101
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Echelmeier A, Kim D, Cruz Villarreal J, Coe J, Quintana S, Brehm G, Egatz-Gomez A, Nazari R, Sierra RG, Koglin JE, Batyuk A, Hunter MS, Boutet S, Zatsepin N, Kirian RA, Grant TD, Fromme P, Ros A. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating. J Appl Crystallogr 2019; 52:997-1008. [PMID: 31636518 DOI: 10.1107/s1600576719010343] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
The role of surface wetting properties and their impact on the performance of 3D printed microfluidic droplet generation devices for serial femtosecond crystallography (SFX) are reported. SFX is a novel crystallography method enabling structure determination of proteins at room temperature with atomic resolution using X-ray free-electron lasers (XFELs). In SFX, protein crystals in their mother liquor are delivered and intersected with a pulsed X-ray beam using a liquid jet injector. Owing to the pulsed nature of the X-ray beam, liquid jets tend to waste the vast majority of injected crystals, which this work aims to overcome with the delivery of aqueous protein crystal suspension droplets segmented by an oil phase. For this purpose, 3D printed droplet generators that can be easily customized for a variety of XFEL measurements have been developed. The surface properties, in particular the wetting properties of the resist materials compatible with the employed two-photon printing technology, have so far not been characterized extensively, but are crucial for stable droplet generation. This work investigates experimentally the effectiveness and the long-term stability of three different surface treatments on photoresist films and glass as models for our 3D printed droplet generator and the fused silica capillaries employed in the other fluidic components of an SFX experiment. Finally, the droplet generation performance of an assembly consisting of the 3D printed device and fused silica capillaries is examined. Stable and reproducible droplet generation was achieved with a fluorinated surface coating which also allowed for robust downstream droplet delivery. Experimental XFEL diffraction data of crystals formed from the large membrane protein complex photosystem I demonstrate the full compatibility of the new injection method with very fragile membrane protein crystals and show that successful droplet generation of crystal-laden aqueous droplets intersected by an oil phase correlates with increased crystal hit rates.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sebastian Quintana
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Gerrit Brehm
- Institute for X-ray Physics, University of Göttingen, Göttingen, Germany
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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102
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Gañán-Calvo AM. Scaling Laws of an Exploding Liquid Column under an Intense Ultrashort X-Ray Pulse. PHYSICAL REVIEW LETTERS 2019; 123:064501. [PMID: 31491190 DOI: 10.1103/physrevlett.123.064501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Indexed: 06/10/2023]
Abstract
A general formulation of the partial destruction of a liquid object in vacuum after the sudden deposition of a very large amount of energy is proposed. That energy instantaneously raises the pressure of a portion of the liquid to extreme values and changes its state, which causes its explosive expansion into vacuum and against the rest of the liquid object. When the deformable object is a liquid capillary column, the model reduces to a universal equation for the evolution of the expanding gap between the two sides of the exploding liquid column. The theoretical analysis contemplates two asymptotic stages for small and large times from the initiation of the blast, whose asymptotic solutions are fitted to available experimental data. A universal approximate analytical solution is obtained. A complete dimensional analysis of the problem and an optimal collapse of experimental data reveal that the proposed solution is in remarkable agreement with experiments of a jet exploding after being irradiated by an ultrashort and intense x-ray pulse from an x-ray free electron laser.
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Affiliation(s)
- Alfonso M Gañán-Calvo
- Departamento de Ingeniería Aerospacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, Camino de los Descubrimientos s/n 41092, Sevilla, Spain
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103
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Standfuss J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr Opin Struct Biol 2019; 57:63-71. [DOI: 10.1016/j.sbi.2019.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/05/2023]
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104
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Kim D, Echelmeier A, Cruz Villarreal J, Gandhi S, Quintana S, Egatz-Gomez A, Ros A. Electric Triggering for Enhanced Control of Droplet Generation. Anal Chem 2019; 91:9792-9799. [PMID: 31260621 DOI: 10.1021/acs.analchem.9b01449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that uses X-ray free-electron lasers (XFEL) to determine structures of biomolecular complexes. Specifically, it benefits the study of atomic resolution structures of large membrane protein complexes and time-resolved reactions with crystallography. One major drawback of SFX studies with XFELs is the consumption of large amounts of a protein crystal sample to collect a complete X-ray diffraction data set for high-resolution crystal structures. This increases the time and resources required for sample preparation and experimentation. The intrinsic pulsed nature of all current X-ray sources is a major reason why such large amounts of sample are required. Any crystal sample that is delivered in the path of the X-ray beam during its "off-time" is wasted. To address this large sample consumption issue, we developed a 3D printed microfluidic system with integrated metal electrodes for water-in-oil droplet generation to dynamically create and manipulate aqueous droplets. We demonstrate on-demand droplet generation using DC potentials and the ability to tune the frequency of droplet generation through the application of AC potentials. More importantly, to assist with the synchronization of droplets and XFEL pulses, we show that the device can induce a phase shift in the base droplet generation frequency. This novel approach to droplet generation has the potential to reduce sample waste by more than 95% for SFX experiments with XFELs performed with liquid jets and can operate under low- and high-pressure liquid injection systems.
