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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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2
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Plumley R, Sun Y, Teitelbaum S, Song S, Sato T, Chollet M, Nelson S, Wang N, Sun P, Robert A, Fuoss P, Sutton M, Zhu D. Speckle correlation as a monitor of X-ray free-electron laser induced crystal lattice deformation. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1470-1476. [PMID: 33147171 DOI: 10.1107/s1600577520011509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
X-ray free-electron lasers (X-FELs) present new opportunities to study ultrafast lattice dynamics in complex materials. While the unprecedented source brilliance enables high fidelity measurement of structural dynamics, it also raises experimental challenges related to the understanding and control of beam-induced irreversible structural changes in samples that can ultimately impact the interpretation of experimental results. This is also important for designing reliable high performance X-ray optical components. In this work, X-FEL beam-induced lattice alterations are investigated by measuring the shot-to-shot evolution of near-Bragg coherent scattering from a single crystalline germanium sample. It is shown that X-ray photon correlation analysis of sequential speckle patterns measurements can be used to monitor the nature and extent of lattice rearrangements. Abrupt, irreversible changes are observed following intermittent high-fluence monochromatic X-ray pulses, thus revealing the existence of a threshold response to X-FEL pulse intensity.
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Affiliation(s)
- Rajan Plumley
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Yanwen Sun
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Samuel Teitelbaum
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Takahiro Sato
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nan Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Peihao Sun
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Aymeric Robert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Paul Fuoss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark Sutton
- Physics Department, McGill University, 845 Sherbrooke St W, Montréal, Quebec, Canada H3A 0G4
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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3
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Flat Field Soft X-ray Spectrometry with Reflection Zone Plates on a Curved Substrate. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10207210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report on the first experimental results obtained with a newly designed instrument for high-resolution soft X-ray spectroscopy, using reflection zone plates (RZPs) on a spherical substrate. The spectrometer was tested with a fluorescence source. High-resolution flat field spectra within ±50% around the design energies were measured at an interval of 150–750 eV, using only two RZPs: the first RZP, with its design energy of 277 eV, covered the band of 150–370 eV, and the second RZP, with a design energy of 459 eV, covered the band of 350–750 eV, where the upper boundary of this energy range was defined by the Ni coating of the RZPs. The absolute quantum efficiency of the spectrometer, including the optical element and the detector, was, on average, above 10%, and reached 20% at the designed energies of the RZPs. The resolving power E/∆E exceeded 600 for energies E inside the core range of 200–550 eV.
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4
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Cox N, Pantazis DA, Lubitz W. Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data. Annu Rev Biochem 2020; 89:795-820. [DOI: 10.1146/annurev-biochem-011520-104801] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOxcomplex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.
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Affiliation(s)
- Nicholas Cox
- Research School of Chemistry, The Australian National University, Canberra ACT 2601, Australia
| | | | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim an der Ruhr, Germany
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5
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Kubin M, Guo M, Kroll T, Löchel H, Källman E, Baker ML, Mitzner R, Gul S, Kern J, Föhlisch A, Erko A, Bergmann U, Yachandra V, Yano J, Lundberg M, Wernet P. Probing the oxidation state of transition metal complexes: a case study on how charge and spin densities determine Mn L-edge X-ray absorption energies. Chem Sci 2018; 9:6813-6829. [PMID: 30310614 PMCID: PMC6115617 DOI: 10.1039/c8sc00550h] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/15/2018] [Indexed: 11/21/2022] Open
Abstract
Transition metals in inorganic systems and metalloproteins can occur in different oxidation states, which makes them ideal redox-active catalysts. To gain a mechanistic understanding of the catalytic reactions, knowledge of the oxidation state of the active metals, ideally in operando, is therefore critical. L-edge X-ray absorption spectroscopy (XAS) is a powerful technique that is frequently used to infer the oxidation state via a distinct blue shift of L-edge absorption energies with increasing oxidation state. A unified description accounting for quantum-chemical notions whereupon oxidation does not occur locally on the metal but on the whole molecule and the basic understanding that L-edge XAS probes the electronic structure locally at the metal has been missing to date. Here we quantify how charge and spin densities change at the metal and throughout the molecule for both redox and core-excitation processes. We explain the origin of the L-edge XAS shift between the high-spin complexes MnII(acac)2 and MnIII(acac)3 as representative model systems and use ab initio theory to uncouple effects of oxidation-state changes from geometric effects. The shift reflects an increased electron affinity of MnIII in the core-excited states compared to the ground state due to a contraction of the Mn 3d shell upon core-excitation with accompanied changes in the classical Coulomb interactions. This new picture quantifies how the metal-centered core hole probes changes in formal oxidation state and encloses and substantiates earlier explanations. The approach is broadly applicable to mechanistic studies of redox-catalytic reactions in molecular systems where charge and spin localization/delocalization determine reaction pathways.
