylakoid membranes of cyanobacteria, algae and plants, catalyzes light-driven oxygen evolution from water and reduction of plastoquinone. Biogenesis of PSII requires coordinated assembly of at least 20 protein subunits, as well as incorporation of various organic and inorganic cofactors. The stepwise assembly process is facilitated by numerous protein factors that have been identified in recent years. Further analysis of this process requires the development or refinement of specific methods for the identification of novel assembly factors and, in particular, elucidation of the unique role of each. Here we summarize current knowledge of PSII biogenesis in cyanobacteria, focusing primarily on the impact of methodological advances and innovations. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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Affiliation(s)
- Steffen Heinz
- Molekulare Pflanzenwissenschaften, Biozentrum LMU München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Pasqual Liauw
- Biochemie der Pflanzen, Ruhr Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Jörg Nickelsen
- Molekulare Pflanzenwissenschaften, Biozentrum LMU München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Marc Nowaczyk
- Biochemie der Pflanzen, Ruhr Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany.
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255
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Zhang T, Yao D, Wang J, Gu Y, Fan H. Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals. ACTA ACUST UNITED AC 2015; 71:2513-8. [PMID: 26627658 DOI: 10.1107/s139900471501603x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/27/2015] [Indexed: 11/10/2022]
Abstract
A post-experimental identification/purification procedure similar to that described in Zhang et al. [(2015), IUCrJ, 2, 322-326] has been proposed for use in the treatment of multiphase protein serial crystallography (SX) diffraction snapshots. As a proof of concept, the procedure was tested using theoretical serial femtosecond crystallography (SFX) data from a mixture containing native and derivatized crystals of a protein. Two known proteins were taken as examples. Multiphase diffraction snapshots were subjected to two rounds of indexing using the program CrystFEL [White et al. (2012). J. Appl. Cryst. 45, 335-341]. In the first round, an ab initio indexing was performed to derive a set of approximate primitive unit-cell parameters, which are roughly the average of those from the native protein and the derivative. These parameters were then used in a second round of indexing as input to CrystFEL. The results were then used to separate the diffraction snapshots into two subsets corresponding to the native and the derivative. For each test sample, integration of the two subsets of snapshots separately led to two sets of three-dimensional diffraction intensities, one belonging to the native and the other to the derivative. Based on these two sets of intensities, a conventional single isomorphous replacement (SIR) procedure solved the structure easily.
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Affiliation(s)
- Tao Zhang
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Deqiang Yao
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Jiawei Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yuanxin Gu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Haifu Fan
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
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256
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Protein-protein interactions: a supra-structural phenomenon demanding trans-disciplinary biophysical approaches. Curr Opin Struct Biol 2015; 35:76-86. [PMID: 26496626 DOI: 10.1016/j.sbi.2015.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/01/2015] [Accepted: 09/28/2015] [Indexed: 01/14/2023]
Abstract
Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can be obtained at increasing resolution, at relevant time-scales and under increasingly relevant experimental conditions, intricate data are interpreted reliably, and the questions posed and answered grow in complexity. With this review, highlights from the study of PPIs using a multitude of biophysical methods, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods.
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257
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Chemical, electrochemical and photochemical molecular water oxidation catalysts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:71-81. [DOI: 10.1016/j.jphotobiol.2014.10.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/08/2014] [Accepted: 10/27/2014] [Indexed: 11/19/2022]
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258
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Wijeratne GB, Day VW, Jackson TA. O-H bond oxidation by a monomeric Mn(III)-OMe complex. Dalton Trans 2015; 44:3295-306. [PMID: 25597362 DOI: 10.1039/c4dt03546a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Manganese-containing, mid-valent oxidants (Mn(III)-OR) that mediate proton-coupled electron-transfer (PCET) reactions are central to a variety of crucial enzymatic processes. The Mn-dependent enzyme lipoxygenase is such an example, where a Mn(III)-OH unit activates fatty acid substrates for peroxidation by an initial PCET. This present work describes the quantitative generation of the Mn(III)-OMe complex, [Mn(III)(OMe)(dpaq)](+) (dpaq = 2-[bis(pyridin-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate) via dioxygen activation by [Mn(II)(dpaq)](+) in methanol at 25 °C. The X-ray diffraction structure of [Mn(III)(OMe)(dpaq)](+) exhibits a Mn-OMe group, with a Mn-O distance of 1.825(4) Å, that is trans to the amide functionality of the dpaq ligand. The [Mn(III)(OMe)(dpaq)](+) complex is quite stable in solution, with a half-life of 26 days in MeCN at 25 °C. [Mn(III)(OMe)(dpaq)](+) can activate phenolic O-H bonds with bond dissociation free energies (BDFEs) of less than 79 kcal mol(-1) and reacts with the weak O-H bond of TEMPOH (TEMPOH = 2,2'-6,6'-tetramethylpiperidine-1-ol) with a hydrogen/deuterium kinetic isotope effect (H/D KIE) of 1.8 in MeCN at 25 °C. This isotope effect, together with other experimental evidence, is suggestive of a concerted proton-electron transfer (CPET) mechanism for O-H bond oxidation by [Mn(III)(OMe)(dpaq)](+). A kinetic and thermodynamic comparison of the O-H bond oxidation reactivity of [Mn(III)(OMe)(dpaq)](+) to other M(III)-OR oxidants is presented as an aid to gain more insight into the PCET reactivity of mid-valent oxidants. In contrast to high-valent counterparts, the limited examples of M(III)-OR oxidants exhibit smaller H/D KIEs and show weaker dependence of their oxidation rates on the driving force of the PCET reaction with O-H bonds.
