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Paulson L, Narayanasamy SR, Shelby ML, Frank M, Trebbin M. Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:011101. [PMID: 38389979 PMCID: PMC10883715 DOI: 10.1063/4.0000229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals and solutions at microscales. Microfluidics are the obvious approach for any high-throughput, nano-to-microliter sample handling, that also requires design flexibility and rapid prototyping to deal with the variable shapes, sizes, and density of crystals. Here, we discuss recent advances in polymer 3D printing for microfluidics-based serial crystallography research and present a demonstration of emerging, large-scale, nano-3D printing approaches leading into the future of 3D sample environment and delivery device fabrication from liquid jet gas-dynamic virtual nozzles devices to fixed-target sample environment technology.
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Affiliation(s)
- Lars Paulson
- Department of Chemistry & Research and Education in Energy, Environment and Water (RENEW), The State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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2
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Trebbin M. Thinner than a knife's edge: 3D-printed liquid sheet jet technology for solution phase XFEL experiments. IUCRJ 2023; 10:638-641. [PMID: 37910141 PMCID: PMC10619446 DOI: 10.1107/s2052252523009429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
In this commentary, we explore the pioneering implementation of 3D-printed thin liquid sheet devices for advanced X-ray scattering and spectroscopy experiments at high-repetition rate XFELs.
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Affiliation(s)
- Martin Trebbin
- University at Buffalo, Department of Chemistry & Research and Education in eNergy, Environment and Water (RENEW), 760 Natural Sciences Complex, Buffalo, NY 14260, USA
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3
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Konold PE, You T, Bielecki J, Valerio J, Kloos M, Westphal D, Bellisario A, Varma Yenupuri T, Wollter A, Koliyadu JCP, Koua FH, Letrun R, Round A, Sato T, Mészáros P, Monrroy L, Mutisya J, Bódizs S, Larkiala T, Nimmrich A, Alvarez R, Adams P, Bean R, Ekeberg T, Kirian RA, Martin AV, Westenhoff S, Maia FRNC. 3D-printed sheet jet for stable megahertz liquid sample delivery at X-ray free-electron lasers. IUCRJ 2023; 10:662-670. [PMID: 37721770 PMCID: PMC10619454 DOI: 10.1107/s2052252523007972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interaction point in such a way that produces data of the highest possible quality and with maximal efficiency. This is hampered by intrinsic constraints posed by the light source and operation within a beamline environment. For liquid samples, the solution typically involves some form of high-speed liquid jet, capable of keeping up with the rate of X-ray pulses. However, conventional jets are not ideal because of radiation-induced explosions of the jet, as well as their cylindrical geometry combined with the X-ray pointing instability of many beamlines which causes the interaction volume to differ for every pulse. This complicates data analysis and contributes to measurement errors. An alternative geometry is a liquid sheet jet which, with its constant thickness over large areas, eliminates the problems related to X-ray pointing. Since liquid sheets can be made very thin, the radiation-induced explosion is reduced, boosting their stability. These are especially attractive for experiments which benefit from small interaction volumes such as fluctuation X-ray scattering and several types of spectroscopy. Although their use has increased for soft X-ray applications in recent years, there has not yet been wide-scale adoption at XFELs. Here, gas-accelerated liquid sheet jet sample injection is demonstrated at the European XFEL SPB/SFX nano focus beamline. Its performance relative to a conventional liquid jet is evaluated and superior performance across several key factors has been found. This includes a thickness profile ranging from hundreds of nanometres to 60 nm, a fourfold increase in background stability and favorable radiation-induced explosion dynamics at high repetition rates up to 1.13 MHz. Its minute thickness also suggests that ultrafast single-particle solution scattering is a possibility.
