1
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Chavas LMG, Coulibaly F, Garriga D. Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography. IUCRJ 2024; 11:476-485. [PMID: 38958014 PMCID: PMC11220871 DOI: 10.1107/s205225252400513x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
A series of events underscoring the significant advancements in micro-crystallization and in vivo crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale.
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Affiliation(s)
| | - Fasséli Coulibaly
- Biomedicine Discovery Institute & Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
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2
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Krause L, Gjørup FH, Jørgensen MRV. xrdPlanner: exploring area detector geometries for powder diffraction and total scattering experiments. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:394-398. [PMID: 38306298 PMCID: PMC10914179 DOI: 10.1107/s1600577523011086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/27/2023] [Indexed: 02/04/2024]
Abstract
xrdPlanner is a software package designed to aid in the planning and preparation of powder X-ray diffraction and total scattering beam times at synchrotron facilities. Many modern beamlines provide a flexible experimental setup and may have several different detectors available. In combination with a range of available X-ray energies, it often makes it difficult for the user to explore the available parameter space relevant for a given experiment prior to the scheduled beam time. xrdPlanner was developed to provide a fast and straightforward tool that allows users to visualize the accessible part of reciprocal space of their experiment at a given combination of photon energy and detector geometry. To plan and communicate the necessary geometry not only saves time but also helps the beamline staff to prepare and accommodate for an experiment. The program is tailored toward powder X-ray diffraction and total scattering experiments but may also be useful for other experiments that rely on an area detector and for which detector placement and achievable momentum-transfer range are important experimental parameters.
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Affiliation(s)
- Lennard Krause
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund, Sweden
| | - Frederik Holm Gjørup
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund, Sweden
- iNANO, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Mads Ry Vogel Jørgensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund, Sweden
- iNANO, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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3
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Hattne J, Clabbers MTB, Martynowycz MW, Gonen T. Electron counting with direct electron detectors in MicroED. Structure 2023; 31:1504-1509.e1. [PMID: 37992709 PMCID: PMC10756876 DOI: 10.1016/j.str.2023.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the number of electrons used for data collection. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease fluence also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. The major concern with electron-counting direct detectors lies at the low end of the resolution spectrum: their limited linear range makes strong low-resolution reflections susceptible to coincidence loss and careful data collection is required to avoid compromising data quality. Nevertheless, these cameras are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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4
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Babu AV, Zhou T, Kandel S, Bicer T, Liu Z, Judge W, Ching DJ, Jiang Y, Veseli S, Henke S, Chard R, Yao Y, Sirazitdinova E, Gupta G, Holt MV, Foster IT, Miceli A, Cherukara MJ. Deep learning at the edge enables real-time streaming ptychographic imaging. Nat Commun 2023; 14:7059. [PMID: 37923741 PMCID: PMC10624836 DOI: 10.1038/s41467-023-41496-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/06/2023] [Indexed: 11/06/2023] Open
Abstract
Coherent imaging techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent imaging methods like ptychography are poised to revolutionize nanoscale materials characterization. However, these advancements are accompanied by significant increase in data and compute needs, which precludes real-time imaging, feedback and decision-making capabilities with conventional approaches. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the oversampling constraints, allowing low-dose imaging using orders of magnitude less data than required by traditional methods.
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Affiliation(s)
- Anakha V Babu
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
- KLA Corporation, Ann Arbor, MI, USA
| | - Tao Zhou
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Saugat Kandel
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Tekin Bicer
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Zhengchun Liu
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - William Judge
- Department of Chemistry, University of Illinois, Chicago, IL, USA
| | - Daniel J Ching
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Yi Jiang
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Sinisa Veseli
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Steven Henke
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Ryan Chard
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Yudong Yao
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | | | | | - Martin V Holt
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Ian T Foster
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA
| | - Antonino Miceli
- Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL, USA.
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5
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Hattne J, Clabbers MTB, Martynowycz MW, Gonen T. Electron-counting in MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547123. [PMID: 37425889 PMCID: PMC10327187 DOI: 10.1101/2023.06.29.547123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the exposure. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease the exposure also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. However, the dynamic range of electron-counting detectors requires careful data collection to avoid errors from coincidence loss. Nevertheless, these detectors are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Max T. B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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6
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Sowerby K, Freitag-Pohl S, Murillo AM, Silber AM, Pohl E. Cysteine synthase: multiple structures of a key enzyme in cysteine synthesis and a potential drug target for Chagas disease and leishmaniasis. Acta Crystallogr D Struct Biol 2023; 79:518-530. [PMID: 37204818 PMCID: PMC10233618 DOI: 10.1107/s2059798323003613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/20/2023] [Indexed: 05/20/2023] Open
Abstract
Chagas disease is a neglected tropical disease (NTD) caused by Trypanosoma cruzi, whilst leishmaniasis, which is caused by over 20 species of Leishmania, represents a group of NTDs endemic to most countries in the tropical and subtropical belt of the planet. These diseases remain a significant health problem both in endemic countries and globally. These parasites and other trypanosomatids, including T. theileri, a bovine pathogen, rely on cysteine biosynthesis for the production of trypanothione, which is essential for parasite survival in hosts. The de novo pathway of cysteine biosynthesis requires the conversion of O-acetyl-L-serine into L-cysteine, which is catalysed by cysteine synthase (CS). These enzymes present potential for drug development against T. cruzi, Leishmania spp. and T. theileri. To enable these possibilities, biochemical and crystallographic studies of CS from T. cruzi (TcCS), L. infantum (LiCS) and T. theileri (TthCS) were conducted. Crystal structures of the three enzymes were determined at resolutions of 1.80 Å for TcCS, 1.75 Å for LiCS and 2.75 Å for TthCS. These three homodimeric structures show the same overall fold and demonstrate that the active-site geometry is conserved, supporting a common reaction mechanism. Detailed structural analysis revealed reaction intermediates of the de novo pathway ranging from an apo structure of LiCS and holo structures of both TcCS and TthCS to the substrate-bound structure of TcCS. These structures will allow exploration of the active site for the design of novel inhibitors. Additionally, unexpected binding sites discovered at the dimer interface represent new potential for the development of protein-protein inhibitors.