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Affiliation(s)
- Gayan B Wijeratne
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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259
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Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy. Nat Chem 2015; 7:961-7. [PMID: 26587711 DOI: 10.1038/nchem.2369] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/04/2015] [Indexed: 12/19/2022]
Abstract
To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.
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260
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Isobe H, Shoji M, Shen JR, Yamaguchi K. Strong Coupling between the Hydrogen Bonding Environment and Redox Chemistry during the S2 to S3 Transition in the Oxygen-Evolving Complex of Photosystem II. J Phys Chem B 2015; 119:13922-33. [DOI: 10.1021/acs.jpcb.5b05740] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hiroshi Isobe
- Photosynthesis
Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- The Institute
of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Mitsuo Shoji
- Graduate School
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Jian-Ren Shen
- Photosynthesis
Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- The Institute
of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
- Institute for
NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan
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261
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Phuthong W, Huang Z, Wittkopp TM, Sznee K, Heinnickel ML, Dekker JP, Frese RN, Prinz FB, Grossman AR. The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes. PLANT PHYSIOLOGY 2015; 169:1318-32. [PMID: 26220954 PMCID: PMC4587457 DOI: 10.1104/pp.15.00706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/24/2015] [Indexed: 05/02/2023]
Abstract
To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach (Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsic domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.
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Affiliation(s)
- Witchukorn Phuthong
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Zubin Huang
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Tyler M Wittkopp
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Kinga Sznee
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Mark L Heinnickel
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Jan P Dekker
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Raoul N Frese
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Fritz B Prinz
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Arthur R Grossman
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
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262
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Murray TD, Lyubimov AY, Ogata CM, Vo H, Uervirojnangkoorn M, Brunger AT, Berger JM. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1987-97. [PMID: 26457423 PMCID: PMC4601365 DOI: 10.1107/s1399004715015011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/11/2015] [Indexed: 11/14/2022]
Abstract
Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.
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Affiliation(s)
- Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Artem Y. Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Craig M. Ogata
- GM/CA@APS, X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Huy Vo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Monarin Uervirojnangkoorn
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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263
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Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T. An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. Sci Rep 2015; 5:14017. [PMID: 26360462 PMCID: PMC4566134 DOI: 10.1038/srep14017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/14/2015] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection.
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Affiliation(s)
| | - Dongqing Pan
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | - Tomohiko Okuda
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | | | - Atsushi Kodan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | - Tomohiro Yamaguchi
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | - Tomohiro Murai
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | - Keiko Gomi
- Research and Development Division, Kikkoman Corporation, Noda, 278-0037, Japan
| | - Naoki Kajiyama
- Research and Development Division, Kikkoman Corporation, Noda, 278-0037, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Mamoru Suzuki
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.,Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo, 679-5148, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Sayo, 679-5148, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, Sayo, 679-5148, Japan
| | | | | | | | | | - So Iwata
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo, 606-8501, Japan
| | - Hiroaki Kato
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan
| | | | - Toru Nakatsu
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, 606-8501, Japan
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264
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Levantino M, Yorke BA, Monteiro DC, Cammarata M, Pearson AR. Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules. Curr Opin Struct Biol 2015; 35:41-8. [PMID: 26342489 DOI: 10.1016/j.sbi.2015.07.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/27/2015] [Accepted: 07/31/2015] [Indexed: 11/17/2022]
Abstract
Time-resolved structural information is key to understand the mechanism of biological processes, such as catalysis and signalling. Recent developments in X-ray sources as well as data collection and analysis methods are making routine time-resolved X-ray crystallography and solution scattering experiments a real possibility for structural biologists. Here we review the information that can be obtained from these techniques and discuss the considerations that must be taken into account when designing a time-resolved experiment.