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Affiliation(s)
- Markus Kubin
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany .
| | - Meiyuan Guo
- Department of Chemistry-Ångström Laboratory , Uppsala University , Sweden .
| | - Thomas Kroll
- SSRL , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Heike Löchel
- Institute for Nanometre Optics and Technology , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany
| | - Erik Källman
- Department of Chemistry-Ångström Laboratory , Uppsala University , Sweden .
| | - Michael L Baker
- The School of Chemistry , The University of Manchester at Harwell , Didcot , OX11 OFA , UK
| | - Rolf Mitzner
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany .
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
- LCLS , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Alexander Föhlisch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany .
- Institut für Physik und Astronomie , Universität Potsdam , Karl-Liebknecht-Strasse 24/25 , 14476 Potsdam , Germany
| | - Alexei Erko
- Institute for Nanometre Optics and Technology , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany
| | - Uwe Bergmann
- Stanford PULSE Institute , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , USA
| | - Vittal Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Marcus Lundberg
- Department of Chemistry-Ångström Laboratory , Uppsala University , Sweden .
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research , Helmholtz-Zentrum Berlin für Materialien und Energie GmbH , Albert-Einstein-Strasse 15 , 12489 Berlin , Germany .
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6
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Abela R, Beaud P, van Bokhoven JA, Chergui M, Feurer T, Haase J, Ingold G, Johnson SL, Knopp G, Lemke H, Milne CJ, Pedrini B, Radi P, Schertler G, Standfuss J, Staub U, Patthey L. Perspective: Opportunities for ultrafast science at SwissFEL. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061602. [PMID: 29376109 PMCID: PMC5758366 DOI: 10.1063/1.4997222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/17/2017] [Indexed: 05/03/2023]
Abstract
We present the main specifications of the newly constructed Swiss Free Electron Laser, SwissFEL, and explore its potential impact on ultrafast science. In light of recent achievements at current X-ray free electron lasers, we discuss the potential territory for new scientific breakthroughs offered by SwissFEL in Chemistry, Biology, and Materials Science, as well as nonlinear X-ray science.
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Affiliation(s)
- Rafael Abela
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Paul Beaud
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jeroen A van Bokhoven
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-FSB, Station 6, 1015 Lausanne, Switzerland
| | - Thomas Feurer
- Institute of Applied Physics, University of Bern, Bern, Switzerland
| | - Johannes Haase
- Laboratory for Catalysis and Sustainable Chemistry, Paul-Scherrer Institute, 5232 Villigen PSI, and Department of Chemistry, ETH-Zürich, 8093 Zürich, Switzerland
| | - Gerhard Ingold
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Steven L Johnson
- Institute for Quantum Electronics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zurich, Switzerland
| | - Gregor Knopp
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Henrik Lemke
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Chris J Milne
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Peter Radi
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
| | | | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Urs Staub
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Luc Patthey
- SwissFEL, Paul-Scherrer Institute, 5232 Villigen PSI, Switzerland
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7
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8
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Choosing the optimal spectroscopic toolkit to understand protein function. Biosci Rep 2017; 37:BSR20160378. [PMID: 28522552 PMCID: PMC5463260 DOI: 10.1042/bsr20160378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/02/2022] Open
Abstract
Spectroscopy was one of the earliest methods used to study the properties and reactions of proteins, and remains one of the most powerful and widely used approaches to this day. A sometimes bewildering range of spectroscopies is now available, applicable to different sample states, timescales and indeed biological questions. This editorial describes some of the most relevant spectroscopic methods together with a selection of illustrative examples.