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Affiliation(s)
- Kate Sowerby
- Department of Chemistry, Durham University, Durham, United Kingdom
| | | | | | | | - Ehmke Pohl
- Department of Chemistry, Durham University, Durham, United Kingdom
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7
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Jasilionis A, Plotka M, Wang L, Dorawa S, Lange J, Watzlawick H, van den Bergh T, Vroling B, Altenbuchner J, Kaczorowska AK, Pohl E, Kaczorowski T, Nordberg Karlsson E, Freitag-Pohl S. AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. Protein Sci 2023; 32:e4585. [PMID: 36721347 PMCID: PMC9929850 DOI: 10.1002/pro.4585] [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: 11/23/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
Bacteriophages encode a wide variety of cell wall disrupting enzymes that aid the viral escape in the final stages of infection. These lytic enzymes have accumulated notable interest due to their potential as novel antibacterials for infection treatment caused by multiple-drug resistant bacteria. Here, the detailed functional and structural characterization of Thermus parvatiensis prophage peptidoglycan lytic amidase AmiP, a globular Amidase_3 type lytic enzyme adapted to high temperatures is presented. The sequence and structure comparison with homologous lytic amidases reveals the key adaptation traits that ensure the activity and stability of AmiP at high temperatures. The crystal structure determined at a resolution of 1.8 Å displays a compact α/β-fold with multiple secondary structure elements omitted or shortened compared with protein structures of similar proteins. The functional characterization of AmiP demonstrates high efficiency of catalytic activity and broad substrate specificity toward thermophilic and mesophilic bacteria strains containing Orn-type or DAP-type peptidoglycan. The here presented AmiP constitutes the most thermoactive and ultrathermostable Amidase_3 type lytic enzyme biochemically characterized with a temperature optimum at 85°C. The extraordinary high melting temperature Tm 102.6°C confirms fold stability up to approximately 100°C. Furthermore, AmiP is shown to be more active over the alkaline pH range with pH optimum at pH 8.5 and tolerates NaCl up to 300 mM with the activity optimum at 25 mM NaCl. This set of beneficial characteristics suggests that AmiP can be further exploited in biotechnology.
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Affiliation(s)
- Andrius Jasilionis
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Lei Wang
- Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | | | | | | | - Josef Altenbuchner
- Institute of Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Ehmke Pohl
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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8
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Leonarski F, Brückner M, Lopez-Cuenca C, Mozzanica A, Stadler HC, Matěj Z, Castellane A, Mesnet B, Wojdyla JA, Schmitt B, Wang M. Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:227-234. [PMID: 36601941 PMCID: PMC9814052 DOI: 10.1107/s1600577522010268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
The JUNGFRAU 4-megapixel (4M) charge-integrating pixel-array detector, when operated at a full 2 kHz frame rate, streams data at a rate of 17 GB s-1. To operate this detector for macromolecular crystallography beamlines, a data-acquisition system called Jungfraujoch was developed. The system, running on a single server with field-programmable gate arrays and general-purpose graphics processing units, is capable of handling data produced by the JUNGFRAU 4M detector, including conversion of raw pixel readout to photon counts, compression and on-the-fly spot finding. It was also demonstrated that 30 GB s-1 can be handled in performance tests, indicating that the operation of even larger and faster detectors will be achievable in the future. The source code is available from a public repository.
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Affiliation(s)
- Filip Leonarski
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Martin Brückner
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Carlos Lopez-Cuenca
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Hans-Christian Stadler
- Scientific Computing, Theory and Data Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Zdeněk Matěj
- MAX IV Laboratory, Lund University, Fotongatan 2, 221 00 Lund, Sweden
| | | | - Bruno Mesnet
- IBM France, 21 av Simone Veil, 06206 Nice, France
| | | | - Bernd Schmitt
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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9
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Levenstein MA, Robertson K, Turner TD, Hunter L, O’Brien C, O’Shaughnessy C, Kulak AN, Le Magueres P, Wojciechowski J, Mykhaylyk OO, Kapur N, Meldrum FC. Serial small- and wide-angle X-ray scattering with laboratory sources. IUCRJ 2022; 9:538-543. [PMID: 36071805 PMCID: PMC9438489 DOI: 10.1107/s2052252522007631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in X-ray instrumentation and sample injection systems have enabled serial crystallography of protein nanocrystals and the rapid structural analysis of dynamic processes. However, this progress has been restricted to large-scale X-ray free-electron laser (XFEL) and synchrotron facilities, which are often oversubscribed and have long waiting times. Here, we explore the potential of state-of-the-art laboratory X-ray systems to perform comparable analyses when coupled to micro- and millifluidic sample environments. Our results demonstrate that commercial small- and wide-angle X-ray scattering (SAXS/WAXS) instruments and X-ray diffractometers are ready to access samples and timescales (≳5 ms) relevant to many processes in materials science including the preparation of pharmaceuticals, nanoparticles and functional crystalline materials. Tests of different X-ray instruments highlighted the importance of the optical configuration and revealed that serial WAXS/XRD analysis of the investigated samples was only possible with the higher flux of a microfocus setup. We expect that these results will also stimulate similar developments for structural biology.
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Affiliation(s)
| | - Karen Robertson
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Thomas D. Turner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Liam Hunter
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Cate O’Brien
- Soft Matter Analytical Laboratory, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Cedrick O’Shaughnessy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Alexander N. Kulak
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Pierre Le Magueres
- Rigaku Americas Corporation, 9009 New Tails Drive, The Woodlands, TX 77381, USA
| | | | - Oleksandr O. Mykhaylyk
- Soft Matter Analytical Laboratory, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - Nikil Kapur
- School of Mechanical Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Fiona C. Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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10
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Liu J, Makowski L. Scanning x-ray microdiffraction: In situ molecular imaging of tissue and materials. Curr Opin Struct Biol 2022; 75:102421. [PMID: 35834949 PMCID: PMC11317818 DOI: 10.1016/j.sbi.2022.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
Scanning x-ray microdiffraction of complex tissues and materials is an emerging method for the study of macromolecular structures in situ, providing information on the way molecular constituents are arranged and interact with their microenvironment. Acting as a bridge between high-resolution images of individual constituents and lower resolution microscopies that generate global views of material, scanning microdiffraction provides an approach to study the functioning of complex tissues across multiple length scales. Here, we discuss the methodology, summarize results from recent studies, and discuss the potential of the technique for future studies coordinated with other biophysical techniques.