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Affiliation(s)
- Patrick E. Konold
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tong You
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Alfredo Bellisario
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - August Wollter
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | | | | | - Romain Letrun
- 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
| | - Petra Mészáros
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Szabolcs Bódizs
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Taru Larkiala
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Bagley Hall, Seattle, WA 98195, USA
| | - Roberto Alvarez
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Patrick Adams
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Richard A. Kirian
- Department of Physics, Arizona State University, 550 E. Tyler Drive, Tempe, AZ 85287, USA
| | - Andrew V. Martin
- School of Science, STEM College, RMIT University, Melbourne, Victoria 3000, Australia
| | - Sebastian Westenhoff
- Department of Chemistry – BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Institute for Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, Ros A. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. LAB ON A CHIP 2023; 23:3016-3033. [PMID: 37294576 PMCID: PMC10503405 DOI: 10.1039/d3lc00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jose Domingo Meza-Aguilar
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mohammad T Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Roberto C Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jay-How Yang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jackson Carrion
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Katherine Morin
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gihan K Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Miguel Angel Ruiz-Fresneda
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Christopher J Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Robert E Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
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5
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Kloudová B, Strmeň T, Vrkoslav V, Chára Z, Pačes O, Cvačka J. Gas Dynamic Virtual Nozzle Sprayer for an Introduction of Liquid Samples in Atmospheric Pressure Ionization Mass Spectrometry. Anal Chem 2023; 95:4196-4203. [PMID: 36800482 PMCID: PMC10016749 DOI: 10.1021/acs.analchem.2c05349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Electrospray may exhibit inadequate ionization efficiency in some applications. In such cases, atmospheric-pressure chemical ionization (APCI) and photoionization (APPI) can be used. Despite a wide application potential, no APCI and APPI sources dedicated to very low sample flow rates exist on the market. Since the ion source performance depends on the transfer of analytes from the liquid to the gas phase, a nebulizer is a critical component of an ion source. Here, we report on the nebulizer with a gas dynamic virtual nozzle (GDVN) and its applicability in APCI at microliter-per-minute flow rates. Nebulizers differing by geometrical parameters were fabricated and characterized regarding the jet breakup regime, droplet size, droplet velocity, and spray angle for liquid flow rates of 0.75-15.0 μL/min. A micro-APCI source with the GDVN nebulizer behaved as a mass-flow-sensitive detector and provided stable and intense analyte signals. Compared to a classical APCI source, an order of magnitude lower detection limit for verapamil was achieved. Mass spectra recorded with the nebulizer in dripping and jetting modes were almost identical and did not differ from normal APCI spectra. Clogging never occurred during the experiments, indicating the high robustness of the nebulizer. Low-flow-rate APCI and APPI sources with a GDVN sprayer promise new applications for low- and medium-polar analytes.
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Affiliation(s)
- Barbora Kloudová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, CZ-128 43 Prague 2, Czech Republic
| | - Timotej Strmeň
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Zdeněk Chára
- Institute of Hydrodynamics of the Czech Academy of Sciences, Pod Pat'ankou 30/5, CZ-166 12 Prague 6, Czech Republic
| | - Ondřej Pačes
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic.,Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, CZ-128 43 Prague 2, Czech Republic
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6
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Jernigan RJ, Logeswaran D, Doppler D, Nagaratnam N, Sonker M, Yang JH, Ketawala G, Martin-Garcia JM, Shelby ML, Grant TD, Mariani V, Tolstikova A, Sheikh MZ, Yung MC, Coleman MA, Zaare S, Kaschner EK, Rabbani MT, Nazari R, Zacks MA, Hayes B, Sierra RG, Hunter MS, Lisova S, Batyuk A, Kupitz C, Boutet S, Hansen DT, Kirian RA, Schmidt M, Fromme R, Frank M, Ros A, Chen JJL, Botha S, Fromme P. Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser. Structure 2023; 31:138-151.e5. [PMID: 36630960 PMCID: PMC9830665 DOI: 10.1016/j.str.2022.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/08/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023]
Abstract
NendoU from SARS-CoV-2 is responsible for the virus's ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.
