1
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Helliwell JR. Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:061301. [PMID: 38107246 PMCID: PMC10725304 DOI: 10.1063/4.0000225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical, experimental and software development. This work was added to the broad research and development program of synchrotron radiation at the UK's SRS. This whole program led to knowledge transfer from the UK's SRS to the ESRF as well as for neutron Laue protein crystallography to the reactor spallation sources and later to spallation neutron sources.
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Affiliation(s)
- John R. Helliwell
- School of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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2
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Rizzato S, Manca G, Lemée MH, Marchiò L, Cesare Marincola F, Guerri A, Ienco A, Serpe A, Deplano P. Halogen-Bonding-Mediated Radical Reactions: The Unexpected Behavior of Piperazine-Based Dithiooxamide Ligands in the Presence of Diiodine. Inorg Chem 2023; 62:694-705. [PMID: 36602377 PMCID: PMC9846695 DOI: 10.1021/acs.inorgchem.2c02340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
N,N'-Dialkylpiperazine-2,3-dithiones (R2pipdt) were recognized as a class of hexa-atomic cyclic dithiooxamide ligands with peculiar charge-transfer donor properties toward soft electron-acceptors such as noble metal cations and diiodine. The latter interaction is nowadays better described as halogen bonding. In the reaction with diiodine, R2pipdt unexpectedly provides the corresponding triiodide salts, differently from the other dithiooxamides, which instead typically achieve ligand·nI2 halogen-bonded adducts. In this paper, we report a combined experimental and theoretical study that allows elucidation of the nature of the cited products and the reasons behind the unpredictable behavior of these ligands. Specifically, low-temperature single-crystal X-ray diffraction measurements on a series of synthetically obtained R2pipdt (R = Me, iPr, Bz)/I3 salts, complemented by neutron diffraction experiments, were able to experimentally highlight the formation of [R2pipdtH]+ cations with a -S-H bond on the dithionic moiety. Differently, with R = Ph, a benzothiazolylium cation, resulting from an intramolecular condensation reaction of the ligand, is obtained. Based on density functional theory (DFT) calculations, a reasonable reaction mechanism where diiodine plays the fundamental role of promoting a halogen-bonding-mediated radical reaction has been proposed. In addition, the comparison of combined experimental and computational results with the corresponding reactions of N,N'-dialkylperhydrodiazepine-2,3-dithione (R2dazdt, a hepta-atomic cyclic dithiooxamide), which provide neutral halogen-bonded adducts, pointed out that the difference in the torsion angle of the free ligands represents the structural key factor in determining the different reactivities of the two systems.
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Affiliation(s)
- Silvia Rizzato
- Dipartimento
di Chimica, Università degli Studi
di Milano, Via Golgi 19, I-20133 Milano, Italy
| | - Gabriele Manca
- Istituto
di Chimica dei Composti Organometallici ICCOM-CNR, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Florence, Italy
| | - Marie-Hélène Lemée
- Institut
Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Luciano Marchiò
- Dipartimento
di Chimica, Scienze della Vita e della Sostenibilità Ambientale, Università di Parma, 43124 Parma, Italy
| | - Flaminia Cesare Marincola
- Dipartimento
di Scienze Chimiche e Geologiche, Università
di Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Annalisa Guerri
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, Via della
Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Andrea Ienco
- Istituto
di Chimica dei Composti Organometallici ICCOM-CNR, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Florence, Italy,
| | - Angela Serpe
- Dipartimento
di Ingegneria Civile, Ambientale e Architettura (DICAAR) and Research
Unit of INSTM, Università di Cagliari, I-09042 Monserrato, Cagliari, Italy,Istituto
di Geologia Ambientale e Geoingegneria del Consiglio Nazionale delle
Ricerche (IGAG-CNR), Piazza d’Armi, 09123 Cagliari, Italy,
| | - Paola Deplano
- Dipartimento
di Scienze Chimiche e Geologiche, Università
di Cagliari, 09042 Monserrato, Cagliari, Italy,Dipartimento
di Ingegneria Civile, Ambientale e Architettura (DICAAR) and Research
Unit of INSTM, Università di Cagliari, I-09042 Monserrato, Cagliari, Italy
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3
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Tandrup T, Lo Leggio L, Meilleur F. Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature. Acta Crystallogr F Struct Biol Commun 2023; 79:1-7. [PMID: 36598350 PMCID: PMC9813973 DOI: 10.1107/s2053230x22011335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes which cleave polysaccharides oxidatively and are important in pathogen biology, carbon cycling and biotechnology. The Lentinus similis family AA9 isoform A (LsAA9_A) has been extensively studied as a model system because its activity towards smaller soluble saccharide substrates has allowed detailed structural characterization of its interaction with a variety of substrates by X-ray crystallography at high resolution. Here, the joint X-ray/neutron room-temperature crystallographic structure of carbohydrate-free LsAA9_A in the copper(II) resting state refined against X-ray and neutron data at 2.1 and 2.8 Å resolution, respectively, is presented. The results provide an experimental determination of the protonation states of the copper(II)-coordinating residues and second-shell residues in LsAA9_A, paving the way for future neutron crystallographic studies of LPMO-carbohydrate complexes.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA,Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA,Correspondence e-mail:
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4
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Harp JM, Lybrand TP, Pallan PS, Coates L, Sullivan B, Egli M. Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Nucleic Acids Res 2022; 50:7721-7738. [PMID: 35819202 PMCID: PMC9303348 DOI: 10.1093/nar/gkac577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
The ribose 2′-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2′-OH orientation (H2′-C2′-O2′-HO2′ torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2′-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3′, 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2′-OD backbone-orientation. GAGA-tetraloop riboses display a 2′-OD base-orientation. An atypical C2′-endo sugar pucker is strictly correlated with a 2′-OD sugar-orientation. Neutrons reveal the strong preference of the 2′-OH to donate in H-bonds and that 2′-OH orientation affects both backbone geometry and ribose pucker. We discuss 2′-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Terry P Lybrand
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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5
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Borgstahl GEO, O'Dell WB, Egli M, Kern JF, Kovalevsky A, Lin JYY, Myles D, Wilson MA, Zhang W, Zwart P, Coates L. EWALD: A macromolecular diffractometer for the second target station. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:064103. [PMID: 35778015 DOI: 10.1063/5.0090810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Revealing the positions of all the atoms in large macromolecules is powerful but only possible with neutron macromolecular crystallography (NMC). Neutrons provide a sensitive and gentle probe for the direct detection of protonation states at near-physiological temperatures and clean of artifacts caused by x rays or electrons. Currently, NMC use is restricted by the requirement for large crystal volumes even at state-of-the-art instruments such as the macromolecular neutron diffractometer at the Spallation Neutron Source. EWALD's design will break the crystal volume barrier and, thus, open the door for new types of experiments, the study of grand challenge systems, and the more routine use of NMC in biology. EWALD is a single crystal diffractometer capable of collecting data from macromolecular crystals on orders of magnitude smaller than what is currently feasible. The construction of EWALD at the Second Target Station will cause a revolution in NMC by enabling key discoveries in the biological, biomedical, and bioenergy sciences.