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9
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Jensen SC, Davis KM, Sullivan B, Hartzler DA, Seidler GT, Casa DM, Kasman E, Colmer HE, Massie AA, Jackson TA, Pushkar Y. X-ray Emission Spectroscopy of Biomimetic Mn Coordination Complexes. J Phys Chem Lett 2017; 8:2584-2589. [PMID: 28524662 DOI: 10.1021/acs.jpclett.7b01209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the function of Mn ions in biological and chemical redox catalysis requires precise knowledge of their electronic structure. X-ray emission spectroscopy (XES) is an emerging technique with a growing application to biological and biomimetic systems. Here, we report an improved, cost-effective spectrometer used to analyze two biomimetic coordination compounds, [MnIV(OH)2(Me2EBC)]2+ and [MnIV(O)(OH)(Me2EBC)]+, the second of which contains a key MnIV═O structural fragment. Despite having the same formal oxidation state (MnIV) and tetradentate ligands, XES spectra from these two compounds demonstrate different electronic structures. Experimental measurements and DFT calculations yield different localized spin densities for the two complexes resulting from MnIV-OH conversion to MnIV═O. The relevance of the observed spectroscopic changes is discussed for applications in analyzing complex biological systems such as photosystem II. A model of the S3 intermediate state of photosystem II containing a MnIV═O fragment is compared to recent time-resolved X-ray diffraction data of the same state.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Katherine M Davis
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daniel A Hartzler
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
| | - Gerald T Seidler
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Diego M Casa
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Elina Kasman
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Hannah E Colmer
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Allyssa A Massie
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University , West Lafayette, Indiana 47907, United States
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10
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The Intersection of Structural and Chemical Biology - An Essential Synergy. Cell Chem Biol 2016; 23:173-182. [PMID: 26933743 DOI: 10.1016/j.chembiol.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Abstract
The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas.
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11
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Lima FA, Saleta ME, Pagliuca RJS, Eleotério MA, Reis RD, Fonseca Júnior J, Meyer B, Bittar EM, Souza-Neto NM, Granado E. XDS: a flexible beamline for X-ray diffraction and spectroscopy at the Brazilian synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1538-1549. [PMID: 27787261 DOI: 10.1107/s160057751601403x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
The majority of the beamlines at the Brazilian Synchrotron Light Source Laboratory (LNLS) use radiation produced in the storage-ring bending magnets and are therefore currently limited in the flux that can be used in the harder part of the X-ray spectrum (above ∼10 keV). A 4 T superconducting multipolar wiggler (SCW) was recently installed at LNLS in order to improve the photon flux above 10 keV and fulfill the demands set by the materials science community. A new multi-purpose beamline was then installed at the LNLS using the SCW as a photon source. The XDS is a flexible beamline operating in the energy range between 5 and 30 keV, designed to perform experiments using absorption, diffraction and scattering techniques. Most of the work performed at the XDS beamline concentrates on X-ray absorption spectroscopy at energies above 18 keV and high-resolution diffraction experiments. More recently, new setups and photon-hungry experiments such as total X-ray scattering, X-ray diffraction under high pressures, resonant X-ray emission spectroscopy, among others, have started to become routine at XDS. Here, the XDS beamline characteristics, performance and a few new experimental possibilities are described.