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Affiliation(s)
- Matteo Levantino
- Department of Physics and Chemistry, University of Palermo, Palermo 90128, Italy
| | - Briony A Yorke
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany
| | - Diana Cf Monteiro
- Astbury Centre for Structural Molecular Biology & School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes 35042, France
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging & Institute of Nanostructure and Solid State Physics, University of Hamburg, Hamburg 22607, Germany.
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265
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Kern J, Yachandra VK, Yano J. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers. Curr Opin Struct Biol 2015; 34:87-98. [PMID: 26342144 DOI: 10.1016/j.sbi.2015.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/23/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.
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Affiliation(s)
- Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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266
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Janna Olmos JD, Kargul J. A quest for the artificial leaf. Int J Biochem Cell Biol 2015; 66:37-44. [DOI: 10.1016/j.biocel.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 01/08/2023]
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267
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Najafpour MM, Ghobadi MZ, Larkum AW, Shen JR, Allakhverdiev SI. The biological water-oxidizing complex at the nano-bio interface. TRENDS IN PLANT SCIENCE 2015; 20:559-68. [PMID: 26183174 DOI: 10.1016/j.tplants.2015.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/30/2015] [Accepted: 06/16/2015] [Indexed: 05/03/2023]
Abstract
Photosynthesis is one of the most important processes on our planet, providing food and oxygen for the majority of living organisms on Earth. Over the past 30 years scientists have made great strides in understanding the central photosynthetic process of oxygenic photosynthesis, whereby water is used to provide the hydrogen and reducing equivalents vital to CO2 reduction and sugar formation. A recent crystal structure at 1.9-1.95Å has made possible an unparalleled map of the structure of photosystem II (PSII) and particularly the manganese-calcium (Mn-Ca) cluster, which is responsible for splitting water. Here we review how knowledge of the water-splitting site provides important criteria for the design of artificial Mn-based water-oxidizing catalysts, allowing the development of clean and sustainable solar energy technologies.
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Affiliation(s)
- Mohammad Mahdi Najafpour
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran; Center of Climate Change and Global Warming, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
| | - Mohadeseh Zarei Ghobadi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Anthony W Larkum
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Suleyman I Allakhverdiev
- Controlled Photobiosynthesis Laboratory, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia; Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow 119991, Russia.
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268
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Tanyag RMP, Bernando C, Jones CF, Bacellar C, Ferguson KR, Anielski D, Boll R, Carron S, Cryan JP, Englert L, Epp SW, Erk B, Foucar L, Gomez LF, Hartmann R, Neumark DM, Rolles D, Rudek B, Rudenko A, Siefermann KR, Ullrich J, Weise F, Bostedt C, Gessner O, Vilesov AF. Communication: X-ray coherent diffractive imaging by immersion in nanodroplets. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:051102. [PMID: 26798821 PMCID: PMC4711653 DOI: 10.1063/1.4933297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/05/2015] [Indexed: 05/12/2023]
Abstract
Lensless x-ray microscopy requires the recovery of the phase of the radiation scattered from a specimen. Here, we demonstrate a de novo phase retrieval technique by encapsulating an object in a superfluid helium nanodroplet, which provides both a physical support and an approximate scattering phase for the iterative image reconstruction. The technique is robust, fast-converging, and yields the complex density of the immersed object. Images of xenon clusters embedded in superfluid helium droplets reveal transient configurations of quantum vortices in this fragile system.
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Affiliation(s)
- Rico Mayro P Tanyag
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | - Charles Bernando
- Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, USA
| | - Curtis F Jones
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | | | - Ken R Ferguson
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Sebastian Carron
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - James P Cryan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik , Giessenbachstraße, 85741 Garching, Germany
| | | | | | | | - Luis F Gomez
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | | | | | | | | | | | - Katrin R Siefermann
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | | | - Fabian Weise
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | | | - Oliver Gessner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
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269
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Mueller C, Marx A, Epp SW, Zhong Y, Kuo A, Balo AR, Soman J, Schotte F, Lemke HT, Owen RL, Pai EF, Pearson AR, Olson JS, Anfinrud PA, Ernst OP, Dwayne Miller RJ. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:054302. [PMID: 26798825 PMCID: PMC4711646 DOI: 10.1063/1.4928706] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 05/18/2023]
Abstract
We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.
