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  1. Article ; Online: Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook.

    Botha, Sabine / Fromme, Petra

    Structure (London, England : 1993)

    2023  Volume 31, Issue 11, Page(s) 1306–1319

    Abstract: Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage ... ...

    Abstract Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
    MeSH term(s) Humans ; Crystallography/methods ; Crystallography, X-Ray ; Pandemics ; COVID-19/epidemiology ; SARS-CoV-2 ; X-Ray Diffraction ; Macromolecular Substances/chemistry
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2023-10-27
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2023.10.005
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  2. Article: The

    Ketawala, Gihan / Reiter, Caitlin M / Fromme, Petra / Botha, Sabine

    Journal of applied crystallography

    2024  Volume 57, Issue Pt 2, Page(s) 529–538

    Abstract: Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, ... ...

    Abstract Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment. This is integrated into an easy-to-use graphical user interface, specifically designed to support the detectors, file formats and software available at most X-ray free electron laser facilities. The highly modular design makes the tool easily expandable to comply with other X-ray sources and detectors, and the supervised learning approach enables even the novice user to sort data containing unwanted artefacts or perform routine data-analysis tasks such as hit finding during an experiment, without needing to write code.
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2020879-0
    ISSN 1600-5767 ; 0021-8898
    ISSN (online) 1600-5767
    ISSN 0021-8898
    DOI 10.1107/S1600576724000116
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  3. Article ; Online: Native Deglycosylation and Size Exclusion Chromatography of Viral Chemokine Binding Proteins for Structural Discovery.

    Boyd, Ryan / Zhang, Liqiang / Fromme, Petra

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2597, Page(s) 251–259

    Abstract: Structural discovery of viral chemokine binding proteins can provide valuable information on the binding domains and protein-protein interfaces (PPI) of these immunologically relevant proteins. Protein expression in mammalian cells produces high-quality ... ...

    Abstract Structural discovery of viral chemokine binding proteins can provide valuable information on the binding domains and protein-protein interfaces (PPI) of these immunologically relevant proteins. Protein expression in mammalian cells produces high-quality protein compared to other expression methods; however, because structural discovery methods such as cryo-EM-based single particle analysis (SPA) and x-ray crystallography use methods which combine data from many individual proteins, these demand a highly monodispersed sample composed of protein with ordered structure. These techniques are often incompatible with flexible glycosyl groups commonly present on proteins produced by mammalian cells and require deglycosylation to enable observation of the conserved tertiary structure beneath these variable, flexible, glycans. Using the Myxoma viral protein M-T7 as a test case, we discuss considerations and preliminary bioinformatic analysis for approaching structural discovery using freely accessible sequence and structure databases to maximize success and guide experiments. We describe a simple deglycosylation optimization protocol utilizing Endo H followed by size exclusion chromatography (SEC) based purification to produce and validate protein suitable for structural discovery. Considerations such as protein concentration and volumes required for crystallography and negative stain electron microscopy are discussed as well as grid blotting techniques for negative stain experiments to validate protein quality.
    MeSH term(s) Animals ; Cryoelectron Microscopy/methods ; Viral Proteins ; Crystallography, X-Ray ; Chromatography, Gel ; Chemokines ; Mammals
    Chemical Substances Viral Proteins ; Chemokines
    Language English
    Publishing date 2022-11-14
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2835-5_18
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  4. Article ; Online: XFELs open a new era in structural chemical biology.

    Fromme, Petra

    Nature chemical biology

    2015  Volume 11, Issue 12, Page(s) 895–899

    MeSH term(s) Lasers ; Models, Molecular ; Molecular Structure ; Proteins/chemistry ; X-Rays
    Chemical Substances Proteins
    Language English
    Publishing date 2015-11-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/nchembio.1968
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    Zs.A 6251: Show issues Location:
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  5. Article ; Online: A novel solution for controlling hardware components of accelerators and beamlines.