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Affiliation(s)
- Gloria E O Borgstahl
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
| | - William B O'Dell
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA and Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Martin Egli
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jan F Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Jiao Y Y Lin
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Dean Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Petrus Zwart
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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6
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. SCIENCE ADVANCES 2022; 8:eabo5083. [PMID: 35622909 PMCID: PMC9140965 DOI: 10.1126/sciadv.abo5083] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 05/04/2023]
Abstract
The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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7
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.07.479477. [PMID: 35169801 PMCID: PMC8845425 DOI: 10.1101/2022.02.07.479477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
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8
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Azadmanesh J, Lutz WE, Coates L, Weiss KL, Borgstahl GEO. Cryotrapping peroxide in the active site of human mitochondrial manganese superoxide dismutase crystals for neutron diffraction. Acta Crystallogr F Struct Biol Commun 2022; 78:8-16. [PMID: 34981770 PMCID: PMC8725007 DOI: 10.1107/s2053230x21012413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022] Open
Abstract
Structurally identifying the enzymatic intermediates of redox proteins has been elusive due to difficulty in resolving the H atoms involved in catalysis and the susceptibility of ligand complexes to photoreduction from X-rays. Cryotrapping ligands for neutron protein crystallography combines two powerful tools that offer the advantage of directly identifying hydrogen positions in redox-enzyme intermediates without radiolytic perturbation of metal-containing active sites. However, translating cryogenic techniques from X-ray to neutron crystallography is not straightforward due to the large crystal volumes and long data-collection times. Here, methods have been developed to visualize the evasive peroxo complex of manganese superoxide dismutase (MnSOD) so that all atoms, including H atoms, could be visualized. The subsequent cryocooling and ligand-trapping methods resulted in neutron data collection to 2.30 Å resolution. The P6122 crystal form of MnSOD is challenging because it has some of the largest unit-cell dimensions (a = b = 77.8, c = 236.8 Å) ever studied using high-resolution cryo-neutron crystallography. The resulting neutron diffraction data permitted the visualization of a dioxygen species bound to the MnSOD active-site metal that was indicative of successful cryotrapping.
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Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - William E. Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA
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9
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Harp JM, Coates L, Sullivan B, Egli M. Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography. Nucleic Acids Res 2021; 49:4782-4792. [PMID: 33872377 PMCID: PMC8096259 DOI: 10.1093/nar/gkab264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
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10
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Kneller D, Phillips G, Weiss KL, Zhang Q, Coates L, Kovalevsky A. Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography. J Med Chem 2021; 64:4991-5000. [PMID: 33755450 PMCID: PMC8009097 DOI: 10.1021/acs.jmedchem.1c00058] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 02/08/2023]
Abstract
The main protease (3CL Mpro) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. To date, no small-molecule clinical drugs are available that specifically inhibit SARS-CoV-2 Mpro. To aid rational drug design, we determined a neutron structure of Mpro in complex with the α-ketoamide inhibitor telaprevir at near-physiological (22 °C) temperature. We directly observed protonation states in the inhibitor complex and compared them with those in the ligand-free Mpro, revealing modulation of the active-site protonation states upon telaprevir binding. We suggest that binding of other α-ketoamide covalent inhibitors can lead to the same protonation state changes in the Mpro active site. Thus, by studying the protonation state changes induced by inhibitors, we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 Mpro.
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Affiliation(s)
- Daniel
W. Kneller
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Gwyndalyn Phillips
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Kevin L. Weiss
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Qiu Zhang
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
| | - Leighton Coates
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
- Second
Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Andrey Kovalevsky
- Neutron
Scattering Division, Oak Ridge National
Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- National
Virtual Biotechnology Laboratory, US Department of Energy, Washington, D.C. 20585, United States
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11
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Schröder GC, O’Dell WB, Swartz PD, Meilleur F. Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions. Acta Crystallogr F Struct Biol Commun 2021; 77:128-133. [PMID: 33830078 PMCID: PMC8034432 DOI: 10.1107/s2053230x21002399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper-oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - William B. O’Dell
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul D. Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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12
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Kneller DW, Phillips G, Weiss KL, Pant S, Zhang Q, O'Neill HM, Coates L, Kovalevsky A. Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography. J Biol Chem 2020; 295:17365-17373. [PMID: 33060199 PMCID: PMC7832724 DOI: 10.1074/jbc.ac120.016154] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Indexed: 01/02/2023] Open
Abstract
The main protease (3CL Mpro) from SARS-CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease. We observe that the catalytic site natively adopts a zwitterionic reactive form in which Cys145 is in the negatively charged thiolate state and His41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged. The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen-bonding networks in the active-site cavity and at the dimer interface. The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature. Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.
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Affiliation(s)
- Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Hugh M O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA; Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; National Virtual Biotechnology Laboratory, United States Department of Energy, Washington, DC, USA.
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13
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Gorfman S. Algorithms for target transformations of lattice basis vectors. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:713-718. [PMID: 33125354 PMCID: PMC7598097 DOI: 10.1107/s2053273320012668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/17/2020] [Indexed: 11/10/2022]
Abstract
Presented here are algorithms for the transformation of lattice basis vectors to a specific target. The algorithms are useful for crystallographic operations in direct and reciprocal spaces alike. The algorithms are demonstrated graphically and numerically. Simple algorithms are proposed for the transformation of lattice basis vectors to a specific target. In the first case, one of the new basis vectors is aligned to a predefined lattice direction, while in the second case, two of the new basis vectors are brought to a lattice plane with predefined Miller indices. The multi-dimensional generalization of the algorithm is available in the supporting materials. The algorithms are useful for such crystallographic operations as simulation of zone planes (i.e. geometry of electron diffraction patterns) or transformation of a unit cell for surface or cleavage energy calculations. The most general multi-dimensional version of the algorithm may be useful for the analysis of quasiperiodic crystals or as an alternative method of calculating Bézout coefficients. The algorithms are demonstrated both graphically and numerically.