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Affiliation(s)
- C Mueller
- Departments of Chemistry and Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Marx
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - S W Epp
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Y Zhong
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - A R Balo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - J Soman
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - F Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
| | - H T Lemke
- LCLS, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - R L Owen
- Diamond Light Source , Harwell Campus for Science and Innovation, Didcot OX11 0DE, United Kingdom
| | | | - A R Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg , CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - J S Olson
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - P A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
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270
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Membrane protein structural biology using X-ray free electron lasers. Curr Opin Struct Biol 2015; 33:115-25. [DOI: 10.1016/j.sbi.2015.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/13/2015] [Accepted: 08/13/2015] [Indexed: 11/20/2022]
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271
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Abdallah BG, Zatsepin NA, Roy-Chowdhury S, Coe J, Conrad CE, Dörner K, Sierra RG, Stevenson HP, Camacho-Alanis F, Grant TD, Nelson G, James D, Calero G, Wachter RM, Spence JCH, Weierstall U, Fromme P, Ros A. Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041719. [PMID: 26798818 PMCID: PMC4711642 DOI: 10.1063/1.4928688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/05/2015] [Indexed: 05/23/2023]
Abstract
The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10-100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
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Affiliation(s)
| | | | | | | | | | | | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, USA
| | - Fernanda Camacho-Alanis
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, USA
| | - Thomas D Grant
- Hauptman-Woodward Medical Research Institute, University at Buffalo , Buffalo, New York 14203, USA
| | | | | | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, USA
| | - Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, USA
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272
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Pawate AS, Šrajer V, Schieferstein J, Guha S, Henning R, Kosheleva I, Schmidt M, Ren Z, Kenis PJA, Perry SL. Towards time-resolved serial crystallography in a microfluidic device. Acta Crystallogr F Struct Biol Commun 2015; 71:823-30. [PMID: 26144226 PMCID: PMC4498702 DOI: 10.1107/s2053230x15009061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR(1)/pR(E46Q) and pR(2)/pR(CW) states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.
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Affiliation(s)
- Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Jeremy Schieferstein
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
| | - Marius Schmidt
- Department of Physics, The University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, USA
- Renz Research Inc., Westmont, Illinois, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah L. Perry
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, Massachusetts, USA
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273
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Li C, Schmidt K, Spence JC. Data collection strategies for time-resolved X-ray free-electron laser diffraction, and 2-color methods. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041714. [PMID: 26798813 PMCID: PMC4711652 DOI: 10.1063/1.4922433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/29/2015] [Indexed: 05/29/2023]
Abstract
We compare three schemes for time-resolved X-ray diffraction from protein nanocrystals using an X-ray free-electron laser. We find expressions for the errors in structure factor measurement using the Monte Carlo pump-probe method of data analysis with a liquid jet, the fixed sample pump-probe (goniometer) method (both diffract-and-destroy, and below the safe damage dose), and a proposed two-color method. Here, an optical pump pulse arrives between X-ray pulses of slightly different energies which hit the same nanocrystal, using a weak first X-ray pulse which does not damage the sample. (Radiation damage is outrun in the other cases.) This two-color method, in which separated Bragg spots are impressed on the same detector readout, eliminates stochastic fluctuations in crystal size, shape, and orientation and is found to require two orders of magnitude fewer diffraction patterns than the currently used Monte Carlo liquid jet method, for 1% accuracy. Expressions are given for errors in structure factor measurement for the four approaches, and detailed simulations provided for cathepsin B and IC3 crystals. While the error is independent of the number of shots for the dose-limited goniometer method, it falls off inversely as the square root of the number of shots for the two-color and Monte Carlo methods, with a much smaller pre-factor for the two-color mode, when the first shot is below the damage threshold.