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Affiliation(s)
- F A Lima
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - M E Saleta
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - R J S Pagliuca
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - M A Eleotério
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - R D Reis
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - J Fonseca Júnior
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - B Meyer
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - E M Bittar
- Centro Brasileiro de Pesquisas Físicas, Rua Doutor Xavier Sigaud 150, CEP 22290-180, Rio de Janeiro (RJ), Brazil
| | - N M Souza-Neto
- Laboratório Nacional de Luz Síncrotron, Caixa Postal 6192, CEP 13084-971, Campinas (SP), Brazil
| | - E Granado
- Instituto de Física `Gleb Wataghin', Universidade de Campinas, CEP 13083-859, Campinas (SP), Brazil
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12
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Sui S, Wang Y, Kolewe KW, Srajer V, Henning R, Schiffman JD, Dimitrakopoulos C, Perry SL. Graphene-based microfluidics for serial crystallography. LAB ON A CHIP 2016; 16:3082-96. [PMID: 27241728 PMCID: PMC4970872 DOI: 10.1039/c6lc00451b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Yuxi Wang
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Kristopher W Kolewe
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Vukica Srajer
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Robert Henning
- BioCARS Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL 60439, USA
| | - Jessica D Schiffman
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Christos Dimitrakopoulos
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
| | - Sarah L Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA 01003, USA.
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13
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A Practical Guide to High-resolution X-ray Spectroscopic Measurements and their Applications in Bioinorganic Chemistry. Isr J Chem 2016. [DOI: 10.1002/ijch.201600037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Barnes CO, Kovaleva EG, Fu X, Stevenson HP, Brewster AS, DePonte DP, Baxter EL, Cohen AE, Calero G. Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography. Arch Biochem Biophys 2016; 602:61-68. [PMID: 26944553 DOI: 10.1016/j.abb.2016.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL) sources has enabled structural studies on microcrystalline protein samples at non-cryogenic temperatures. However, the identification and optimization of conditions that produce well diffracting microcrystals remains an experimental challenge. Here, we report parallel SFX and transmission electron microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate 2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions and morphology, as well as similar crystal size and density, the indexing efficiency of the diffraction data collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the H200Q variant sample. While not reported herein, the 1.75 Å resolution structure of the H200Q variant was determined from ∼16 min of beam time, demonstrating the utility of TEM analysis in evaluating sample monodispersity and lattice quality, parameters critical to the efficiency of SFX experiments.
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Affiliation(s)
- Christopher O Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Elena G Kovaleva
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Hilary P Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Aaron S Brewster
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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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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Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015; 10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.
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Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics , 1340 Jefferson Park Avenue, Charlottesville, VA 22908 , USA +1 434 243 6865 ; +1 434 243 2981 ;
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17
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Tran R, Kern J, Hattne J, Koroidov S, Hellmich J, Alonso-Mori R, Sauter NK, Bergmann U, Messinger J, Zouni A, Yano J, Yachandra VK. The Mn₄Ca photosynthetic water-oxidation catalyst studied by simultaneous X-ray spectroscopy and crystallography using an X-ray free-electron laser. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130324. [PMID: 24914152 DOI: 10.1098/rstb.2013.0324] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The structure of photosystem II and the catalytic intermediate states of the Mn₄CaO₅ cluster involved in water oxidation have been studied intensively over the past several years. An understanding of the sequential chemistry of light absorption and the mechanism of water oxidation, however, requires a new approach beyond the conventional steady-state crystallography and X-ray spectroscopy at cryogenic temperatures. In this report, we present the preliminary progress using an X-ray free-electron laser to determine simultaneously the light-induced protein dynamics via crystallography and the local chemistry that occurs at the catalytic centre using X-ray spectroscopy under functional conditions at room temperature.
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Affiliation(s)
- Rosalie Tran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Julia Hellmich
- Institut für Biologie, Humboldt-Universität Berlin, Berlin 10099, Germany
| | | | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uwe Bergmann
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität Berlin, Berlin 10099, Germany
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vittal K Yachandra
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85282, USA
| | - Henry N Chapman
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg 22607, Germany
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