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Affiliation(s)
- Semën Gorfman
- Department of Materials Science and Engineering, Tel Aviv University, Wolfson Building for Mechanical Engineering, Tel Aviv 6997801, Israel
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14
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Kamiński R, Szarejko D, Pedersen MN, Hatcher LE, Łaski P, Raithby PR, Wulff M, Jarzembska KN. Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction. J Appl Crystallogr 2020; 53:1370-1375. [PMID: 33122973 DOI: 10.1107/s1600576720011929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/29/2020] [Indexed: 11/10/2022] Open
Abstract
A simple yet efficient instrument-model refinement method for X-ray diffraction data is presented and discussed. The method is based on least-squares minimization of differences between respective normalized (i.e. unit length) reciprocal vectors computed for adjacent frames. The approach was primarily designed to work with synchrotron X-ray Laue diffraction data collected for small-molecule single-crystal samples. The method has been shown to work well on both simulated and experimental data. Tests performed on simulated data sets for small-molecule and protein crystals confirmed the validity of the proposed instrument-model refinement approach. Finally, examination of data sets collected at both BioCARS 14-ID-B (Advanced Photon Source) and ID09 (European Synchrotron Radiation Facility) beamlines indicated that the approach is capable of retrieving goniometer parameters (e.g. detector distance or primary X-ray beam centre) reliably, even when their initial estimates are rather inaccurate.
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Affiliation(s)
- Radosław Kamiński
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dariusz Szarejko
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Martin N Pedersen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Lauren E Hatcher
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.,School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Piotr Łaski
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paul R Raithby
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Michael Wulff
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Katarzyna N Jarzembska
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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15
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Kneller DW, Phillips G, Kovalevsky A, Coates L. Room-temperature neutron and X-ray data collection of 3CL M pro from SARS-CoV-2. Acta Crystallogr F Struct Biol Commun 2020; 76:483-487. [PMID: 33006576 PMCID: PMC7531248 DOI: 10.1107/s2053230x20011814] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/27/2020] [Indexed: 01/16/2023] Open
Abstract
The replication of SARS-CoV-2 produces two large polyproteins, pp1a and pp1ab, that are inactive until cleavage by the viral chymotrypsin-like cysteine protease enzyme (3CL Mpro) into a series of smaller functional proteins. At the heart of 3CL Mpro is an unusual catalytic dyad formed by the side chains of His41 and Cys145 and a coordinated water molecule. The catalytic mechanism by which the enzyme operates is still unknown, as crucial information on the protonation states within the active site is unclear. To experimentally determine the protonation states of the catalytic site and of the other residues in the substrate-binding cavity, and to visualize the hydrogen-bonding networks throughout the enzyme, room-temperature neutron and X-ray data were collected from a large H/D-exchanged crystal of ligand-free (apo) 3CL Mpro.
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Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
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16
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Hiromoto T, Nishikawa K, Inoue S, Matsuura H, Hirano Y, Kurihara K, Kusaka K, Cuneo M, Coates L, Tamada T, Higuchi Y. Towards cryogenic neutron crystallography on the reduced form of [NiFe]-hydrogenase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:946-953. [PMID: 33021496 DOI: 10.1107/s2059798320011365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022]
Abstract
A membrane-bound hydrogenase from Desulfovibrio vulgaris Miyazaki F is a metalloenzyme that contains a binuclear Ni-Fe complex in its active site and mainly catalyzes the oxidation of molecular hydrogen to generate a proton gradient in the bacterium. The active-site Ni-Fe complex of the aerobically purified enzyme shows its inactive oxidized form, which can be reactivated through reduction by hydrogen. Here, in order to understand how the oxidized form is reactivated by hydrogen and further to directly evaluate the bridging of a hydride ligand in the reduced form of the Ni-Fe complex, a neutron structure determination was undertaken on single crystals grown in a hydrogen atmosphere. Cryogenic crystallography is being introduced into the neutron diffraction research field as it enables the trapping of short-lived intermediates and the collection of diffraction data to higher resolution. To optimize the cooling of large crystals under anaerobic conditions, the effects on crystal quality were evaluated by X-rays using two typical methods, the use of a cold nitrogen-gas stream and plunge-cooling into liquid nitrogen, and the former was found to be more effective in cooling the crystals uniformly than the latter. Neutron diffraction data for the reactivated enzyme were collected at the Japan Photon Accelerator Research Complex under cryogenic conditions, where the crystal diffracted to a resolution of 2.0 Å. A neutron diffraction experiment on the reduced form was carried out at Oak Ridge National Laboratory under cryogenic conditions and showed diffraction peaks to a resolution of 2.4 Å.
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Affiliation(s)
- Takeshi Hiromoto
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Seiya Inoue
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Hiroaki Matsuura
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Matthew Cuneo
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Hyogo 678-1297, Japan
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17
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Arnaud A, Guediche W, Remacha C, Romero E, Proudhon H. A laboratory transmission diffraction Laue setup to evaluate single-crystal quality. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720006317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A scanning laboratory Laue transmission setup is developed to probe extended quasi-monocrystalline samples. Orientation mapping is achieved by controlling the collimation of the incident beam and scanning the position of the specimen. An automated indexing algorithm for transmission Laue patterns is presented, together with a forward simulation model adapted for a laboratory setup. The effect of the main parameters of the system is studied with the aim of achieving exposure times of the order of one second. Applications are presented to probe the orientation of an extended part and detect disoriented regions within the bulk. Finally, the analysis of diffraction spot shapes shows that the misorientation within the illuminated volume can be measured, and a new method is proposed to evaluate its complete mean lattice rotation tensor.
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18
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Dejoie C, Tamura N. Pattern-matching indexing of Laue and monochromatic serial crystallography data for applications in materials science. J Appl Crystallogr 2020; 53:824-836. [PMID: 32684897 PMCID: PMC7312145 DOI: 10.1107/s160057672000521x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/13/2020] [Indexed: 11/11/2022] Open
Abstract
Serial crystallography data can be challenging to index, as each frame is processed individually, rather than being processed as a whole like in conventional X-ray single-crystal crystallography. An algorithm has been developed to index still diffraction patterns arising from small-unit-cell samples. The algorithm is based on the matching of reciprocal-lattice vector pairs, as developed for Laue microdiffraction data indexing, combined with three-dimensional pattern matching using a nearest-neighbors approach. As a result, large-bandpass data (e.g. 5-24 keV energy range) and monochromatic data can be processed, the main requirement being prior knowledge of the unit cell. Angles calculated in the vicinity of a few theoretical and experimental reciprocal-lattice vectors are compared, and only vectors with the highest number of common angles are selected as candidates to obtain the orientation matrix. Global matching on the entire pattern is then checked. Four indexing options are available, two for the ranking of the theoretical reciprocal-lattice vectors and two for reducing the number of possible candidates. The algorithm has been used to index several data sets collected under different experimental conditions on a series of model samples. Knowing the crystallographic structure of the sample and using this information to rank the theoretical reflections based on the structure factors helps the indexing of large-bandpass data for the largest-unit-cell samples. For small-bandpass data, shortening the candidate list to determine the orientation matrix should be based on matching pairs of reciprocal-lattice vectors instead of triplet matching.