    Khokhriakov, Igor / Merkulova, Olga / Nozik, Alexander / Fromme, Petra / Mazalova, Victoria

    Journal of synchrotron radiation

    2022  Volume 29, Issue Pt 3, Page(s) 644–653

    Abstract: A novel approach to the remote-control system for the compact multi-crystal energy-dispersive spectrometer for X-ray emission spectroscopy (XES) applications has been developed. This new approach is based on asynchronous communication between software ... ...

    Abstract A novel approach to the remote-control system for the compact multi-crystal energy-dispersive spectrometer for X-ray emission spectroscopy (XES) applications has been developed. This new approach is based on asynchronous communication between software components and on reactive design principles. In this paper, the challenges faced, their solutions, as well as the implementation and future development prospects are identified. The main motivation of this work was the development of a new holistic communication protocol that can be implemented to control various hardware components allowing both independent operation and easy integration into different SCADA systems.
    MeSH term(s) Software ; Spectrometry, X-Ray Emission ; Synchrotrons
    Language English
    Publishing date 2022-04-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2021413-3
    ISSN 1600-5775 ; 0909-0495
    ISSN (online) 1600-5775
    ISSN 0909-0495
    DOI 10.1107/S1600577522002685
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  6. Article ; Online: Methods for Crystallization and Structural Determination of M-T7 Protein from Myxoma Virus.

    Gisriel, Christopher / Fromme, Petra / Martin-Garcia, Jose M

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2225, Page(s) 125–162

    Abstract: The myxoma virus has become of interest in human medicine in the last two decades as it has the ability to infect many types of human cancer cells and is being used as a platform to develop viro-therapeutic agents that suppress aggressive and damaging ... ...

    Abstract The myxoma virus has become of interest in human medicine in the last two decades as it has the ability to infect many types of human cancer cells and is being used as a platform to develop viro-therapeutic agents that suppress aggressive and damaging immune responses and inflammation. Furthermore, the myxoma virus encodes proteins that have strong immunosuppressive effects, and several of the myxoma virus-encoded immunomodulators are being developed to treat systemic inflammatory syndromes such as cardiovascular disease and transplant rejection. Myxoma virus encodes the M-T7 protein, the most abundantly secreted protein expressed in myxoma virus-infected cells, originally identified as a rabbit species-specific interferon-gamma (IFN-γ) receptor homolog and as a chemokine-modulating protein binding a wide range of mammalian chemokines. M-T7 is a critical virulence factor for viral pathogenesis that increases virus lethality when expressed. Although M-T7 has been extensively studied using biochemical and biophysical techniques and its interactome map is well known, its three-dimensional (3D) structure remains elusive. Obtaining the 3D structure of M-T7 would be greatly beneficial and is a crucial step toward advancing M-T7 research through understanding the molecular function and activity of M-T7 as a novel therapeutic reagent and to rationally develop this protein as a drug. This chapter provides an overview of the structural determination techniques, especially X-ray crystallography, that can be applied toward the goal of achieving the first high-resolution structure of M-T7. In addition, details of up-and-coming methods are discussed, including X-ray diffraction at X-ray free electron lasers (XFELs), nuclear magnetic resonance (NMR), cryo-electron microscopy (cryo-EM), Micro-electron diffraction (Micro-ED), and small-angle X-ray scattering (SAXS), and their potential applications to M-T7 structural biology.
    MeSH term(s) Amino Acid Sequence ; Cloning, Molecular ; Cryoelectron Microscopy ; Crystallization/methods ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Models, Molecular ; Myxoma virus/chemistry ; Receptors, Interferon/chemistry ; Receptors, Interferon/genetics ; Receptors, Interferon/ultrastructure ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/ultrastructure ; Scattering, Small Angle ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/ultrastructure ; Virulence Factors/genetics ; Virulence Factors/metabolism ; X-Ray Diffraction/instrumentation ; X-Ray Diffraction/methods
    Chemical Substances M-T7 protein, Myxoma virus ; Receptors, Interferon ; Recombinant Proteins ; Viral Proteins ; Virulence Factors
    Language English
    Publishing date 2021-03-26
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1012-1_8
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  7. Article ; Online: Regulation of light energy conversion between linear and cyclic electron flow within photosystem II controlled by the plastoquinone/quinol redox poise.