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Affiliation(s)
- Daihyun Kim
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Austin Echelmeier
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sahir Gandhi
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Sebastian Quintana
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Ana Egatz-Gomez
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
| | - Alexandra Ros
- School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States.,Center for Applied Structural Discovery, The Biodesign Institute , Arizona State University , Tempe , Arizona 85281 , United States
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105
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Echelmeier A, Sonker M, Ros A. Microfluidic sample delivery for serial crystallography using XFELs. Anal Bioanal Chem 2019; 411:6535-6547. [PMID: 31250066 DOI: 10.1007/s00216-019-01977-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) is an emerging field for structural biology. One of its major impacts lies in the ability to reveal the structure of complex proteins previously inaccessible with synchrotron-based crystallography techniques and allowing time-resolved studies from femtoseconds to seconds. The nature of this serial technique requires new approaches for crystallization, data analysis, and sample delivery. With continued advancements in microfabrication techniques, various developments have been reported in the past decade for innovative and efficient microfluidic sample delivery for crystallography experiments using XFELs. This article summarizes the recent developments in microfluidic sample delivery with liquid injection and fixed-target approaches, which allow exciting new research with XFELs. Graphical abstract.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA.
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106
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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107
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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108
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Mancuso AP, Aquila A, Batchelor L, Bean RJ, Bielecki J, Borchers G, Doerner K, Giewekemeyer K, Graceffa R, Kelsey OD, Kim Y, Kirkwood HJ, Legrand A, Letrun R, Manning B, Lopez Morillo L, Messerschmidt M, Mills G, Raabe S, Reimers N, Round A, Sato T, Schulz J, Signe Takem C, Sikorski M, Stern S, Thute P, Vagovič P, Weinhausen B, Tschentscher T. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:660-676. [PMID: 31074429 PMCID: PMC6510195 DOI: 10.1107/s1600577519003308] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/07/2019] [Indexed: 05/22/2023]
Abstract
The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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Affiliation(s)
- 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 3086, Australia
- Correspondence e-mail:
| | - Andrew Aquila
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | | | | | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Steffen Raabe
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Nadja Reimers
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | | | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Prasad Thute
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Patrik Vagovič
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
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109
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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110
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MHz data collection of a microcrystalline mixture of different jack bean proteins. Sci Data 2019; 6:18. [PMID: 30944333 PMCID: PMC6472352 DOI: 10.1038/s41597-019-0010-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/05/2019] [Indexed: 11/14/2022] Open
Abstract
We provide a detailed description of a serial femtosecond crystallography (SFX) dataset collected at the European X-ray free-electron laser facility (EuXFEL). The EuXFEL is the first high repetition rate XFEL delivering MHz X-ray pulse trains at 10 Hz. The short spacing (<1 µs) between pulses requires fast flowing microjets for sample injection and high frame rate detectors. A data set was recorded of a microcrystalline mixture of at least three different jack bean proteins (urease, concanavalin A, concanavalin B). A one megapixel Adaptive Gain Integrating Pixel Detector (AGIPD) was used which has not only a high frame rate but also a large dynamic range. This dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development and for data analysis training for prospective XFEL users. Design Type(s) | protocol testing objective | Measurement Type(s) | protein structure data | Technology Type(s) | x ray crystallography | Factor Type(s) | | Sample Characteristic(s) | Canavalia |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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111
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Roseker W, Lee S, Walther M, Rysov R, Sprung M, Grübel G. Spatial and temporal pre-alignment of an X-ray split-and-delay unit by laser light interferometry. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:045106. [PMID: 31042974 DOI: 10.1063/1.5089496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
We present a novel experimental setup for performing a precise pre-alignment of a hard X-ray split-and-delay unit based on low coherence light interferometry and high-precision penta-prisms. A split-and-delay unit is a sophisticated perfect crystal-optics device that splits an incoming X-ray pulse into two sub-pulses and generates a controlled time-delay between them. While the availability of a split-and-delay system will make ultrafast time-correlation and X-ray pump-probe experiments possible at free-electron lasers, its alignment process can be very tedious and time-consuming due to its complex construction. By implementing our experimental setup at beamline P10 of PETRA III, we were able to reduce the time of alignment to less than 3 h. We also propose an alternate method for finding the zero-time delay crossing without the use of X-rays or pulsed laser sources. The successful demonstration of this method brings prospect for operating the split-and-delay systems under alignment-time-critical environments such as X-ray free electron laser facilities.