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Affiliation(s)
- Catherine Dejoie
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Nobumichi Tamura
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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19
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Kita A, Morimoto Y. Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state. J Appl Crystallogr 2020; 53:837-840. [PMID: 32684898 DOI: 10.1107/s1600576720005488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 04/20/2020] [Indexed: 11/11/2022] Open
Abstract
Neutron diffraction studies of hydrogen/deuterium-exchanged hen egg-white lysozyme were performed by a joint X-ray and neutron refinement to elucidate the hydrogen/deuterium exchange behavior. Large crystals for neutron work, consisting of molecules that were exchanged before crystallization, were obtained by repeatedly adding protein solution to the crystal batch using deuterated precipitant reagent. There are differences in hydrogen/deuterium exchange behavior compared with previous crystallographic or NMR studies, which could be due to intermolecular interactions in the crystal or to different lengths of exchange period.
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Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sen-nan, Osaka 590-0494, Japan
| | - Yukio Morimoto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sen-nan, Osaka 590-0494, Japan
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20
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Szarejko D, Kamiński R, Łaski P, Jarzembska KN. Seed-skewness algorithm for X-ray diffraction signal detection in time-resolved synchrotron Laue photocrystallography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:405-413. [PMID: 32153279 PMCID: PMC7064106 DOI: 10.1107/s1600577520000077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
A one-dimensional seed-skewness algorithm adapted for X-ray diffraction signal detection is presented and discussed. The method, primarily designed for photocrystallographic time-resolved Laue data processing, was shown to work well for the type of data collected at the Advanced Photon Source and European Synchrotron Radiation Facility. Nevertheless, it is also applicable in the case of standard single-crystal X-ray diffraction data. The reported algorithm enables reasonable separation of signal from the background in single one-dimensional data vectors as well as the capability to determine small changes of reflection shapes and intensities resulting from exposure of the sample to laser light. Otherwise, the procedure is objective, and relies only on skewness computation and its subsequent minimization. The new algorithm was proved to yield comparable results to the Kruskal-Wallis test method [Kalinowski, J. A. et al. (2012). J. Synchrotron Rad. 19, 637], while the processing takes a similar amount of time. Importantly, in contrast to the Kruskal-Wallis test, the reported seed-skewness approach does not need redundant input data, which allows for faster data collections and wider applications. Furthermore, as far as the structure refinement is concerned, the reported algorithm leads to the excited-state geometry closest to the one modelled using the quantum-mechanics/molecular-mechanics approach reported previously [Jarzembska, K. N. et al. (2014). Inorg. Chem. 53, 10594], when the t and s algorithm parameters are set to the recommended values of 0.2 and 3.0, respectively.
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Affiliation(s)
- Dariusz Szarejko
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Radosław Kamiński
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Piotr Łaski
- Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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21
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Gevorkov Y, Barty A, Brehm W, White TA, Tolstikova A, Wiedorn MO, Meents A, Grigat RR, Chapman HN, Yefanov O. pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots. Acta Crystallogr A Found Adv 2020; 76:121-131. [PMID: 32124850 PMCID: PMC7053222 DOI: 10.1107/s2053273319015559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.
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Affiliation(s)
- Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rolf-Rainer Grigat
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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22
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Meilleur F, Kovalevsky A, Myles DAA. IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor. Methods Enzymol 2020; 634:69-85. [PMID: 32093843 DOI: 10.1016/bs.mie.2019.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm3 and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.
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Affiliation(s)
- Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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23
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Sullivan B, Archibald R, Azadmanesh J, Vandavasi VG, Langan PS, Coates L, Lynch V, Langan P. BraggNet: integrating Bragg peaks using neural networks. J Appl Crystallogr 2019; 52:854-863. [PMID: 31396028 PMCID: PMC6662992 DOI: 10.1107/s1600576719008665] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 06/17/2019] [Indexed: 10/14/2023] Open
Abstract
Neutron crystallography offers enormous potential to complement structures from X-ray crystallography by clarifying the positions of low-Z elements, namely hydrogen. Macromolecular neutron crystallography, however, remains limited, in part owing to the challenge of integrating peak shapes from pulsed-source experiments. To advance existing software, this article demonstrates the use of machine learning to refine peak locations, predict peak shapes and yield more accurate integrated intensities when applied to whole data sets from a protein crystal. The artificial neural network, based on the U-Net architecture commonly used for image segmentation, is trained using about 100 000 simulated training peaks derived from strong peaks. After 100 training epochs (a round of training over the whole data set broken into smaller batches), training converges and achieves a Dice coefficient of around 65%, in contrast to just 15% for negative control data sets. Integrating whole peak sets using the neural network yields improved intensity statistics compared with other integration methods, including k-nearest neighbours. These results demonstrate, for the first time, that neural networks can learn peak shapes and be used to integrate Bragg peaks. It is expected that integration using neural networks can be further developed to increase the quality of neutron, electron and X-ray crystallography data.
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Affiliation(s)
- Brendan Sullivan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Rick Archibald
- Computer Science and Mathematics Division, Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, Nebraska 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Patricia S. Langan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Vickie Lynch
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Paul Langan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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24
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Kurdzesau F. Energy-dispersive Laue experiments with X-ray tube and PILATUS detector: precise determination of lattice constants. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576718017193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A PILATUS detector in combination with a conventional sealed X-ray tube was used for the development of the energy-dispersive Laue diffraction technique, which can be applied for precise measurements of single-crystal lattice constants in transmission and reflection modes without moving the sample. Exploiting the ability of PILATUS detectors to suppress counting of X-ray photons below a certain energy threshold allows one to recover the wavelength of diffracted Bragg reflections, reconstruct the three-dimensional reciprocal-space pattern, index X-ray diffraction peaks, and find the orientation and lattice parameters of the crystal without any a priori information about the sample. By making some geometrical assumptions and using a set of fast in situ calibration procedures, it is possible to simultaneously refine lattice constants and hardware correction factors, which simplifies the sample preparation and measurement strategies. Several samples [silicon, quartz, fluorite (CaF2), o′-Al13Co4 quasicrystal approximant, Laves (MgZn2) and Bergman (Mg32(Al,Zn)49) phases] were studied with the developed technique, and 0.01 Å and 0.1° precisions were routinely reached for lattice vector lengths and angles, respectively. The use of the developed methods is only limited by the energy resolution of the PILATUS detector, where lattice vectors with >27 Å length cannot be reliably resolved.