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Affiliation(s)
- Jiliang Liu
- The European Radiation Synchrotron Facility (ESRF), Grenoble, France
| | - Lee Makowski
- Bioengineering Department, Northeastern University, Boston, MA, USA.
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11
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Hirano K, Sugiyama H, Nishimura R, Wakabayashi D, Suzuki Y, Igarashi N, Funamori N. X-ray zooming optics for analyzer-based multi-contrast computed tomography. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:787-793. [PMID: 35511011 PMCID: PMC9070698 DOI: 10.1107/s1600577522001412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
An X-ray analyzer-based optics with a zoom function is proposed for observing various samples with apparent-absorption contrast, phase contrast and scattering contrast. The proposed X-ray optics consists of a collimator crystal and an analyzer crystal arranged in a nondispersive (+, -) geometry with a sample placed between them. For the implementation of the zoom function, an asymmetrically cut crystal in the rotated-inclined geometry was used for the analyzer. Proof-of-principle experiments were performed at the vertical wiggler beamline BL-14B of the Photon Factory. First, the magnification was set to 1×, and then it was zoomed into the optimal magnification (10×). At these magnifications, tri-modal contrast cross-sectional images of a sample were obtained by computed tomography. It was confirmed that the image quality at 10× was superior to that at 1×. This achievement opens up new possibilities for observing an entire sample or regions of interest within a sample at optimal magnification, and is expected to be useful for materials science, condensed matter physics, archeology and biomedical science.
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Affiliation(s)
- Keiichi Hirano
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroshi Sugiyama
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Ryutaro Nishimura
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Daisuke Wakabayashi
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yoshio Suzuki
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Noriyuki Igarashi
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobumasa Funamori
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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12
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Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA binding site. J Biol Chem 2022; 298:101571. [PMID: 35007529 PMCID: PMC8844858 DOI: 10.1016/j.jbc.2022.101571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023] Open
Abstract
Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin antibiotics in Gram-positive bacteria and mycobacteria. Although structural information for ErmAM, ErmC, and ErmE exists from Gram-positive bacteria, little is known about the Erms in mycobacteria, as there are limited biochemical data and no structures available. Here, we present crystal structures of Erm38 from Mycobacterium smegmatis in apoprotein and cofactor-bound forms. Based on structural analysis and mutagenesis, we identified several catalytically critical, positively charged residues at a putative RNA-binding site. We found that mutation of any of these sites is sufficient to abolish methylation activity, whereas the corresponding RNA-binding affinity of Erm38 remains unchanged. The methylation reaction thus appears to require a precise ensemble of amino acids to accurately position the RNA substrate, such that the target nucleotide can be methylated. In addition, we computationally constructed a model of Erm38 in complex with a 32-mer RNA substrate. This model shows the RNA substrate stably bound to Erm38 by a patch of positively charged residues. Furthermore, a π-π stacking interaction between a key aromatic residue of Erm38 and a target adenine of the RNA substrate forms a critical interaction needed for methylation. Taken together, these data provide valuable insights into Erm–RNA interactions, which will aid subsequent structure-based drug design efforts.
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13
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Koch RJ, Roth N, Liu Y, Ivashko O, Dippel AC, Petrovic C, Iversen BB, V Zimmermann M, Bozin ES. On single-crystal total scattering data reduction and correction protocols for analysis in direct space. Acta Crystallogr A Found Adv 2021; 77:611-636. [PMID: 34726636 DOI: 10.1107/s2053273321010159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
Data reduction and correction steps and processed data reproducibility in the emerging single-crystal total-scattering-based technique of three-dimensional differential atomic pair distribution function (3D-ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high-energy X-ray beam and a flat-panel area detector. Computational overhead as pertains to data sampling and the associated data-processing steps is also discussed. Various aspects of the final 3D-ΔPDF reproducibility are explicitly tested by varying the data-processing order and included steps, and by carrying out a crystal-to-crystal data comparison. Situations in which the 3D-ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D-ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in-depth analysis of some of the effects of the data-processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field.
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Affiliation(s)
- Robert J Koch
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nikolaj Roth
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, DK-8000, Aarhus, Denmark
| | - Yiu Liu
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleh Ivashko
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | - Cedomir Petrovic
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Bo B Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, DK-8000, Aarhus, Denmark
| | | | - Emil S Bozin
- Condensed Matter Physics and Materials Science Division, Brookhaven National Laboratory, Upton, NY 11973, USA
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14
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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15
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Hadian-Jazi M, Sadri A, Barty A, Yefanov O, Galchenkova M, Oberthuer D, Komadina D, Brehm W, Kirkwood H, Mills G, de Wijn R, Letrun R, Kloos M, Vakili M, Gelisio L, Darmanin C, Mancuso AP, Chapman HN, Abbey B. Data reduction for serial crystallography using a robust peak finder. J Appl Crystallogr 2021; 54:1360-1378. [PMID: 34667447 PMCID: PMC8493619 DOI: 10.1107/s1600576721007317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of 'robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or 'vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
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Affiliation(s)
- Marjan Hadian-Jazi
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
- Australian Nuclear Science and Technology Organisation (ANSTO), Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alireza Sadri
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dana Komadina
- 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
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - 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 Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
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16
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Terrill NJ, Dent AJ, Dobson B, Beale AM, Allen L, Bras W. Past, present and future-sample environments for materials research studies in scattering and spectroscopy; a UK perspective. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:483002. [PMID: 34479225 DOI: 10.1088/1361-648x/ac2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Small angle x-ray scattering and x-ray absorption fine structure are two techniques that have been employed at synchrotron sources ever since their inception. Over the course of the development of the techniques, the introduction of sample environments for added value experiments has grown dramatically. This article reviews past successes, current developments and an exploration of future possibilities for these two x-ray techniques with an emphasis on the developments in the United Kingdom between 1980-2020.