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Affiliation(s)
- Rebecca J Jernigan
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Dhenugen Logeswaran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Diandra Doppler
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Nirupa Nagaratnam
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mukul Sonker
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jay-How Yang
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Gihan Ketawala
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Jose M Martin-Garcia
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Megan L Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Michelle Z Sheikh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Mimi Cho Yung
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Sahba Zaare
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Fulton School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Emily K Kaschner
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Mohammad Towshif Rabbani
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Reza Nazari
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Michele A Zacks
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Richard A Kirian
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, WI 53211, USA
| | - Raimund Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Alexandra Ros
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Julian J-L Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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7
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Zupan B, Peña-Murillo GE, Zahoor R, Gregorc J, Šarler B, Knoška J, Gañán-Calvo AM, Chapman HN, Bajt S. An experimental study of liquid micro-jets produced with a gas dynamic virtual nozzle under the influence of an electric field. Front Mol Biosci 2023; 10:1006733. [PMID: 36743214 PMCID: PMC9892056 DOI: 10.3389/fmolb.2023.1006733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
The results of an experimental study of micro-jets produced with a gas dynamic virtual nozzle (GDVN) under the influence of an electric field are provided and discussed for the first time. The experimental study is performed with a 50% volume mixture of water and ethanol, and nitrogen focusing gas. The liquid sample and gas Reynolds numbers range from 0.09-5.4 and 0-190, respectively. The external electrode was positioned 400-500 μm downstream of the nozzle tip and an effect of electric potential between the electrode and the sample liquid from 0-7 kV was investigated. The jetting parametric space is examined as a function of operating gas and liquid flow rates, outlet chamber pressure, and an external electric field. The experimentally observed jet diameter, length and velocity ranged from 1-25 μm, 50-500 μm and 0.5-10 m/s, respectively. The jetting shape snapshots were processed automatically using purposely developed computer vision software. The velocity of the jet was calculated from the measured jet diameter and the sample flow rate. It is found that micro-jets accelerate in the direction of the applied electric field in the downstream direction at a constant acceleration as opposed to the standard GDVNs. New jetting modes were observed, where either the focusing gas or the electric forces dominate, encouraging further theoretical and numerical studies towards optimized system design. The study shows the potential to unlock a new generation of low background sample delivery for serial diffraction measurements of weakly scattering objects.
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Affiliation(s)
- Bor Zupan
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | | | - Rizwan Zahoor
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Gregorc
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Božidar Šarler
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia,Laboratory for Simulation of Materials and Processes, Institute of Metals and Technology, Ljubljana, Slovenia
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Alfonso M. Gañán-Calvo
- Departamento de Ingeniería Aeroespacial y Mecánica de Fluidos, Universidad de Sevilla, Sevilla, Spain,Laboratory of Engineering for Energy and Environmental Sustainability, Universidad de Sevilla, Sevilla, Spain
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany,*Correspondence: Saša Bajt,
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8
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Khotmungkhun K, Prathumwan R, Chotiyasilp A, Watcharasresomroeng B, Subannajui K. Mechanical property of pixel extrusion and pin forming for polymer, ceramic, and metal formation. Heliyon 2023; 9:e12871. [PMID: 36711282 PMCID: PMC9879782 DOI: 10.1016/j.heliyon.2023.e12871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
The rapid material fabrications in pixel shape were mechanically studied in comparison with FDM and STL 3D printing technique. The pixel extrusion technique was the extrusion with a set of holes in the die. By controlling the flow of each hole in the die, the shape could be adjustable. The pixel molding technique composed of a set of pins. By adjusting the length of pin inside the mold, the shape of cavity could be designed. Compared to 3D printing which requires the material deposition with 2D scanning for several layers, 3D material fabrication by pixel extrusion and pixel molding were much faster; however, their resolutions were still much worse compared to 3D printing at the moment. SEM, Tensile test, flexural test, including hardness were used to observe the properties of pixel extrusion and pixel molding. The pixel molding technique was also used to fabricate many materials to compare the properties such as cement, iron, and silica. Apparently, materials could be formed and mechanical properties were investigated.
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Affiliation(s)
- Kittikhun Khotmungkhun
- Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Nonthaburi, 11000, Thailand
- School of Materials Science and Innovation, Material Science and Engineering Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rat Prathumwan
- School of Materials Science and Innovation, Material Science and Engineering Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Arkorn Chotiyasilp
- School of Materials Science and Innovation, Material Science and Engineering Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Kittitat Subannajui
- School of Materials Science and Innovation, Material Science and Engineering Program, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Corresponding author.