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Affiliation(s)
- Chufeng Li
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
| | - Kevin Schmidt
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
| | - John C Spence
- Department of Physics, Arizona State University , Tempe, Arizona 85287, USA
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274
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Dao EH, Sierra RG, Laksmono H, Lemke HT, Alonso-Mori R, Coey A, Larsen K, Baxter EL, Cohen AE, Soltis SM, DeMirci H. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041706. [PMID: 26798805 PMCID: PMC4711619 DOI: 10.1063/1.4919407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aaron Coey
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Kevin Larsen
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
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275
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Pomés A, Chruszcz M, Gustchina A, Minor W, Mueller GA, Pedersen LC, Wlodawer A, Chapman MD. 100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology. J Allergy Clin Immunol 2015; 136:29-37.e10. [PMID: 26145985 PMCID: PMC4502579 DOI: 10.1016/j.jaci.2015.05.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/21/2015] [Accepted: 05/14/2015] [Indexed: 01/07/2023]
Abstract
Current knowledge of molecules involved in immunology and allergic disease results from the significant contributions of x-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and x-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact 3-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind LPSs can also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. In turn, this surface determines antibody specificity and cross-reactivity, which are important factors for the selection of allergen panels used for molecular diagnosis and the interpretation of clinical symptoms. This review celebrates the contributions of x-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases.
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Affiliation(s)
- Anna Pomés
- Basic Research, INDOOR Biotechnologies, Charlottesville, Va.
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Md
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physic, University of Virginia, Charlottesville, Va
| | - Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Md
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276
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Panneels V, Wu W, Tsai CJ, Nogly P, Rheinberger J, Jaeger K, Cicchetti G, Gati C, Kick LM, Sala L, Capitani G, Milne C, Padeste C, Pedrini B, Li XD, Standfuss J, Abela R, Schertler G. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041718. [PMID: 26798817 PMCID: PMC4711639 DOI: 10.1063/1.4922774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 05/19/2023]
Abstract
Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.
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Affiliation(s)
- Valérie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Wenting Wu
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Przemek Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jan Rheinberger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Kathrin Jaeger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Gregor Cicchetti
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | | | - Leonhard M Kick
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Scientific Computing, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Chris Milne
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Celestino Padeste
- Lab for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Xiao-Dan Li
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Rafael Abela
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
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277
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Lawrence RM, Conrad CE, Zatsepin NA, Grant TD, Liu H, James D, Nelson G, Subramanian G, Aquila A, Hunter MS, Liang M, Boutet S, Coe J, Spence JCH, Weierstall U, Liu W, Fromme P, Cherezov V, Hogue BG. Serial femtosecond X-ray diffraction of enveloped virus microcrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041720. [PMID: 26798819 PMCID: PMC4711640 DOI: 10.1063/1.4929410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 05/22/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | | | | | | | | | | | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California , Los Angeles, California 90089, USA
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278
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Conrad CE, Basu S, James D, Wang D, Schaffer A, Roy-Chowdhury S, Zatsepin NA, Aquila A, Coe J, Gati C, Hunter MS, Koglin JE, Kupitz C, Nelson G, Subramanian G, White TA, Zhao Y, Zook J, Boutet S, Cherezov V, Spence JCH, Fromme R, Weierstall U, Fromme P. A novel inert crystal delivery medium for serial femtosecond crystallography. IUCRJ 2015; 2:421-30. [PMID: 26177184 PMCID: PMC4491314 DOI: 10.1107/s2052252515009811] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/21/2015] [Indexed: 05/21/2023]
Abstract
Serial femtosecond crystallography (SFX) has opened a new era in crystallo-graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.
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Affiliation(s)
- Chelsie E. Conrad
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Daniel James
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Dingjie Wang
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Alexander Schaffer
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Shatabdi Roy-Chowdhury
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Nadia A. Zatsepin
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, University of Wisconsin-Milwaukee, 1900 East Kenwood Boulevard, Milwaukee, WI 53211, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Ganesh Subramanian
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yun Zhao
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - James Zook
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, 3430 S. Vermont Avenue, Los Angeles, CA 90089, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
- Department of Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1504, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, PO Box 875001, Tempe, AZ 85287-5001, USA
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279
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Hao Y, Inhester L, Hanasaki K, Son SK, Santra R. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041707. [PMID: 26798806 PMCID: PMC4711638 DOI: 10.1063/1.4919794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/24/2015] [Indexed: 05/16/2023]
Abstract
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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280
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Chavas LMG, Gumprecht L, Chapman HN. Possibilities for serial femtosecond crystallography sample delivery at future light sources. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041709. [PMID: 26798808 PMCID: PMC4711622 DOI: 10.1063/1.4921220] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) uses X-ray pulses from free-electron laser (FEL) sources that can outrun radiation damage and thereby overcome long-standing limits in the structure determination of macromolecular crystals. Intense X-ray FEL pulses of sufficiently short duration allow the collection of damage-free data at room temperature and give the opportunity to study irreversible time-resolved events. SFX may open the way to determine the structure of biological molecules that fail to crystallize readily into large well-diffracting crystals. Taking advantage of FELs with high pulse repetition rates could lead to short measurement times of just minutes. Automated delivery of sample suspensions for SFX experiments could potentially give rise to a much higher rate of obtaining complete measurements than at today's third generation synchrotron radiation facilities, as no crystal alignment or complex robotic motions are required. This capability will also open up extensive time-resolved structural studies. New challenges arise from the resulting high rate of data collection, and in providing reliable sample delivery. Various developments for fully automated high-throughput SFX experiments are being considered for evaluation, including new implementations for a reliable yet flexible sample environment setup. Here, we review the different methods developed so far that best achieve sample delivery for X-ray FEL experiments and present some considerations towards the goal of high-throughput structure determination with X-ray FELs.