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Affiliation(s)
| | - Andrew J Dent
- Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Barry Dobson
- Sagentia Ltd, Harston Mill, Harston Mill, CB22 7GG, United Kingdom
| | - Andrew M Beale
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
- The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom
| | - Lisa Allen
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
- The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom
| | - Wim Bras
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, One Bethel Valley Road TN 37831, United States of America
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17
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Jiang N, Zhang D. Solution Self-Assembly of Coil-Crystalline Diblock Copolypeptoids Bearing Alkyl Side Chains. Polymers (Basel) 2021; 13:3131. [PMID: 34578031 PMCID: PMC8473287 DOI: 10.3390/polym13183131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Polypeptoids, a class of synthetic peptidomimetic polymers, have attracted increasing attention due to their potential for biotechnological applications, such as drug/gene delivery, sensing and molecular recognition. Recent investigations on the solution self-assembly of amphiphilic block copolypeptoids highlighted their capability to form a variety of nanostructures with tailorable morphologies and functionalities. Here, we review our recent findings on the solutions self-assembly of coil-crystalline diblock copolypeptoids bearing alkyl side chains. We highlight the solution self-assembly pathways of these polypeptoid block copolymers and show how molecular packing and crystallization of these building blocks affect the self-assembly behavior, resulting in one-dimensional (1D), two-dimensional (2D) and multidimensional hierarchical polymeric nanostructures in solution.
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Affiliation(s)
- Naisheng Jiang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Donghui Zhang
- Macromolecular Studies Group, Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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18
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Baba S, Matsuura H, Kawamura T, Sakai N, Nakamura Y, Kawano Y, Mizuno N, Kumasaka T, Yamamoto M, Hirata K. Guidelines for de novo phasing using multiple small-wedge data collection. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1284-1295. [PMID: 34475278 PMCID: PMC8415328 DOI: 10.1107/s1600577521008067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/05/2021] [Indexed: 05/30/2023]
Abstract
Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5-20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for de novo structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.
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Affiliation(s)
- Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Kawamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Naoki Sakai
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuki Nakamura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshiaki Kawano
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Nobuhiro Mizuno
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Masaki Yamamoto
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kunio Hirata
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-gun, Hyogo 679-5148, Japan
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19
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Guimarães BG, Golinelli-Pimpaneau B. De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing. Curr Res Struct Biol 2021; 3:112-120. [PMID: 34235491 PMCID: PMC8244422 DOI: 10.1016/j.crstbi.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 10/25/2022] Open
Abstract
Single-wavelength anomalous dispersion (SAD)-phasing using sulfur as the unique anomalous scatterer is a powerful method to solve the phase problem in protein crystallography. However, it is not yet widely used by non-expert crystallographers. We report here the structure determination of the double stranded RNA binding domain of human dihydrouridine synthase using the sulfur-SAD method and highly redundant data collected at 1.8 Å ("off-edge"), at which the estimated overall anomalous signal was 1.08%. High multiplicity data were collected on a single crystal rotated along the ϕ or ω axis at different κ angles, with the primary beam intensity being attenuated from 50% to 95%, compared to data collection at 0.98 Å, to reduce radiation damage. SHELXD succeeded to locate 14 out 15 sulfur sites only using the data sets recorded with highest beam attenuation, which provided phases sufficient for structure solving. In an attempt to stimulate the use of sulfur-SAD phasing by a broader community of crystallographers, we describe our experimental strategy together with a compilation of previous successful cases, suggesting that sulfur-SAD phasing should be attempted for determining the de novo structure of any protein with average sulfur content diffracting better than 3 Å resolution.
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Affiliation(s)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75005 Paris, France
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20
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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21
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Gruzinov AY, Schroer MA, Manalastas-Cantos K, Kikhney AG, Hajizadeh NR, Schulz F, Franke D, Svergun DI, Blanchet CE. Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:812-823. [PMID: 33949989 PMCID: PMC8127372 DOI: 10.1107/s1600577521003404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/30/2021] [Indexed: 05/09/2023]
Abstract
Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X-rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
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Affiliation(s)
- Andrey Yu. Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Karen Manalastas-Cantos
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Center for Data and Computing in Natural Science, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Alexey G. Kikhney
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nelly R. Hajizadeh
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Novartis, Novartis Campus, Fabrikstrasse 2, 4056 Basel, Switzerland
| | - Florian Schulz
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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22
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Angular super-resolution retrieval in small-angle X-ray scattering. Sci Rep 2020; 10:16038. [PMID: 32994517 PMCID: PMC7525553 DOI: 10.1038/s41598-020-73030-2] [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: 06/03/2020] [Accepted: 08/31/2020] [Indexed: 11/21/2022] Open
Abstract
Small-angle X-ray scattering (SAXS) techniques enable convenient nanoscopic characterization for various systems and conditions. Unlike synchrotron-based setups, lab-based SAXS systems intrinsically suffer from lower X-ray flux and limited angular resolution. Here, we develop a two-step retrieval methodology to enhance the angular resolution for given experimental conditions. Using minute hardware additions, we show that translating the X-ray detector in subpixel steps and modifying the incoming beam shape results in a set of 2D scattering images, which is sufficient for super-resolution SAXS retrieval. The technique is verified experimentally to show superior resolution. Such advantages have a direct impact on the ability to resolve finer nanoscopic structures and can be implemented in most existing SAXS apparatuses both using synchrotron- and laboratory-based sources.
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23
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Doukov T, Herschlag D, Yabukarski F. Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. J Appl Crystallogr 2020; 53:1493-1501. [PMID: 33312102 PMCID: PMC7710493 DOI: 10.1107/s1600576720013503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/08/2020] [Indexed: 11/10/2022] Open
Abstract
Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.
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Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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24
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Goh BC, Chua YK, Qian X, Lin J, Savko M, Dedon PC, Lescar J. Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of β-lactam antibiotics. J Struct Biol 2020; 212:107610. [DOI: 10.1016/j.jsb.2020.107610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
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25
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Hybrid pixel direct detector for electron energy loss spectroscopy. Ultramicroscopy 2020; 217:113067. [DOI: 10.1016/j.ultramic.2020.113067] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 11/22/2022]
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26
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Makinde ZO, van der Heijden NJ, Domigan LJ, McGillivray DJ, Williams DE. Aligned Assembly in a 2-D Gel of a Water-Soluble Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11292-11302. [PMID: 32882136 DOI: 10.1021/acs.langmuir.0c01944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We demonstrate the assembly of a compact, gel-like Langmuir-Blodgett film of rods formed by self-assembly of a β-sheet-forming water-soluble peptide, Ac-IKHLSVN-NH2, at the surface of aqueous electrolytes. We characterize surface pressure hysteresis and demonstrate shear stiffening of the surface caused by area cycling, which we interpret as due to rearrangement and alignment of the rods. We show strong effects of the electrolyte on the assembly of the elementary rods, which can be related to the Hofmeister series and interpreted by effects on the interaction energies mediated by ions and water. Formation of β-sheet structures and assembly of these into surface-segregated semicrystalline gels was strongly promoted by ammonium sulfate electrolyte. With ammonium sulfate electrolyte as subphase for Langmuir-Blodgett film deposition, shear stiffening by surface area cycling resulted in very compact films on transfer to a substrate.