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9
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, Ros A. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. BIOPHYSICAL REPORTS 2022; 2:100081. [PMID: 36425668 PMCID: PMC9680787 DOI: 10.1016/j.bpr.2022.100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Robert E. Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Frederic Poitevin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sebastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - J. Domingo Meza-Aguilar
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jose M. Martin-Garcia
- Institute Physical-Chemistry Rocasolano, Spanish National Research Council, Madrid, Spain
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Richard A. Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
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10
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Wells DJ, Berntsen P, Balaur E, Kewish CM, Adams P, Aquila A, Binns J, Boutet S, Broomhall H, Caleman C, Christofferson A, Conn CE, Dahlqvist C, Flueckiger L, Gian Roque F, Greaves TL, Hejazian M, Hunter M, Hadian Jazi M, Jönsson HO, Pathirannahalage SK, Kirian RA, Kozlov A, Kurta RP, Marman H, Mendez D, Morgan A, Nugent K, Oberthuer D, Quiney H, Reinhardt J, Saha S, Sellberg JA, Sierra R, Wiedorn M, Abbey B, Martin AV, Darmanin C. Observations of phase changes in monoolein during high viscous injection. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:602-614. [PMID: 35510993 PMCID: PMC9070699 DOI: 10.1107/s1600577522001862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.
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Affiliation(s)
- Daniel J. Wells
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter Berntsen
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Eugeniu Balaur
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Cameron M. Kewish
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia
- Department of Chemistry and Physics, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Patrick Adams
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jack Binns
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hayden Broomhall
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Caroline Dahlqvist
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Leonie Flueckiger
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Francisco Gian Roque
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Tamar L. Greaves
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Majid Hejazian
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marjan Hadian Jazi
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - H. Olof Jönsson
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | | | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Kozlov
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Hugh Marman
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Derek Mendez
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Morgan
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Keith Nugent
- Research School of Physics, The Australian National University, Acton, ACT, Australia
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Harry Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Juliane Reinhardt
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Saumitra Saha
- ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonas A. Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Raymond Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Max Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Brian Abbey
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Andrew V. Martin
- School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Connie Darmanin
- La Trobe Institute for Molecular Science, Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Science, La Trobe University, Bundoora, VIC 3086, Australia
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11
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Assalauova D, Ignatenko A, Isensee F, Trofimova D, Vartanyants IA. Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:444-454. [PMID: 35719305 PMCID: PMC9172041 DOI: 10.1107/s1600576722002667] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
A convolutional neural network is applied for the single-hit diffraction-pattern classification step in single-particle-imaging experiments at X-ray free-electron lasers. This approach can be employed not only after the experiment but, importantly, also during an experiment and can significantly reduce the size of data storage for further analysis stages. Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.
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12
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Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:331-346. [PMID: 35254295 PMCID: PMC8900844 DOI: 10.1107/s1600577521013370] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.
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Affiliation(s)
| | | | - Juraj Knoška
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Florian Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, TU Dortmund, Otto-Hahn-Straße 4, 44221 Dortmund, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Elisa Delmas
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Simon Dold
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5AZ, United Kingdom
| | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Heymann
- Institute for Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia
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13
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, 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, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany,School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Correspondence e-mail:
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14
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Ignatenko A, Assalauova D, Bobkov SA, Gelisio L, Teslyuk AB, Ilyin VA, Vartanyants IA. Classification of diffraction patterns in single particle imaging experiments performed at x-ray free-electron lasers using a convolutional neural network. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abd916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Single particle imaging (SPI) is a promising method of native structure determination, which has undergone fast progress with the development of x-ray free-electron lasers. Large amounts of data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus non-single hits). Classification and object detection are areas where deep neural networks currently outperform other approaches. In this work, we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting transfer learning, a moderate amount of data is sufficient to train the neural network. We demonstrate here that a convolutional neural network can be successfully used to classify data from SPI experiments. We compare the results of classification for the two different networks, with different depth and architecture, by applying them to the same SPI data with different data representation. The best results are obtained for diffracted intensity represented by color images on a linear scale using YOLOv2 for classification. It shows an accuracy of about 95% with precision and recall of about 50% and 60%, respectively, in comparison to manual data classification.
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15
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Hejazian M, Balaur E, Abbey B. Recent Advances and Future Perspectives on Microfluidic Mix-and-Jet Sample Delivery Devices. MICROMACHINES 2021; 12:531. [PMID: 34067131 PMCID: PMC8151207 DOI: 10.3390/mi12050531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
The integration of the Gas Dynamic Virtual Nozzle (GDVN) and microfluidic technologies has proven to be a promising sample delivery solution for biomolecular imaging studies and has the potential to be transformative for a range of applications in physics, biology, and chemistry. Here, we review the recent advances in the emerging field of microfluidic mix-and-jet sample delivery devices for the study of biomolecular reaction dynamics. First, we introduce the key parameters and dimensionless numbers involved in their design and characterisation. Then we critically review the techniques used to fabricate these integrated devices and discuss their advantages and disadvantages. We then summarise the most common experimental methods used for the characterisation of both the mixing and jetting components. Finally, we discuss future perspectives on the emerging field of microfluidic mix-and-jet sample delivery devices. In summary, this review aims to introduce this exciting new topic to the wider microfluidics community and to help guide future research in the field.