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25
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Knihtila R, Volmar AY, Meilleur F, Mattos C. Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:111-115. [PMID: 30713162 DOI: 10.1107/s2053230x18018125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 11/11/2022]
Abstract
Neutron protein crystallography (NPC) reveals the three-dimensional structures of proteins, including the positions of H atoms. The technique is particularly suited to elucidate ambiguous catalytic steps in complex biochemical reactions. While NPC uniquely complements biochemical assays and X-ray structural analyses by revealing the protonation states of ionizable groups at and around the active site of enzymes, the technique suffers from a major drawback: large single crystals must be grown to compensate for the relatively low flux of neutron beams. However, in addition to revealing the positions of hydrogens involved in enzyme catalysis, NPC has the advantage over X-ray crystallography that the crystals do not suffer radiation damage. The lack of radiation damage can be exploited to conduct in crystallo parametric studies. Here, the use of a single crystal of the small GTPase Ras to collect three neutron data sets at pD 8.4, 9.0 and 9.4 is reported, enabling an in crystallo titration study using NPC. In addition to revealing the behavior of titratable groups in the active site, the data sets will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks, Tyr32, Tyr96 and Tyr137, with pKa values expected to be in the range sampled in our experiments.
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Affiliation(s)
- Ryan Knihtila
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alicia Y Volmar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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26
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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27
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The Neutron Macromolecular Crystallography Instruments at Oak Ridge National Laboratory: Advances, Challenges, and Opportunities. CRYSTALS 2018. [DOI: 10.3390/cryst8100388] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The IMAGINE and MaNDi instruments, located at Oak Ridge National Laboratory High Flux Isotope Reactor and Spallation Neutron Source, respectively, are powerful tools for determining the positions of hydrogen atoms in biological macromolecules and their ligands, orienting water molecules, and for differentiating chemical states in macromolecular structures. The possibility to model hydrogen and deuterium atoms in neutron structures arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction studies at the 1.5–2.5 Å resolutions, which are typical for protein crystals. Neutrons have the additional benefit for structural biology of not inducing radiation damage to protein crystals, which can be critical in the study of metalloproteins. Here we review the specifications of the IMAGINE and MaNDi beamlines and illustrate their complementarity. IMAGINE is suitable for crystals with unit cell edges up to 150 Å using a quasi-Laue technique, whereas MaNDi provides neutron crystallography resources for large unit cell samples with unit cell edges up to 300 Å using the time of flight (TOF) Laue technique. The microbial culture and crystal growth facilities which support the IMAGINE and MaNDi user programs are also described.
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28
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Haberl B, Dissanayake S, Wu Y, Myles DAA, Dos Santos AM, Loguillo M, Rucker GM, Armitage DP, Cochran M, Andrews KM, Hoffmann C, Cao H, Matsuda M, Meilleur F, Ye F, Molaison JJ, Boehler R. Next-generation diamond cell and applications to single-crystal neutron diffraction. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:092902. [PMID: 30278728 DOI: 10.1063/1.5031454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
A diamond cell optimized for single-crystal neutron diffraction is described. It is adapted for work at several of the single-crystal diffractometers of the Spallation Neutron Source and the High Flux Isotope Reactor at the Oak Ridge National Laboratory (ORNL). A simple spring design improves portability across the facilities and affords load maintenance from offline pressurization and during temperature cycling. Compared to earlier prototypes, pressure stability of polycrystalline diamond (Versimax®) has been increased through double-conical designs and ease of use has been improved through changes to seat and piston setups. These anvils allow ∼30%-40% taller samples than possible with comparable single-crystal anvils. Hydrostaticity and the important absence of shear pressure gradients have been established with the use of glycerin as a pressure medium. Large single-crystal synthetic diamonds have also been used for the first time with such a clamp-diamond anvil cell for pressures close to 20 GPa. The cell is made from a copper beryllium alloy and sized to fit into ORNL's magnets for future ultra-low temperature and high-field studies. We show examples from the Spallation Neutron Source's SNAP and CORELLI beamlines and the High Flux Isotope Reactor's HB-3A and IMAGINE beamlines.
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Affiliation(s)
- Bianca Haberl
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Sachith Dissanayake
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yan Wu
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Dean A A Myles
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Antonio M Dos Santos
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mark Loguillo
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald M Rucker
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Douglas P Armitage
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Malcolm Cochran
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Katie M Andrews
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Christina Hoffmann
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huibo Cao
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Masaaki Matsuda
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Flora Meilleur
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Feng Ye
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jamie J Molaison
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Reinhard Boehler
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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29
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Abstract
The factors affecting the accuracy of structural refinements from image-plate neutron Laue diffractometers are analysed. From this analysis, an improved data-processing method is developed which optimizes the intensity corrections for exposure scaling, wavelength distribution, absorption and extinction corrections, and the wavelength/spatial/time dependence of the image-plate detector efficiencies. Of equal importance is an analysis of the sources of uncertainty in the final corrected intensities, without which bias of the merged intensities occurs, due to the dominance of measurements with small statistical errors though potentially large systematic errors. A new aspect of the impact of detector crosstalk on the counting statistics of area detectors is reported and shown to be significant for the case of neutron Laue diffraction. These methods have been implemented in software which processes data from the KOALA instrument at ANSTO and the now decommissioned VIVALDI instrument at ILL (Grenoble, France). A comparison with earlier data-analysis methods shows a significant improvement in accuracy of the refined structures.
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30
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Meents A, Wiedorn MO, Srajer V, Henning R, Sarrou I, Bergtholdt J, Barthelmess M, Reinke PYA, Dierksmeyer D, Tolstikova A, Schaible S, Messerschmidt M, Ogata CM, Kissick DJ, Taft MH, Manstein DJ, Lieske J, Oberthuer D, Fischetti RF, Chapman HN. Pink-beam serial crystallography. Nat Commun 2017; 8:1281. [PMID: 29097720 PMCID: PMC5668288 DOI: 10.1038/s41467-017-01417-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/14/2017] [Indexed: 02/02/2023] Open
Abstract
Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.
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Affiliation(s)
- A Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany.
| | - M O Wiedorn
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - V Srajer
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - R Henning
- Center for Advanced Radiation Sources, The University of Chicago, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - I Sarrou
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - J Bergtholdt
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - P Y A Reinke
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D Dierksmeyer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - A Tolstikova
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - S Schaible
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - M Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - C M Ogata
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - D J Kissick
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - M H Taft
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - D J Manstein
- Medizinische Hochschule Hannover (MHH), Institut für Biophysikalische Chemie, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - J Lieske
- Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - D Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - R F Fischetti
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL, 60439, USA
| | - H N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
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31
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Fullagar WK, Paziresh M, Latham SJ, Myers GR, Kingston AM. The index of dispersion as a metric of quanta - unravelling the Fano factor. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:675-695. [PMID: 28762978 DOI: 10.1107/s2052520617009222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
In statistics, the index of dispersion (or variance-to-mean ratio) is unity (σ2/〈x〉 = 1) for a Poisson-distributed process with variance σ2 for a variable x that manifests as unit increments. Where x is a measure of some phenomenon, the index takes on a value proportional to the quanta that constitute the phenomenon. That outcome might thus be anticipated to apply for an enormously wide variety of applied measurements of quantum phenomena. However, in a photon-energy proportional radiation detector, a set of M witnessed Poisson-distributed measurements {W1, W2,… WM} scaled so that the ideal expectation value of the quantum is unity, is generally observed to give σ2/〈W〉 < 1 because of detector losses as broadly indicated by Fano [Phys. Rev. (1947), 72, 26]. In other cases where there is spectral dispersion, σ2/〈W〉 > 1. Here these situations are examined analytically, in Monte Carlo simulations, and experimentally. The efforts reveal a powerful metric of quanta broadly associated with such measurements, where the extension has been made to polychromatic and lossy situations. In doing so, the index of dispersion's variously established yet curiously overlooked role as a metric of underlying quanta is indicated. The work's X-ray aspects have very diverse utility and have begun to find applications in radiography and tomography, where the ability to extract spectral information from conventional intensity detectors enables a superior level of material and source characterization.