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Affiliation(s)
- Zainab O Makinde
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Nadine J van der Heijden
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Laura J Domigan
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
- Department of Chemical and Materials Engineering, The University of Auckland, Auckland 1010, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - David E Williams
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
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27
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Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCRJ 2020; 7:728-736. [PMID: 32695419 PMCID: PMC7340269 DOI: 10.1107/s2052252520007411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, Grenoble Cedex 9, 38044, France
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28
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Krause L, Tolborg K, Grønbech TBE, Sugimoto K, Iversen BB, Overgaard J. Accurate high-resolution single-crystal diffraction data from a Pilatus3 X CdTe detector. J Appl Crystallogr 2020; 53:635-649. [PMID: 32684879 PMCID: PMC7312157 DOI: 10.1107/s1600576720003775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/14/2020] [Indexed: 11/10/2022] Open
Abstract
Hybrid photon-counting detectors are widely established at third-generation synchrotron facilities and the specifications of the Pilatus3 X CdTe were quickly recognized as highly promising in charge-density investigations. This is mainly attributable to the detection efficiency in the high-energy X-ray regime, in combination with a dynamic range and noise level that should overcome the perpetual problem of detecting strong and weak data simultaneously. These benefits, however, come at the expense of a persistent problem for high diffracted beam flux, which is particularly problematic in single-crystal diffraction of materials with strong scattering power and sharp diffraction peaks. Here, an in-depth examination of data collected on an inorganic material, FeSb2, and an organic semiconductor, rubrene, revealed systematic differences in strong intensities for different incoming beam fluxes, and the implemented detector intensity corrections were found to be inadequate. Only significant beam attenuation for the collection of strong reflections was able to circumvent this systematic error. All data were collected on a bending-magnet beamline at a third-generation synchrotron radiation facility, so undulator and wiggler beamlines and fourth-generation synchrotrons will be even more prone to this error. On the other hand, the low background now allows for an accurate measurement of very weak intensities, and it is shown that it is possible to extract structure factors of exceptional quality using standard crystallographic software for data processing (SAINT-Plus, SADABS and SORTAV), although special attention has to be paid to the estimation of the background. This study resulted in electron-density models of substantially higher accuracy and precision compared with a previous investigation, thus for the first time fulfilling the promise of photon-counting detectors for very accurate structure factor measurements.
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Affiliation(s)
- Lennard Krause
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Kasper Tolborg
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Thomas Bjørn Egede Grønbech
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Kunihisa Sugimoto
- SPring-8, JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Bo Brummerstedt Iversen
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus 8000, Denmark
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29
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Kuwajima K. The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins. Biomolecules 2020; 10:biom10030407. [PMID: 32155758 PMCID: PMC7175247 DOI: 10.3390/biom10030407] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 11/16/2022] Open
Abstract
From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms of protein folding. This article describes how the presence of the two types of folding behavior has been confirmed experimentally, and discusses the relationships between the two-state and the non-two-state folding reactions, on the basis of available data on the correlations of the folding rate constant with various structure-based properties, which are determined primarily by the backbone topology of proteins. Finally, a two-stage hierarchical model is proposed as a general mechanism of protein folding. In this model, protein folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the molten globule state as a folding intermediate. The two-state folding is thus merely a simplified version of the hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ; Tel.: +81-90-5435-6540
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul 02455, Korea
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30
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Vos BE, Martinez-Torres C, Burla F, Weisel JW, Koenderink GH. Revealing the molecular origins of fibrin's elastomeric properties by in situ X-ray scattering. Acta Biomater 2020; 104:39-52. [PMID: 31923718 DOI: 10.1016/j.actbio.2020.01.002] [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: 10/08/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 01/01/2023]
Abstract
Fibrin is an elastomeric protein forming highly extensible fiber networks that provide the scaffold of blood clots. Here we reveal the molecular mechanisms that explain the large extensibility of fibrin networks by performing in situ small angle X-ray scattering measurements while applying a shear deformation. We simultaneously measure shear-induced alignment of the fibers and changes in their axially ordered molecular packing structure. We show that fibrin networks exhibit distinct structural responses that set in consecutively as the shear strain is increased. They exhibit an entropic response at small strains (<5%), followed by progressive fiber alignment (>25% strain) and finally changes in the fiber packing structure at high strain (>100%). Stretching reduces the fiber packing order and slightly increases the axial periodicity, indicative of molecular unfolding. However, the axial periodicity changes only by 0.7%, much less than the 80% length increase of the fibers, suggesting that fiber elongation mainly stems from uncoiling of the natively disordered αC-peptide linkers that laterally bond the molecules. Upon removal of the load, the network structure returns to the original isotropic state, but the fiber structure becomes more ordered and adopts a smaller packing periodicity compared to the original state. We conclude that the hierarchical packing structure of fibrin fibers, with built-in disorder, makes the fibers extensible and allows for mechanical annealing. Our results provide a basis for interpreting the molecular basis of haemostatic and thrombotic disorders associated with clotting and provide inspiration to design resilient bio-mimicking materials. STATEMENT OF SIGNIFICANCE: Fibrin provides structural integrity to blood clots and is also widely used as a scaffold for tissue engineering. To fulfill their biological functions, fibrin networks have to be simultaneously compliant like skin and resilient against rupture. Here, we unravel the structural origin underlying this remarkable mechanical behaviour. To this end, we performed in situ measurements of fibrin structure across multiple length scales by combining X-ray scattering with shear rheology. Our findings show that fibrin sustains large strains by undergoing a sequence of structural changes on different scales with increasing strain levels. This demonstrates new mechanistic aspects of an important biomaterial's structure and its mechanical function, and serves as an example in the design of biomimicking materials.