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Affiliation(s)
- W Roseker
- Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - S Lee
- Frontier in Extreme Physics, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
| | - M Walther
- Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - R Rysov
- Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Sprung
- Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - G Grübel
- Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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112
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Kirkwood HJ, Letrun R, Tanikawa T, Liu J, Nakatsutsumi M, Emons M, Jezynski T, Palmer G, Lederer M, Bean R, Buck J, Di Dio Cafisio S, Graceffa R, Grünert J, Göde S, Höppner H, Kim Y, Konopkova Z, Mills G, Makita M, Pelka A, Preston TR, Sikorski M, Takem CMS, Giewekemeyer K, Chollet M, Vagovic P, Chapman HN, Mancuso AP, Sato T. Initial observations of the femtosecond timing jitter at the European XFEL. OPTICS LETTERS 2019; 44:1650-1653. [PMID: 30933113 DOI: 10.1364/ol.44.001650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Intense, ultrashort, and high-repetition-rate X-ray pulses, combined with a femtosecond optical laser, allow pump-probe experiments with fast data acquisition and femtosecond time resolution. However, the relative timing of the X-ray pulses and the optical laser pulses can be controlled only to a level of the intrinsic error of the instrument which, without characterization, limits the time resolution of experiments. This limitation inevitably calls for a precise determination of the relative arrival time, which can be used after measurement for sorting and tagging the experimental data to a much finer resolution than it can be controlled to. The observed root-mean-square timing jitter between the X-ray and the optical laser at the SPB/SFX instrument at European XFEL was 308 fs. This first measurement of timing jitter at the European XFEL provides an important step in realizing ultrafast experiments at this novel X-ray source. A method for determining the change in the complex refractive index of samples is also presented.
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113
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Schmidt M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int J Mol Sci 2019; 20:ijms20061401. [PMID: 30897736 PMCID: PMC6470897 DOI: 10.3390/ijms20061401] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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Schulz J, Bielecki J, Doak RB, Dörner K, Graceffa R, Shoeman RL, Sikorski M, Thute P, Westphal D, Mancuso AP. A versatile liquid-jet setup for the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:339-345. [PMID: 30855241 PMCID: PMC6412181 DOI: 10.1107/s1600577519000894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
The SPB/SFX instrument of the European XFEL provides unique possibilities for high-throughput serial femtosecond crystallography. This publication presents the liquid-jet sample delivery setup of this instrument. The setup is compatible with state-of-the-art gas dynamic virtual nozzle systems as well as high-viscosity extruders and provides space and flexibility for other liquid injection devices and future upgrades. The liquid jets are confined in a differentially pumped catcher assembly and can be replaced within a couple of minutes through a load-lock. A two-microscope imaging system allows visual control of the jets from two perspectives.