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Affiliation(s)
- L M G Chavas
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - L Gumprecht
- Center for Free-Electron Laser Science, DESY , Notkestraße 85, 22607 Hamburg, Germany
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281
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Feld GK, Heymann M, Benner WH, Pardini T, Tsai CJ, Boutet S, Coleman MA, Hunter MS, Li X, Messerschmidt M, Opathalage A, Pedrini B, Williams GJ, Krantz BA, Fraden S, Hau-Riege S, Evans JE, Segelke BW, Frank M. Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715010493] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.
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282
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Zorman S, Botte M, Jiang Q, Collinson I, Schaffitzel C. Advances and challenges of membrane–protein complex production. Curr Opin Struct Biol 2015; 32:123-30. [DOI: 10.1016/j.sbi.2015.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 01/14/2023]
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283
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Chen J, Kell A, Acharya K, Kupitz C, Fromme P, Jankowiak R. Critical assessment of the emission spectra of various photosystem II core complexes. PHOTOSYNTHESIS RESEARCH 2015; 124:253-265. [PMID: 25832780 DOI: 10.1007/s11120-015-0128-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
We evaluate low-temperature (low-T) emission spectra of photosystem II core complexes (PSII-cc) previously reported in the literature, which are compared with emission spectra of PSII-cc obtained in this work from spinach and for dissolved PSII crystals from Thermosynechococcus (T.) elongatus. This new spectral dataset is used to interpret data published on membrane PSII (PSII-m) fragments from spinach and Chlamydomonas reinhardtii, as well as PSII-cc from T. vulcanus and intentionally damaged PSII-cc from spinach. This study offers new insight into the assignment of emission spectra reported on PSII-cc from different organisms. Previously reported spectra are also compared with data obtained at different saturation levels of the lowest energy state(s) of spinach and T. elongatus PSII-cc via hole burning in order to provide more insight into emission from bleached and/or photodamaged complexes. We show that typical low-T emission spectra of PSII-cc (with closed RCs), in addition to the 695 nm fluorescence band assigned to the intact CP47 complex (Reppert et al. J Phys Chem B 114:11884-11898, 2010), can be contributed to by several emission bands, depending on sample quality. Possible contributions include (i) a band near 690-691 nm that is largely reversible upon temperature annealing, proving that the band originates from CP47 with a bleached low-energy state near 693 nm (Neupane et al. J Am Chem Soc 132:4214-4229, 2010; Reppert et al. J Phys Chem B 114:11884-11898, 2010); (ii) CP43 emission at 683.3 nm (not at 685 nm, i.e., the F685 band, as reported in the literature) (Dang et al. J Phys Chem B 112:9921-9933, 2008; Reppert et al. J Phys Chem B 112:9934-9947, 2008); (iii) trap emission from destabilized CP47 complexes near 691 nm (FT1) and 685 nm (FT2) (Neupane et al. J Am Chem Soc 132:4214-4229, 2010); and (iv) emission from the RC pigments near 686-687 nm. We suggest that recently reported emission of single PSII-cc complexes from T. elongatus may not represent intact complexes, while those obtained for T. elongatus presented in this work most likely represent intact PSII-cc, since they are nearly indistinguishable from emission spectra obtained for various PSII-m fragments.
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Affiliation(s)
- Jinhai Chen
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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284
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A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering. Sci Rep 2015; 5:10451. [PMID: 26022615 PMCID: PMC4448500 DOI: 10.1038/srep10451] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/14/2015] [Indexed: 12/02/2022] Open
Abstract
At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.