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31
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Franke D, Hajizadeh NR, Svergun DI. Simulation of small-angle X-ray scattering data of biological macromolecules in solution. J Appl Crystallogr 2020; 53:536-539. [PMID: 32280325 PMCID: PMC7133063 DOI: 10.1107/s1600576720000527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/14/2020] [Indexed: 11/21/2022] Open
Abstract
An application is presented to simulate images on an area detector for isotropic small-angle X-ray scattering, explicitly accounting for the experimental geometry and yielding radially averaged 1D scattering patterns with statistically appropriate variations. This article presents IMSIM, an application to simulate two-dimensional small-angle X-ray scattering patterns and, further, one-dimensional profiles from biological macromolecules in solution. IMSIM implements a statistical approach yielding two-dimensional images in TIFF, CBF or EDF format, which may be readily processed by existing data-analysis pipelines. Intensities and error estimates of one-dimensional patterns obtained from the radial average of the two-dimensional images exhibit the same statistical properties as observed with actual experimental data. With initial input on an absolute scale, [cm−1]/c[mg ml−1], the simulated data frames may also be scaled to absolute scale such that the forward scattering after subtraction of the background is proportional to the molecular weight of the solute. The effects of changes of concentration, exposure time, flux, wavelength, sample–detector distance, detector dimensions, pixel size, and the mask as well as incident beam position can be considered for the simulation. The simulated data may be used in method development, for educational purposes, and also to determine the most suitable beamline setup for a project prior to the application and use of the actual beamtime. IMSIM is available as part of the ATSAS software package (3.0.0) and is freely available for academic use (http://www.embl-hamburg.de/biosaxs/download.html).
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Affiliation(s)
- Daniel Franke
- European Molecular Biology Laboratory, Notkestrasse 85 c/o DESY, Hamburg, 22607, Germany
| | - Nelly R Hajizadeh
- European Molecular Biology Laboratory, Notkestrasse 85 c/o DESY, Hamburg, 22607, Germany.,ETH, ScopeM IDA Group, HPZ G 35.1, John-von-Neumann-Weg 9, 8093, Zurich, Switzerland
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Notkestrasse 85 c/o DESY, Hamburg, 22607, Germany
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32
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Abstract
Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.
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Affiliation(s)
- Birger Dittrich
- Novartis Campus
- Novartis Pharma AG
- Basel CH-4002
- Switzerland
- Institut für Anorganische Chemie und Strukturchemie
| | - Christoph Sever
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Jens Lübben
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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33
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High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur. Molecules 2019; 24:molecules24244451. [PMID: 31817305 PMCID: PMC6943606 DOI: 10.3390/molecules24244451] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022] Open
Abstract
The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.
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34
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Wang T, Tian N, Chen J, Huang L, Sun G, Gong J, Liu D. Revisiting flow-induced crystallization of polyethylene inversely: An in situ swelling SANS study. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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Freitag-Pohl S, Jasilionis A, Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E. Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol 2019; 75:1028-1039. [PMID: 31692476 PMCID: PMC6834076 DOI: 10.1107/s2059798319013330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022] Open
Abstract
As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.
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Affiliation(s)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Rebeka Kovačič
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Hildegard Watzlawick
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lei Wang
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Magdalena Płotka
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Anna Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | | | | | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, England
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36
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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37
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Abstract
Until recently X-ray crystallography has been the standard technique for virus structure determinations. Available X-ray sources have continuously improved over the decades, leading to the realization of X-ray free-electron lasers (XFELs). They provide high-intensity femtosecond X-ray pulses, which allow for new kinds of experiments by making use of the diffraction-before-destruction principle. By overcoming classical dose constraints, they at least in principle allow researchers to perform X-ray virus structure determination for single particles at room temperature. Simultaneously, the availability of XFELs led to the development of the method of serial femtosecond crystallography, where a crystal structure is determined from the measurement of hundreds to thousands of microcrystals. In the case of virus crystallography this method does not require freezing of the crystals and allows researchers to perform experiments under non-equilibrium conditions (e.g., by laser-induced temperature jumps or rapid chemical mixing), which is currently not possible with electron microscopy.
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Affiliation(s)
- A. Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - M.O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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38
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Kihara S, De Zoysa GH, Shahlori R, Vadakkedath PG, Ryan TM, Mata JP, Sarojini V, McGillivray DJ. Solution structure of linear battacin lipopeptides - the effect of lengthening fatty acid chain. SOFT MATTER 2019; 15:7501-7508. [PMID: 31528955 DOI: 10.1039/c9sm00932a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, lipopeptides have received attention for their enhanced antimicrobial activity, especially against multi-drug resistant (MDR) pathogens. We have previously reported that the bacterial soil extracted, novel cyclic lipopeptide, battacin, and its synthetic analogues have enhanced antimicrobial activity against various Gram negative, Gram positive and fungal pathogens. In particular, the modification of the hydrophobic fatty acid chain and molecular structure has improved its activity. We have used small angle X-ray scattering (SAXS) and circular dichroism (CD) to characterise the low resolution structure of battacin lipopeptides containing covalently bonded fatty acid chains and the one without it. In the absence of fatty acids or with short fatty acid chain, the peptides adopted an extended random coil structure that is best described barbell-like shape, while fatty acids that are sufficiently long induced an aggregation into a ∼4.0 nm diameter core shell sphere. While the kinked structure found within this barbell shape may have a role in antimicrobial activities, the self-assembly of the battacin analogue with the longest fatty acid chain may have a correlation to the declined antibacterial activities.
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Affiliation(s)
- Shinji Kihara
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand.
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39
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Tolstikova A, Levantino M, Yefanov O, Hennicke V, Fischer P, Meyer J, Mozzanica A, Redford S, Crosas E, Opara NL, Barthelmess M, Lieske J, Oberthuer D, Wator E, Mohacsi I, Wulff M, Schmitt B, Chapman HN, Meents A. 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector. IUCRJ 2019; 6:927-937. [PMID: 31576225 PMCID: PMC6760437 DOI: 10.1107/s205225251900914x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/25/2019] [Indexed: 05/18/2023]
Abstract
Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.