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Affiliation(s)
- J. Schulz
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - J. Bielecki
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - R. B. Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - K. Dörner
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - R. Graceffa
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - R. L. Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - M. Sikorski
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - P. Thute
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
| | - D. Westphal
- Department of Cell and Molecular Biology (ICM), Uppsala University, Husargatan 3, Uppsala 75124, Sweden
| | - A. P. Mancuso
- European XFEL, Holzkoppel 4, Schenefeld 22869, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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116
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Bohne S, Heymann M, Chapman HN, Trieu HK, Bajt S. 3D printed nozzles on a silicon fluidic chip. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:035108. [PMID: 30927802 DOI: 10.1063/1.5080428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/26/2019] [Indexed: 05/22/2023]
Abstract
Serial femtosecond crystallography is a new method for protein structure determination utilizing intense and destructive X-ray pulses generated by free-electron lasers. The approach requires the means to deliver hydrated protein crystals to a focused X-ray beam and replenish them at the repetition rate of the pulses. A liquid-jet sample delivery system where a gas dynamic virtual nozzle is printed directly on a silicon-glass microfluidic chip using a 2-photon-polymerization 3D printing process is implemented. This allows for rapid prototyping and high-precision production of nozzles to suit the characteristics of a particular sample and opens up the possibility for high-throughput and versatile sample delivery systems that can integrate microfluidic components for sample detection, characterisation, or control. With the hybrid system described here, stable liquid jets with diameters between 1.5 µm at liquid flow rate of 1.5 µl/min and more than 20 µm at liquid flow rate of 100 µl/min under atmospheric and vacuum conditions are generated. The combination of 2D lithography with direct 3D printing may streamline the integration of free-form-features and also facilitate scale-up production of such integrated microfluidic devices that may be useful in many other applications such as flow cytometry and optofluidics.
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Affiliation(s)
- Sven Bohne
- Hamburg University of Technology, Eissendorfer Str. 42, 21073 Hamburg, Germany
| | - Michael Heymann
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Hoc Khiem Trieu
- Hamburg University of Technology, Eissendorfer Str. 42, 21073 Hamburg, Germany
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Building 99, 22607 Hamburg, Germany
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117
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Grünbein ML, Nass Kovacs G. Sample delivery for serial crystallography at free-electron lasers and synchrotrons. Acta Crystallogr D Struct Biol 2019; 75:178-191. [PMID: 30821706 PMCID: PMC6400261 DOI: 10.1107/s205979831801567x] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.
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Affiliation(s)
- Marie Luise Grünbein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Allahgholi A, Becker J, Delfs A, Dinapoli R, Goettlicher P, Greiffenberg D, Henrich B, Hirsemann H, Kuhn M, Klanner R, Klyuev A, Krueger H, Lange S, Laurus T, Marras A, Mezza D, Mozzanica A, Niemann M, Poehlsen J, Schwandt J, Sheviakov I, Shi X, Smoljanin S, Steffen L, Sztuk-Dambietz J, Trunk U, Xia Q, Zeribi M, Zhang J, Zimmer M, Schmitt B, Graafsma H. The Adaptive Gain Integrating Pixel Detector at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:74-82. [PMID: 30655470 PMCID: PMC6337892 DOI: 10.1107/s1600577518016077] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
The Adaptive Gain Integrating Pixel Detector (AGIPD) is an X-ray imager, custom designed for the European X-ray Free-Electron Laser (XFEL). It is a fast, low-noise integrating detector, with an adaptive gain amplifier per pixel. This has an equivalent noise of less than 1 keV when detecting single photons and, when switched into another gain state, a dynamic range of more than 104 photons of 12 keV. In burst mode the system is able to store 352 images while running at up to 6.5 MHz, which is compatible with the 4.5 MHz frame rate at the European XFEL. The AGIPD system was installed and commissioned in August 2017, and successfully used for the first experiments at the Single Particles, Clusters and Biomolecules (SPB) experimental station at the European XFEL since September 2017. This paper describes the principal components and performance parameters of the system.
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Affiliation(s)
- Aschkan Allahgholi
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julian Becker
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Annette Delfs
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Peter Goettlicher
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Beat Henrich
- Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Helmut Hirsemann
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Klanner
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alexander Klyuev
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Hans Krueger
- University of Bonn, Nussallee 12, 53115 Bonn, Germany
| | - Sabine Lange
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alessandro Marras
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institut, 5232 Villigen, Switzerland
| | | | - Magdalena Niemann
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jennifer Poehlsen
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joern Schwandt
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Igor Sheviakov
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Xintian Shi
- Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sergej Smoljanin
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lothar Steffen
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Ulrich Trunk
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Qingqing Xia
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mourad Zeribi
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jiaguo Zhang
- Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Manfred Zimmer
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Heinz Graafsma
- Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- Mid Sweden University, Holmgatan 10, S-85170 Sundsvall, Sweden
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119
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