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285
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Shoji M, Isobe H, Yamanaka S, Suga M, Akita F, Shen JR, Yamaguchi K. On the guiding principles for lucid understanding of the damage-free S1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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286
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Guerra F, Adam S, Bondar AN. Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. J Mol Graph Model 2015; 58:30-9. [DOI: 10.1016/j.jmgm.2015.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
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287
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Liang M, Williams GJ, Messerschmidt M, Seibert MM, Montanez PA, Hayes M, Milathianaki D, Aquila A, Hunter MS, Koglin JE, Schafer DW, Guillet S, Busse A, Bergan R, Olson W, Fox K, Stewart N, Curtis R, Miahnahri AA, Boutet S. The Coherent X-ray Imaging instrument at the Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:514-9. [PMID: 25931062 PMCID: PMC4416669 DOI: 10.1107/s160057751500449x] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/04/2015] [Indexed: 05/19/2023]
Abstract
The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100 nm focus and one a 1 µm focus, are available, each with multiple diagnostics, sample injection, pump-probe and detector capabilities. The flexibility of CXI has enabled it to host a diverse range of experiments, from biological to extreme matter.
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Affiliation(s)
- Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Paul A. Montanez
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matt Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Despina Milathianaki
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Donald W. Schafer
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Serge Guillet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Armin Busse
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert Bergan
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - William Olson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kay Fox
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nathaniel Stewart
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robin Curtis
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alireza Alan Miahnahri
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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288
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Boutet S, Foucar L, Barends TRM, Botha S, Doak RB, Koglin JE, Messerschmidt M, Nass K, Schlichting I, Seibert MM, Shoeman RL, Williams GJ. Characterization and use of the spent beam for serial operation of LCLS. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:634-43. [PMID: 25931079 PMCID: PMC4416680 DOI: 10.1107/s1600577515004002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/26/2015] [Indexed: 05/30/2023]
Abstract
X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.
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Affiliation(s)
- Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Sabine Botha
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - R. Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jason E. Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Karol Nass
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - M. Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Garth J. Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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289
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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290
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Coe J, Kupitz C, Basu S, Conrad CE, Roy-Chowdhury S, Fromme R, Fromme P. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser. Methods Enzymol 2015; 557:459-82. [PMID: 25950978 PMCID: PMC4558102 DOI: 10.1016/bs.mie.2015.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Photosystem II (PSII) is a membrane protein supercomplex that executes the initial reaction of photosynthesis in higher plants, algae, and cyanobacteria. It captures the light from the sun to catalyze a transmembrane charge separation. In a series of four charge separation events, utilizing the energy from four photons, PSII oxidizes two water molecules to obtain dioxygen, four protons, and four electrons. The light reactions of photosystems I and II (PSI and PSII) result in the formation of an electrochemical transmembrane proton gradient that is used for the production of ATP. Electrons that are subsequently transferred from PSI via the soluble protein ferredoxin to ferredoxin-NADP(+) reductase that reduces NADP(+) to NADPH. The products of photosynthesis and the elemental oxygen evolved sustain all higher life on Earth. All oxygen in the atmosphere is produced by the oxygen-evolving complex in PSII, a process that changed our planet from an anoxygenic to an oxygenic atmosphere 2.5 billion years ago. In this chapter, we provide recent insight into the mechanisms of this process and methods used in probing this question.
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Affiliation(s)
- Jesse Coe
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Christopher Kupitz
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Shibom Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Chelsie E Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | | | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA.