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Affiliation(s)
- A. Tolstikova
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - M. Levantino
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - O. Yefanov
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - V. Hennicke
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - P. Fischer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Meyer
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - A. Mozzanica
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - S. Redford
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - E. Crosas
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - N. L. Opara
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
- C-CINA, Biozentrum, University of Basel, Mattenstrasse 26, 4002 Basel, Switzerland
| | - M. Barthelmess
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - J. Lieske
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - D. Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - E. Wator
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow 30-387, Poland
| | - I. Mohacsi
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Wulff
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - B. Schmitt
- Paul Scherrer Institute, 111 Forschungsstrasse, 5232 Villigen, Switzerland
| | - 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, University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Germany
| | - A. Meents
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen Synchrotron, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
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40
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Spectroscopic imaging with single acquisition ptychography and a hyperspectral detector. Sci Rep 2019; 9:12278. [PMID: 31439864 PMCID: PMC6706576 DOI: 10.1038/s41598-019-48642-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/31/2019] [Indexed: 11/24/2022] Open
Abstract
We present a new method of single acquisition spectroscopic imaging with high spatial resolution. The technique is based on the combination of polychromatic synchrotron radiation and ptychographic imaging with a recently developed energy discriminating detector. We demonstrate the feasibility with a Ni-Cu test sample recorded at I13-1 of the Diamond Light Source, UK. The two elements can be clearly distinguished and the Ni absorption edge is identified. The results prove the feasibility of obtaining high-resolution structural and chemical images within a single acquisition using a polychromatic X-ray beam. The capability of resolving the absorption edge applies to a wide range of research areas, such as magnetic domains imaging and element specific investigations in biological, materials, and earth sciences. The method utilises the full available radiation spectrum and is therefore well suited for broadband radiation sources.
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41
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Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q. Synchrotron microcrystal native-SAD phasing at a low energy. IUCRJ 2019; 6:532-542. [PMID: 31316798 PMCID: PMC6608635 DOI: 10.1107/s2052252519004536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 05/31/2023]
Abstract
De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements - primarily sulfur in proteins and phospho-rus in nucleic acids - increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.
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Affiliation(s)
- Gongrui Guo
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ping Zhu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Martin R. Fuchs
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wuxian Shi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yuan Gao
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sean McSweeney
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
- Photon Science, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
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42
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Ciatto G, Aubert N, Lecroard M, Engblom C, Fontaine P, Dubuisson JM, Abiven YM, Janolin PE, Kiat JM, Dumont Y, Berini B, Fouchet A, Keller N. FORTE - a multipurpose high-vacuum diffractometer for tender X-ray diffraction and spectroscopy at the SIRIUS beamline of Synchrotron SOLEIL. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1374-1387. [PMID: 31274467 DOI: 10.1107/s1600577519003722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
A new high-vacuum multipurpose diffractometer (called FORTE from the French acronyms of the project) has recently been installed at the tender/hard X-ray SIRIUS beamline of Synchrotron SOLEIL, France. The geometry chosen allows one to work either in the classical Eulerian four-circle geometry for bulk X-ray diffraction (XRD) or in the z-axis geometry for surface XRD. The diffractometer nicely fits the characteristics of the SIRIUS beamline, optimized to work in the 1.1-4.5 keV range, and allows one to perform unprecedented diffraction anomalous fine structure (DAFS) experiments in the tender X-ray region, also around non-specular reflections, covering a large reciprocal-space volume. Installation of an X-ray fluorescence detector on a dedicated flange allows simultaneous DAFS and X-ray absorption (XAS) measurements. The access to the tender X-ray region paves the way to resonant investigations around the L-edges of second-row transition elements which are constituents of functional oxide materials. It also enables access to several edges of interest for semiconductors. Finally, the control architecture based on synchronized Delta Tau units opens up exciting perspectives for improvement of the mechanical sphere of confusion.
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Affiliation(s)
- G Ciatto
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - N Aubert
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - M Lecroard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - C Engblom
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - P Fontaine
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - J M Dubuisson
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - Y M Abiven
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48 F-91192 Gif sur Yvette CEDEX, France
| | - P E Janolin
- Laboratoire SPMS, UMR CNRS-CentraleSupélec, Bâtiment Gustave Eiffel - MB.105, 8-10 rue Joliot-Curie, 91190 Gif-Sur-Yvette CEDEX, France
| | - J M Kiat
- Laboratoire SPMS, UMR CNRS-CentraleSupélec, Bâtiment Gustave Eiffel - MB.105, 8-10 rue Joliot-Curie, 91190 Gif-Sur-Yvette CEDEX, France
| | - Y Dumont
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - B Berini
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - A Fouchet
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
| | - N Keller
- Groupe d'Etudes de la Matière Condensée (GEMaC), Université Versailles Saint-Quentin en Yvelines - CNRS, Université Paris-Saclay, Versailles, France
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43
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Förster A, Brandstetter S, Schulze-Briese C. Transforming X-ray detection with hybrid photon counting detectors. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180241. [PMID: 31030653 PMCID: PMC6501887 DOI: 10.1098/rsta.2018.0241] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 05/22/2023]
Abstract
Hybrid photon counting (HPC) detectors have radically transformed basic research at synchrotron light sources since 2006. They excel at X-ray diffraction applications in the energy range from 2 to 100 keV. The main reasons for their superiority are the direct detection of individual photons and the accurate determination of scattering and diffraction intensities over an extremely high dynamic range. The detectors were first adopted in macromolecular crystallography where they revolutionized data collection. They were soon also used for small-angle scattering, coherent scattering, powder X-ray diffraction, spectroscopy and increasingly high-energy applications. Here, we will briefly survey the history of HPC detectors, explain their technology and then show in detail how improved detection has transformed a wide range of experimental techniques. We will end with an outlook to the future, which will probably see HPC technology find even broader use, for example, in electron microscopy and medical applications. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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44
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Heidler J, Pantelic R, Wennmacher JTC, Zaubitzer C, Fecteau-Lefebvre A, Goldie KN, Müller E, Holstein JJ, van Genderen E, De Carlo S, Gruene T. Design guidelines for an electron diffractometer for structural chemistry and structural biology. Acta Crystallogr D Struct Biol 2019; 75:458-466. [PMID: 31063148 PMCID: PMC6503764 DOI: 10.1107/s2059798319003942] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 11/11/2022] Open
Abstract
3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies. In this work, the combination of an EIGER hybrid pixel detector with a transmission electron microscope to construct a productive electron diffractometer is described. The construction not only refers to the combination of hardware but also to the calibration of the system, so that it provides rapid access to the experimental parameters that are necessary for processing diffraction data. Until fully integrated electron diffractometers become available, this describes a setup for productive and efficient operation in chemical crystallography.