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Affiliation(s)
- Wilfred K Fullagar
- Applied Mathematics, RSPE, Oliphant Building 60, Mills Road, Australian National University, Canberra, ACT 2601, Australia
| | - Mahsa Paziresh
- Applied Mathematics, RSPE, Oliphant Building 60, Mills Road, Australian National University, Canberra, ACT 2601, Australia
| | - Shane J Latham
- Applied Mathematics, RSPE, Oliphant Building 60, Mills Road, Australian National University, Canberra, ACT 2601, Australia
| | - Glenn R Myers
- Applied Mathematics, RSPE, Oliphant Building 60, Mills Road, Australian National University, Canberra, ACT 2601, Australia
| | - Andrew M Kingston
- Applied Mathematics, RSPE, Oliphant Building 60, Mills Road, Australian National University, Canberra, ACT 2601, Australia
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32
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Fullagar WK, Uhlig J, Mandal U, Kurunthu D, El Nahhas A, Tatsuno H, Honarfar A, Parnefjord Gustafsson F, Sundström V, Palosaari MRJ, Kinnunen KM, Maasilta IJ, Miaja-Avila L, O'Neil GC, Joe YI, Swetz DS, Ullom JN. Beating Darwin-Bragg losses in lab-based ultrafast x-ray experiments. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044011. [PMID: 28396880 PMCID: PMC5367090 DOI: 10.1063/1.4978742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
The use of low temperature thermal detectors for avoiding Darwin-Bragg losses in lab-based ultrafast experiments has begun. An outline of the background of this new development is offered, showing the relevant history and initiative taken by this work.
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Affiliation(s)
| | - Jens Uhlig
- Department of Chemical Physics, Lund University , Box 124, Lund SE-22100, Sweden
| | | | | | - Amal El Nahhas
- Department of Chemical Physics, Lund University , Box 124, Lund SE-22100, Sweden
| | - Hideyuki Tatsuno
- Department of Chemical Physics, Lund University , Box 124, Lund SE-22100, Sweden
| | - Alireza Honarfar
- Department of Chemical Physics, Lund University , Box 124, Lund SE-22100, Sweden
| | | | - Villy Sundström
- Department of Chemical Physics, Lund University , Box 124, Lund SE-22100, Sweden
| | - Mikko R J Palosaari
- Nanoscience Center, Department of Physics, University of Jyväskylä , P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Kimmo M Kinnunen
- Nanoscience Center, Department of Physics, University of Jyväskylä , P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Ilari J Maasilta
- Nanoscience Center, Department of Physics, University of Jyväskylä , P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Luis Miaja-Avila
- National Institute of Standards and Technology , Boulder, Colorado 80305, USA
| | - Galen C O'Neil
- National Institute of Standards and Technology , Boulder, Colorado 80305, USA
| | - Young Il Joe
- National Institute of Standards and Technology , Boulder, Colorado 80305, USA
| | - Daniel S Swetz
- National Institute of Standards and Technology , Boulder, Colorado 80305, USA
| | - Joel N Ullom
- National Institute of Standards and Technology , Boulder, Colorado 80305, USA
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Chen JCH, Unkefer CJ. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography. IUCRJ 2017; 4:72-86. [PMID: 28250943 PMCID: PMC5331467 DOI: 10.1107/s205225251601664x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.
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Affiliation(s)
- Julian C.-H. Chen
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Clifford J. Unkefer
- Bioscience Division, Protein Crystallography Station, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Send S, Abboud A, Wiesner N, Shokr M, Klaus M, Genzel C, Conka-Nurdan T, Schlosser D, Huth M, Hartmann R, Strüder L, Pietsch U. Application of a pnCCD for energy-dispersive Laue diffraction with ultra-hard X-rays. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576715023997] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In this work the spectroscopic performance of a pnCCD detector in the ultra-hard energy range between 40 and 140 keV is tested by means of an energy-dispersive Laue diffraction experiment on a GaAs crystal. About 100 Bragg peaks were collected in a single-shot exposure of the arbitrarily oriented sample to white synchrotron radiation provided by a wiggler at BESSY II and resolved in a large reciprocal-space volume. The positions and energies of individual Laue spots could be determined with a spatial accuracy of less than one pixel and a relative energy resolution better than 1%. In this way the unit-cell parameters of GaAs were extracted with an accuracy of 0.5%, allowing for a complete indexing of the recorded Laue pattern. Despite the low quantum efficiency of the pnCCD (below 7%), experimental structure factors could be obtained from the three-dimensional data sets, taking into account photoelectric absorption as well as Compton scattering processes inside the detector. The agreement between measured and theoretical kinematical structure factors calculated from the known crystal structure is of the order of 10%. The results of this experiment demonstrate the potential of pnCCD detectors for applications in X-ray structure analysis using the complete energy spectrum of synchrotron radiation.