    Gates, Colin / Ananyev, Gennady / Roy-Chowdhury, Shatabdi / Fromme, Petra / Dismukes, G Charles

    Photosynthesis research

    2022  Volume 156, Issue 1, Page(s) 113–128

    Abstract: Ultrapurified Photosystem II complexes crystalize as uniform microcrystals (PSIIX) of unprecedented homogeneity that allow observation of details previously unachievable, including the longest sustained oscillations of flash-induced ... ...

    Abstract Ultrapurified Photosystem II complexes crystalize as uniform microcrystals (PSIIX) of unprecedented homogeneity that allow observation of details previously unachievable, including the longest sustained oscillations of flash-induced O
    MeSH term(s) Photosystem II Protein Complex/metabolism ; Electron Transport ; Plastoquinone/metabolism ; Electrons ; Protons ; Photosynthesis/physiology ; Hydroquinones ; Oxidation-Reduction ; Water/chemistry
    Chemical Substances Photosystem II Protein Complex ; Plastoquinone (OAC30J69CN) ; Protons ; hydroquinone (XV74C1N1AE) ; Hydroquinones ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-11-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1475688-2
    ISSN 1573-5079 ; 0166-8595
    ISSN (online) 1573-5079
    ISSN 0166-8595
    DOI 10.1007/s11120-022-00985-w
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  8. Article: Split-Second Reactions.

    Fromme, Petra / Spence, John C H

    Scientific American

    2017  Volume 316, Issue 5, Page(s) 62–67

    MeSH term(s) Crystallization ; Crystallography, X-Ray/methods ; Eye ; Humans ; Lasers ; Ocular Physiological Phenomena ; Photosynthesis ; Plant Leaves/metabolism ; Plant Leaves/radiation effects ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Plant Proteins/ultrastructure ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/ultrastructure ; Sunlight ; Vision, Ocular ; X-Rays
    Chemical Substances Plant Proteins ; Receptors, G-Protein-Coupled
    Language English
    Publishing date 2017-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 246-x
    ISSN 1946-7087 ; 0036-8733
    ISSN (online) 1946-7087
    ISSN 0036-8733
    DOI 10.1038/scientificamerican0517-62
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    Zs.A 1209: Show issues Location:
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  9. Article ; Online: Structure determination based on continuous diffraction from macromolecular crystals.

    Chapman, Henry N / Fromme, Petra

    Current opinion in structural biology

    2017  Volume 45, Page(s) 170–177

    Abstract: Bright and coherent X-ray sources, such free-electron lasers, have spurred large activities in developing new methods to obtain the structures of biological macromolecules. In particular, single-molecule diffraction is highly desired, as it would abolish ...

    Abstract Bright and coherent X-ray sources, such free-electron lasers, have spurred large activities in developing new methods to obtain the structures of biological macromolecules. In particular, single-molecule diffraction is highly desired, as it would abolish the need for crystallization. It provides considerably more diffraction intensity information than needed to solve a structure, unlike crystal diffraction, which is usually insufficient for direct phasing. To overcome the challenge of weak scattering signals of single molecules, the direct phasing approaches in coherent diffractive imaging have been combined with crystals in several imaginative ways. One of these, using crystals with translational disorder, has been used to phase continuous femtosecond X-ray diffraction data from photosystem II complexes, offering a paradigm shift in crystallography.
    MeSH term(s) Crystallography, X-Ray/methods ; Macromolecular Substances/chemistry
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2017-09-14
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2017.07.008
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    Zs.A 3206: Show issues Location:
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  10. Article: DatView

    Stander, Natasha / Fromme, Petra / Zatsepin, Nadia

    Journal of applied crystallography

    2019  Volume 52, Issue Pt 6, Page(s) 1440–1448

    Abstract: ... ...

    Abstract DatView
    Language English
    Publishing date 2019-10-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2020879-0
    ISSN 1600-5767 ; 0021-8898
    ISSN (online) 1600-5767
    ISSN 0021-8898
    DOI 10.1107/S1600576719012044
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