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291
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Han XB, Li YG, Zhang ZM, Tan HQ, Lu Y, Wang EB. Polyoxometalate-Based Nickel Clusters as Visible Light-Driven Water Oxidation Catalysts. J Am Chem Soc 2015; 137:5486-93. [DOI: 10.1021/jacs.5b01329] [Citation(s) in RCA: 306] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xin-Bao Han
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Yang-Guang Li
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Zhi-Ming Zhang
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Hua-Qiao Tan
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - Ying Lu
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
| | - En-Bo Wang
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, Jilin 130024, P.R. China
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292
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Hilton JK, Rath P, Helsell CVM, Beckstein O, Van Horn WD. Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors. Biochemistry 2015; 54:2401-13. [DOI: 10.1021/acs.biochem.5b00071] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jacob K. Hilton
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Parthasarathi Rath
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Cole V. M. Helsell
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Oliver Beckstein
- Center
for Biological Physics and Department of Physics, Arizona State University, 550 East Tyler Mall, Tempe, Arizona 85287, United States
| | - Wade D. Van Horn
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
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293
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Vogt L, Vinyard DJ, Khan S, Brudvig GW. Oxygen-evolving complex of Photosystem II: an analysis of second-shell residues and hydrogen-bonding networks. Curr Opin Chem Biol 2015; 25:152-8. [DOI: 10.1016/j.cbpa.2014.12.040] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 12/20/2014] [Accepted: 12/25/2014] [Indexed: 12/22/2022]
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294
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Abstract
Technical progress in laser-sources and detectors has allowed the temporal and spatial resolution of chemical reactions down to femtoseconds and Å-units. In photon-excitable systems the key to chemical kinetics, trajectories across the vibrational saddle landscape, are experimentally accessible. Simple and thus well-defined chemical compounds are preferred objects for calibrating new methodologies and carving out paradigms of chemical dynamics, as shown in several contributions to this Faraday Discussion. Aerobic life on earth is powered by solar energy, which is captured by microorganisms and plants. Oxygenic photosynthesis relies on a three billion year old molecular machinery which is as well defined as simpler chemical constructs. It has been analysed to a very high precision. The transfer of excitation between pigments in antennae proteins, of electrons between redox-cofactors in reaction centres, and the oxidation of water by a Mn4Ca-cluster are solid state reactions. ATP, the general energy currency of the cell, is synthesized by a most agile, rotary molecular machine. While the efficiency of photosynthesis competes well with photovoltaics at the time scale of nanoseconds, it is lower by an order of magnitude for crops and again lower for bio-fuels. The enormous energy demand of mankind calls for engineered (bio-mimetic or bio-inspired) solar-electric and solar-fuel devices.
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Affiliation(s)
- Wolfgang Junge
- Dept. Biology & Chemistry, University of Osnabrück, R. 35/E42 Barbarastrasse 11, 49076 Osnabrück, Germany.
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295
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Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:928-40. [PMID: 25849403 PMCID: PMC4388268 DOI: 10.1107/s1399004715002308] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismail Emre Araci
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aina E. Cohen
- SLAC National Accelerator Laboratory, Stanford, CA 94305, USA
| | | | | | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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296
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Theoretical studies of the damage-free S1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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297
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Weckert E. The potential of future light sources to explore the structure and function of matter. IUCRJ 2015; 2:230-45. [PMID: 25866660 PMCID: PMC4392416 DOI: 10.1107/s2052252514024269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/03/2014] [Indexed: 05/15/2023]
Abstract
Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Low-emittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.
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298
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Schlichting I. Serial femtosecond crystallography: the first five years. IUCRJ 2015; 2:246-55. [PMID: 25866661 PMCID: PMC4392417 DOI: 10.1107/s205225251402702x] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Protein crystallography using synchrotron radiation sources has had a tremendous impact on biology, having yielded the structures of thousands of proteins and given detailed insight into their mechanisms. However, the technique is limited by the requirement for macroscopic crystals, which can be difficult to obtain, as well as by the often severe radiation damage caused in diffraction experiments, in particular when using tiny crystals. To slow radiation damage, data collection is typically performed at cryogenic temperatures. With the advent of free-electron lasers (FELs) capable of delivering extremely intense femtosecond X-ray pulses, this situation appears to be remedied, allowing the structure determination of undamaged macromolecules using either macroscopic or microscopic crystals. The latter are exposed to the FEL beam in random orientations and their diffraction data are collected at cryogenic or room temperature in a serial fashion, since each crystal is destroyed upon a single exposure. The new approaches required for crystal growth and delivery, and for diffraction data analysis, including de novo phasing, are reviewed. The opportunities and challenges of SFX are described, including applications such as time-resolved measurements and the analysis of radiation damage-prone systems.
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Affiliation(s)
- Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
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299
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Jönsson HO, Tîmneanu N, Östlin C, Scott HA, Caleman C. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:256-66. [PMID: 25723927 DOI: 10.1107/s1600577515002878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/10/2015] [Indexed: 05/07/2023]
Abstract
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10(4) to 10(7) J cm(-2) with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
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Affiliation(s)
- H Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Christofer Östlin
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Howard A Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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300
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Askerka M, Vinyard DJ, Wang J, Brudvig GW, Batista VS. Analysis of the Radiation-Damage-Free X-ray Structure of Photosystem II in Light of EXAFS and QM/MM Data. Biochemistry 2015; 54:1713-6. [DOI: 10.1021/acs.biochem.5b00089] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikhail Askerka
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - David J. Vinyard
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Jimin Wang
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Gary W. Brudvig
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
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