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Laulumaa S, Blakeley MP, Raasakka A, Moulin M, Härtlein M, Kursula P. Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Acta Crystallogr F Struct Biol Commun 2015; 71:1391-5. [PMID: 26527266 PMCID: PMC4631588 DOI: 10.1107/s2053230x15017902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/24/2015] [Indexed: 11/11/2022] Open
Abstract
The molecular details of the formation of the myelin sheath, a multilayered membrane in the nervous system, are to a large extent unknown. P2 is a peripheral membrane protein from peripheral nervous system myelin, which is believed to play a role in this process. X-ray crystallographic studies and complementary experiments have provided information on the structure-function relationships in P2. In this study, a fully deuterated sample of human P2 was produced. Crystals that were large enough for neutron diffraction were grown by a ten-month procedure of feeding, and neutron diffraction data were collected to a resolution of 2.4 Å from a crystal of 0.09 mm(3) in volume. The neutron crystal structure will allow the positions of H atoms in P2 and its fatty-acid ligand to be visualized, as well as shedding light on the fine details of the hydrogen-bonding networks within the P2 ligand-binding cavity.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- European Spallation Source, Lund, Sweden
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
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Dejoie C, Smeets S, Baerlocher C, Tamura N, Pattison P, Abela R, McCusker LB. Serial snapshot crystallography for materials science with SwissFEL. IUCRJ 2015; 2:361-70. [PMID: 25995845 PMCID: PMC4420546 DOI: 10.1107/s2052252515006740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
New opportunities for studying (sub)microcrystalline materials with small unit cells, both organic and inorganic, will open up when the X-ray free electron laser (XFEL) presently being constructed in Switzerland (SwissFEL) comes online in 2017. Our synchrotron-based experiments mimicking the 4%-energy-bandpass mode of the SwissFEL beam show that it will be possible to record a diffraction pattern of up to 10 randomly oriented crystals in a single snapshot, to index the resulting reflections, and to extract their intensities reliably. The crystals are destroyed with each XFEL pulse, but by combining snapshots from several sets of crystals, a complete set of data can be assembled, and crystal structures of materials that are difficult to analyze otherwise will become accessible. Even with a single shot, at least a partial analysis of the crystal structure will be possible, and with 10-50 femtosecond pulses, this offers tantalizing possibilities for time-resolved studies.
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Affiliation(s)
- Catherine Dejoie
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Stef Smeets
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Christian Baerlocher
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
| | - Nobumichi Tamura
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Philip Pattison
- Swiss-Norwegian Beamlines, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble, 38042, France
- Laboratory of Crystallography, EPFL, Rte de la Sorge, Lausanne, 1015, Switzerland
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Lynne B. McCusker
- Laboratory of Crystallography, ETH Zurich, Vladimir-Prelog-Weg 5, Zurich, 8093, Switzerland
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Coppens P, Fournier B. New methods in time-resolved Laue pump-probe crystallography at synchrotron sources. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:280-287. [PMID: 25723930 PMCID: PMC4344360 DOI: 10.1107/s1600577514026538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/02/2014] [Indexed: 06/04/2023]
Abstract
Newly developed methods for time-resolved studies using the polychromatic and in particular the pink-Laue technique, suitable for medium and small-size unit cells typical in chemical crystallography, are reviewed. The order of the sections follows that of a typical study, starting with a description of the pink-Laue technique, followed by the strategy of data collection for analysis with the RATIO method. Novel procedures are described for spot integration, orientation matrix determination for relatively sparse diffraction patterns, scaling of multi-crystal data sets, use of Fourier maps for initial assessment and analysis of results, and least-squares refinement of photo-induced structural and thermal changes. In the calculation of Fourier maps a ground-state structure model, typically based on monochromatic results, is employed as reference, and the laser-ON structure factors for the Fourier summations are obtained by multiplying the reference ground-state structure factors by the square root of the experimental ON/OFF ratios. A schematic of the procedure followed is included in the conclusion section.
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Affiliation(s)
- Philip Coppens
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| | - Bertrand Fournier
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
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Perry SL, Guha S, Pawate AS, Henning R, Kosheleva I, Srajer V, Kenis PJA, Ren Z. In situ serial Laue diffraction on a microfluidic crystallization device. J Appl Crystallogr 2014; 47:1975-1982. [PMID: 25484843 PMCID: PMC4248567 DOI: 10.1107/s1600576714023322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/22/2014] [Indexed: 11/10/2022] Open
Abstract
Renewed interest in room-temperature diffraction has been prompted by the desire to observe structural dynamics of proteins as they function. Serial crystallography, an experimental strategy that aggregates small pieces of data from a large uniform pool of crystals, has been demonstrated at synchrotrons and X-ray free-electron lasers. This work utilizes a microfluidic crystallization platform for serial Laue diffraction from macroscopic crystals and proposes that a collection of small slices of Laue data from many individual crystals is a realistic solution to the difficulties in dynamic studies of irreversible biochemical reactions.
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Affiliation(s)
- Sarah L. Perry
- Department of Chemical Engineering, The University of Massachusetts Amherst, Amherst, MA, USA
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Sudipto Guha
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Ashtamurthy S. Pawate
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
| | - Paul J. A. Kenis
- Department of Chemical and Biomolecular Engineering, The University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, IL, USA
- Renz Research Inc., Westmont, IL, USA
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Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCRJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
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Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
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40
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Sippel KH, Bacik J, Quiocho FA, Fisher SZ. Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station. Acta Crystallogr F Struct Biol Commun 2014; 70:819-22. [PMID: 24915101 PMCID: PMC4051545 DOI: 10.1107/s2053230x14009704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP-phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by accepting a phosphate hydrogen. PBP phosphate affinity is relatively consistent across a broad pH range, indicating the capacity to bind monobasic (H2PO4-) and dibasic (HPO4(2-)) phosphate; however, the mechanism by which it might accommodate the second hydrogen of monobasic phosphate is unclear. To answer this question, neutron diffraction studies were initiated. Large single crystals with a volume of 8 mm3 were grown and subjected to hydrogen/deuterium exchange. A 2.5 Å resolution data set was collected on the Protein Crystallography Station at the Los Alamos Neutron Science Center. Initial refinement of the neutron data shows significant nuclear density, and refinement is ongoing. This is the first report of a neutron study from this superfamily.
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Affiliation(s)
- K. H. Sippel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - J. Bacik
- Bioscience Division B-11, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - F. A. Quiocho
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - S. Z. Fisher
- Scientific Activities Division, European Spallation Source, 221 00 Lund, Sweden
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41
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Dejoie C, McCusker LB, Baerlocher C, Kunz M, Tamura N. Can Laue microdiffraction be used to solve and refine complex inorganic structures? J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813026307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The white-beam Laue diffraction experiment is an attractive alternative to the more conventional monochromatic one for single-crystal structure analysis, because it takes full advantage of the X-ray energy spectrum of a synchrotron source and requires no rotation of the crystal in the beam. Therefore, it could be used for structural characterizations underin situoroperandoconditions. The potential of Laue diffraction was recognized and exploited by the protein community many years ago, and the methodology, which involved positioning and rotating the crystal in the beam, has been successfully applied to the determination of both protein and small-molecule crystal structures. Here, it is proposed that the specificities of Laue diffraction are exploited to study randomly oriented stationary microcrystals of inorganic materials. In order to determine the best strategy for collecting a reasonable quantity of data from stationary crystals, a series of simulations on four model structures for three experimental setups have been performed. It is shown that the structures of the four samples can be solved with the dual-space method inSHELX, even though the data sets are highly incomplete and much of the low-resolution part is missing. The experimental setup and data collection strategy for measuring such microcrystals have been developed on BL12.3.2 at the Advanced Light Source in Berkeley. The intensities of reflections with one and two harmonics can be extracted reliably by exploiting the tunable low-energy threshold of a Pilatus detector. In this way, the number of usable reflections can be increased from 75 to 95%. Such Laue microdiffraction data have been measured and used successfully to refine the structures of the model samples.