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Affiliation(s)
- Jonas Heidler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | | | - Christian Zaubitzer
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, University Basel, 4058 Basel, Switzerland
| | | | - Julian J Holstein
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto Hahn Strasse 6, 44227 Dortmund, Germany
| | | | | | - Tim Gruene
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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45
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Vanina PY, Vakhrushev SB, Naberezhnov AA, Bosak AA. Multiscale local ordering in the prototypical uniaxial relaxor Sr 0.6Ba 0.4Nb 2O 6 single crystal at room temperature. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:175401. [PMID: 30703762 DOI: 10.1088/1361-648x/ab03b2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The structure and diffuse scattering in uniaxial relaxor Sr0.6Ba0.4Nb2O6 single crystal have been studied by x-ray diffraction at room temperature. Two different kinds of local ordering with different correlation lengths and different shapes of correlation functions have been revealed. The values of correlation lengths have been determined from analysis of experimental data. These types of orderings are connected with the intrinsic structure of crystal and can promote the appearance of relaxor properties.
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Affiliation(s)
- P Yu Vanina
- Peter the Great Saint-Petersburg Рolytechnic University, 29 Polytechnicheskaya, 195251 St.-Petersburg, Russia
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46
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Basu S, Finke A, Vera L, Wang M, Olieric V. Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source. Acta Crystallogr D Struct Biol 2019; 75:262-271. [PMID: 30950397 PMCID: PMC6450063 DOI: 10.1107/s2059798319003103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/01/2019] [Indexed: 01/19/2023] Open
Abstract
Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin-biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Aaron Finke
- MacCHESS, Cornell University, Ithaca, New York, USA
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
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47
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Montgomery JM, Lipp MJ. Advanced Spectral Analysis Program. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:023903. [PMID: 30831719 DOI: 10.1063/1.5048311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Advanced Spectral Analysis Program is a LabVIEW-based program intended for rapid and accurate analysis of large sets of spectral data. It can handle a range of different types of data including angle-resolved and energy-dispersive powder diffraction and Raman spectra. We present it here with a focus on high-temperature high-pressure powder diffraction. The program contains a novel graphical user interface that allows rapid manual fitting and indexing of peaks which require precise fitting ranges and includes tools for fitting any Bravais lattice and arbitrary user-defined multivariate equations of state. The program allows the user to simultaneously view and manipulate multiple data sets from an experiment. The user can save and load analysis progress at any point, allowing for repeatable calculations to be performed, and to allow the fast comparison of different analysis parameters.
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Affiliation(s)
- J M Montgomery
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - M J Lipp
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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48
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Clabbers MTB, Gruene T, van Genderen E, Abrahams JP. Reducing dynamical electron scattering reveals hydrogen atoms. Acta Crystallogr A Found Adv 2019; 75:82-93. [PMID: 30575586 PMCID: PMC6302931 DOI: 10.1107/s2053273318013918] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/02/2018] [Indexed: 11/26/2022] Open
Abstract
Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.
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Affiliation(s)
- Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Tim Gruene
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
| | | | - Jan Pieter Abrahams
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Paul Scherrer Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden Institute of Biology, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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49
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Leonarski F, Redford S, Mozzanica A, Lopez-Cuenca C, Panepucci E, Nass K, Ozerov D, Vera L, Olieric V, Buntschu D, Schneider R, Tinti G, Froejdh E, Diederichs K, Bunk O, Schmitt B, Wang M. Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector. Nat Methods 2018; 15:799-804. [PMID: 30275593 DOI: 10.1038/s41592-018-0143-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022]
Abstract
The accuracy of X-ray diffraction data is directly related to how the X-ray detector records photons. Here we describe the application of a direct-detection charge-integrating pixel-array detector (JUNGFRAU) in macromolecular crystallography (MX). JUNGFRAU features a uniform response on the subpixel level, linear behavior toward high photon rates, and low-noise performance across the whole dynamic range. We demonstrate that these features allow accurate MX data to be recorded at unprecedented speed. We also demonstrate improvements over previous-generation detectors in terms of data quality, using native single-wavelength anomalous diffraction (SAD) phasing, for thaumatin, lysozyme, and aminopeptidase N. Our results suggest that the JUNGFRAU detector will substantially improve the performance of synchrotron MX beamlines and equip them for future synchrotron light sources.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Sophie Redford
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Aldo Mozzanica
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | | | | | - Karol Nass
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Dmitry Ozerov
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Dominik Buntschu
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Roman Schneider
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Gemma Tinti
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Erik Froejdh
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Kay Diederichs
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Bernd Schmitt
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland.
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland.
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50
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Zobel D, Strumpel M. Electron density: historical remarks with a focus on the Berlin school. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The history of electron density (ED) research is surveyed and its historical highlights in the 20th century are summarized. The progress, reached at the beginnig of the 21st century, is described including contributions from the Berlin school. Key experimental advances concern X-ray sources and synchrotron radiation, measuring reflection data at very low temperatures (down to ~10 K), as well as the introduction of area detectors. Methodological progress was reached by new software systems for the refinement and analysis of ED data sets. This allowed to obtain quantitative ED properties, making use of Bader’s Quantum Theory of Atoms in Molecules (QTAIM). More recently methods, which combine experimental X-ray data and quantum-chemically derived wave functions, established the rapidly developing new field of “Quantum Crystallography.”
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Affiliation(s)
- Dieter Zobel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
| | - Marianna Strumpel
- Institute for Chemistry and Biochemistry, Inorganic Chemistry , Freie Universität Berlin, Fabeckstrasse 36a , 14195 Berlin , Germany
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