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Affiliation(s)
| | | | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, VIC 3086, Australia; (M.H.); (E.B.)
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16
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Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. The XBI BioLab for life science experiments at the European XFEL. J Appl Crystallogr 2021; 54:7-21. [PMID: 33833637 PMCID: PMC7941304 DOI: 10.1107/s1600576720013989] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/19/2020] [Indexed: 11/26/2022] Open
Abstract
The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.
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Affiliation(s)
- Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Ekaterina Round
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Yasmin Gül
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jana Makroczyová
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Domingo Meza
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Philipp Heuser
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Inari Kursula
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK – 8000 Aarhus C, Denmark
| | - Elena Tereschenko
- Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky prospekt, Moscow, 117333, Russian Federation
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Charlotte Uetrecht
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Jozef Ulicný
- Department of Biophysics, Institute of Physics, Faculty of Science, P. J. Šafárik University, Jesenná 5, 04154 Košice, Slovak Republic
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnici 835, 25241 Dolní Břežany, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
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17
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Li H, Nazari R, Abbey B, Alvarez R, Aquila A, Ayyer K, Barty A, Berntsen P, Bielecki J, Pietrini A, Bucher M, Carini G, Chapman HN, Contreras A, Daurer BJ, DeMirci H, Flűckiger L, Frank M, Hajdu J, Hantke MF, Hogue BG, Hosseinizadeh A, Hunter MS, Jönsson HO, Kirian RA, Kurta RP, Loh D, Maia FRNC, Mancuso AP, Morgan AJ, McFadden M, Muehlig K, Munke A, Reddy HKN, Nettelblad C, Ourmazd A, Rose M, Schwander P, Marvin Seibert M, Sellberg JA, Sierra RG, Sun Z, Svenda M, Vartanyants IA, Walter P, Westphal D, Williams G, Xavier PL, Yoon CH, Zaare S. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Sci Data 2020; 7:404. [PMID: 33214568 PMCID: PMC7678860 DOI: 10.1038/s41597-020-00745-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022] Open
Abstract
Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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Affiliation(s)
- Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Physics Department, Stanford University, 450 Serra Mall, Stanford, California, 94305, USA
| | - Reza Nazari
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Roberto Alvarez
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA.
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Berntsen
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Johan Bielecki
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Maximilian Bucher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Gabriella Carini
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - Henry N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alice Contreras
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Hasan DeMirci
- Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Koc University, Rumelifeneri, Sariyer Rumeli Feneri Yolu, 34450, Sariyer/Istanbul, Turkey
| | - Leonie Flűckiger
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-452, Livermore, California, 94550, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnicic 835, 25241, Dolní Břežany, Czech Republic
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Brenda G Hogue
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Ahmad Hosseinizadeh
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Mark S Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - H Olof Jönsson
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Richard A Kirian
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | | | - Duane Loh
- Department of Physics, National University of Singapore, 14 Science Drive 4, Blk S1A, Level 2, S1A-02-07, Lee Wee Kheng Building, Singapore, 117557, Singapore
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - 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
| | - Andrew J Morgan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Matthew McFadden
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Kerstin Muehlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Hemanth Kumar Narayana Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Abbas Ourmazd
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Max Rose
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Schwander
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Jonas A Sellberg
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Zhibin Sun
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Photon Science Division, Paul Scherrer Institute, CH-5232, Villigen PSI, Switzerland
| | - Martin Svenda
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Ivan A Vartanyants
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
- NRNU MEPhI, Kashirskoe shosse 31, 115409, Moscow, Russia
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Garth Williams
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - P Lourdu Xavier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Sahba Zaare
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
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18
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCRJ 2020; 7:1102-1113. [PMID: 33209321 PMCID: PMC7642788 DOI: 10.1107/s2052252520012798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Sergey Bobkov
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
| | - Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
| | - Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA
| | - Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | | | - Anton Teslyuk
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Viacheslav A. Ilyin
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
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