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Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DAA. The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2157-60. [DOI: 10.1107/s0907444913019604] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/15/2013] [Indexed: 11/11/2022]
Abstract
The first high-resolution neutron protein structure of perdeuterated rubredoxin fromPyrococcus furiosus(PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 Å resolution were collected from a relatively small 0.7 mm3PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.5 Å) from crystals with volume <1.0 mm3and with unit-cell edges <100 Å. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6°, respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (λmin= 2.0, 2.8, 3.3 Å to λmax= 3.0, 4.0, 4.5, ∼20 Å). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect thesePfRd data was 5–10 times smaller than those previously reported.
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43
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Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DAA. Neutron scattering techniques and applications in structural biology. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.16. [PMID: 23546619 DOI: 10.1002/0471140864.ps1716s72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutron scattering is exquisitely sensitive to the position, concentration, and dynamics of hydrogen atoms in materials and is a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, nondestructive suite of instruments for biophysical characterization that provides spatial and dynamic information spanning from Ångstroms to microns and from picoseconds to microseconds, respectively. Applications in structural biology range from the atomic-resolution analysis of individual hydrogen atoms in enzymes through to meso- and macro-scale analysis of complex biological structures, membranes, and assemblies. The large difference in neutron scattering length between hydrogen and deuterium allows contrast variation experiments to be performed and enables H/D isotopic labeling to be used for selective and systematic analysis of the local structure, dynamics, and interactions of multi-component systems. This overview describes the available techniques and summarizes their practical application to the study of biomolecular systems.
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Affiliation(s)
- John F Ankner
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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44
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Helliwell JR. Honouring the two Braggs: the first X-ray crystal structure and the first X-ray spectrometer. CRYSTALLOGR REV 2013. [DOI: 10.1080/0889311x.2013.797410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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45
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Dejoie C, McCusker LB, Baerlocher C, Abela R, Patterson BD, Kunz M, Tamura N. Using a non-monochromatic microbeam for serial snapshot crystallography. J Appl Crystallogr 2013. [DOI: 10.1107/s0021889813005888] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The new X-ray free-electron laser source (SwissFEL) that is currently being developed at PSI will provide a broad-bandpass mode with an energy bandwidth of about 4%. By using the full energy range, a new option for structural studies of crystalline materials may become possible. The proof of concept of broad-bandpass diffraction presented here is based on Laue single-crystal microdiffraction and the experimental setup on BL12.3.2 at the Advanced Light Source in Berkeley. Diffraction patterns for 100 randomly oriented stationary crystallites of theMFI-type zeolite ZSM-5 were simulated assuming several bandwidths, and the statistical and structural results are discussed. With a 4% energy bandwidth, the number of reflection intensities measured in a single shot is significantly higher than with monochromatic radiation. Furthermore, the problem of partial reflection measurement, which is inherent to the monochromatic mode with stationary crystals, can be overcome.
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46
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Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography. Proc Natl Acad Sci U S A 2012; 109:15301-6. [PMID: 22949690 DOI: 10.1073/pnas.1208341109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions are clearly defined, including a potential O─H…π interaction between a water molecule and the aromatic ring of residue Y44, as well as a number of potential C─H…O hydrogen bonds. Hydrogen bonding networks that are ambiguous in the 0.85 Å ultrahigh resolution X-ray structure can be resolved by accurate orientation of water molecules. Furthermore, the high resolution of the reported structure has allowed for the anisotropic description of 36 deuterium atoms in the protein. The visibility of hydrogen and deuterium atoms in the nuclear density maps is discussed in relation to the resolution of the neutron data.
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Kalinowski JA, Fournier B, Makal A, Coppens P. The LaueUtil toolkit for Laue photocrystallography. II. Spot finding and integration. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:637-646. [PMID: 22713901 PMCID: PMC3380659 DOI: 10.1107/s0909049512022637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/18/2012] [Indexed: 06/01/2023]
Abstract
A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis to identify clusters of high value pixels which form an appropriate mask corresponding to a reflection peak. The method does not require prior assumptions such as fitting of a profile or definition of an integration box. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peak's integration box. Applications in Laue photocrystallography are presented.
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Affiliation(s)
- Jarosław A. Kalinowski
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bertrand Fournier
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| | - Anna Makal
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| | - Philip Coppens
- Chemistry Department, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
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Medjoubi K, Thompson A, Bérar JF, Clemens JC, Delpierre P, Da Silva P, Dinkespiler B, Fourme R, Gourhant P, Guimaraes B, Hustache S, Idir M, Itié JP, Legrand P, Menneglier C, Mercere P, Picca F, Samama JP. Energy resolution of the CdTe-XPAD detector: calibration and potential for Laue diffraction measurements on protein crystals. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:323-331. [PMID: 22514165 DOI: 10.1107/s0909049512004463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/02/2012] [Indexed: 05/31/2023]
Abstract
The XPAD3S-CdTe, a CdTe photon-counting pixel array detector, has been used to measure the energy and the intensity of the white-beam diffraction from a lysozyme crystal. A method was developed to calibrate the detector in terms of energy, allowing incident photon energy measurement to high resolution (approximately 140 eV), opening up new possibilities in energy-resolved X-ray diffraction. In order to demonstrate this, Laue diffraction experiments were performed on the bending-magnet beamline METROLOGIE at Synchrotron SOLEIL. The X-ray energy spectra of diffracted spots were deduced from the indexed Laue patterns collected with an imaging-plate detector and then measured with both the XPAD3S-CdTe and the XPAD3S-Si, a silicon photon-counting pixel array detector. The predicted and measured energy of selected diffraction spots are in good agreement, demonstrating the reliability of the calibration method. These results open up the way to direct unit-cell parameter determination and the measurement of high-quality Laue data even at low resolution. Based on the success of these measurements, potential applications in X-ray diffraction opened up by this type of technology are discussed.
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Affiliation(s)
- Kadda Medjoubi
- Synchrotron Soleil, BP 48, Saint-Aubin, Gif sur Yvette 91192, France.
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Chen JCH, Fisher Z, Kovalevsky AY, Mustyakimov M, Hanson BL, Zhurov VV, Langan P. Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:119-23. [PMID: 22297981 PMCID: PMC3274385 DOI: 10.1107/s1744309111051499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 11/30/2011] [Indexed: 03/04/2023]
Abstract
The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.
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Affiliation(s)
- Julian C-H Chen
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.
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50
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Helliwell JR. The evolution of synchrotron radiation and the growth of its importance in crystallography. CRYSTALLOGR REV 2012. [DOI: 10.1080/0889311x.2011.631919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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