1
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Chavas LMG, Coulibaly F, Garriga D. Bridging the microscopic divide: a comprehensive overview of micro-crystallization and in vivo crystallography. IUCRJ 2024; 11:476-485. [PMID: 38958014 PMCID: PMC11220871 DOI: 10.1107/s205225252400513x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
A series of events underscoring the significant advancements in micro-crystallization and in vivo crystallography were held during the 26th IUCr Congress in Melbourne, positioning microcrystallography as a pivotal field within structural biology. Through collaborative discussions and the sharing of innovative methodologies, these sessions outlined frontier approaches in macromolecular crystallography. This review provides an overview of this rapidly moving field in light of the rich dialogues and forward-thinking proposals explored during the congress workshop and microsymposium. These advances in microcrystallography shed light on the potential to reshape current research paradigms and enhance our comprehension of biological mechanisms at the molecular scale.
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Affiliation(s)
| | - Fasséli Coulibaly
- Biomedicine Discovery Institute & Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
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2
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Hasegawa H. Temperature-dependent intracellular crystallization of firefly luciferase in mammalian cells is suppressed by D-luciferin and stabilizing inhibitors. Exp Cell Res 2024; 440:114131. [PMID: 38876374 DOI: 10.1016/j.yexcr.2024.114131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Firefly luciferase (Fluc) from Photinus pyralis is one of the most widely used reporter proteins in biomedical research. Despite its widespread use, Fluc's protein phase transition behaviors and phase separation characteristics have not received much attention. Current research uncovers Fluc's intrinsic property to phase separate in mammalian cells upon a simple cell culture temperature change. Specifically, Fluc spontaneously produced needle-shaped crystal-like inclusion bodies upon temperature shift to the hypothermic temperatures ranging from 25 °C to 31 °C. The crystal-like inclusion bodies were not associated with or surrounded by membranous organelles and were likely built from the cytosolic pool of Fluc. Furthermore, the crystal-like inclusion formation was suppressed when cells were cultured in the presence of D-luciferin and its synthetic analog, as well as the benzothiazole family of so-called stabilizing inhibitors. These two classes of compounds inhibited intracellular Fluc crystallization by different modes of action as they had contrasting effects on steady-state luciferase protein accumulation levels. This study suggests that, under substrate insufficient conditions, the excess Fluc phase separates into a crystal-like state that can modulate intracellular soluble enzyme availability and protein turnover rate.
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Affiliation(s)
- Haruki Hasegawa
- Discovery Protein Science, Department of Large Molecule Discovery and Research Data Science Amgen Inc., South San Francisco, CA 94080, USA.
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3
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Kardoost A, Schönherr R, Deiter C, Redecke L, Lorenzen K, Schulz J, de Diego I. Convolutional neural network approach for the automated identification of in cellulo crystals. J Appl Crystallogr 2024; 57:266-275. [PMID: 38596734 PMCID: PMC11001417 DOI: 10.1107/s1600576724000682] [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: 03/22/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
In cellulo crystallization is a rare event in nature. Recent advances that have made use of heterologous overexpression can promote the intracellular formation of protein crystals, but new tools are required to detect and characterize these targets in the complex cell environment. The present work makes use of Mask R-CNN, a convolutional neural network (CNN)-based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim of extracting relevant information to support a semi-automated screening pipeline, in order to aid the development of the intracellular protein crystallization approach.
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Affiliation(s)
- Amirhossein Kardoost
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Schleswig-Holstein, Germany
| | - Carsten Deiter
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Schleswig-Holstein, Germany
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kristina Lorenzen
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Joachim Schulz
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Iñaki de Diego
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
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4
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Schönherr R, Boger J, Lahey-Rudolph JM, Harms M, Kaiser J, Nachtschatt S, Wobbe M, Duden R, König P, Bourenkov G, Schneider TR, Redecke L. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun 2024; 15:1709. [PMID: 38402242 PMCID: PMC10894269 DOI: 10.1038/s41467-024-45985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024] Open
Abstract
With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - J Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Hamburg, Germany
- X-ray technology lab, TH Lübeck - University of Applied Sciences Lübeck, Lübeck, Germany
| | - Mareike Harms
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Marla Wobbe
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Rainer Duden
- Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany.
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
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5
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- 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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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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Nipah Virus Infection Generates Ordered Structures in Cellulo. Viruses 2022; 14:v14071523. [PMID: 35891503 PMCID: PMC9317923 DOI: 10.3390/v14071523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/16/2022] [Accepted: 07/08/2022] [Indexed: 02/06/2023] Open
Abstract
Nipah virus (NiV) is a zoonotic paramyxovirus with a fatality rate of up to 92% in humans. While several pathogenic mechanisms used by NiV to counteract host immune defense responses have been described, all of the processes that take place in cells during infection are not fully characterized. Here, we describe the formation of ordered intracellular structures during NiV infection. We observed that these structures are formed specifically during NiV infection, but not with other viruses from the same Mononegavirales order (namely Ebola virus) or from other orders such as Bunyavirales (Junín virus). We also determined the kinetics of the appearance of these structures and their cellular localization at the cellular periphery. Finally, we confirmed the presence of these NiV-specific ordered structures using structured illumination microscopy (SIM), as well as their localization by transmission electron microscopy (TEM), scanning electron microscopy (SEM), and correlative light and electron microscopy (CLEM). Herein, we describe a cytopathogenic mechanism that provides a new insight into NiV biology. These newly described ordered structures could provide a target for novel antiviral approaches.
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Hochmair J, Exner C, Franck M, Dominguez-Baquero A, Diez L, Brognaro H, Kraushar ML, Mielke T, Radbruch H, Kaniyappan S, Falke S, Mandelkow E, Betzel C, Wegmann S. Molecular crowding and RNA synergize to promote phase separation, microtubule interaction, and seeding of Tau condensates. EMBO J 2022; 41:e108882. [PMID: 35298090 PMCID: PMC9156969 DOI: 10.15252/embj.2021108882] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Biomolecular condensation of the neuronal microtubule‐associated protein Tau (MAPT) can be induced by coacervation with polyanions like RNA, or by molecular crowding. Tau condensates have been linked to both functional microtubule binding and pathological aggregation in neurodegenerative diseases. We find that molecular crowding and coacervation with RNA, two conditions likely coexisting in the cytosol, synergize to enable Tau condensation at physiological buffer conditions and to produce condensates with a strong affinity to charged surfaces. During condensate‐mediated microtubule polymerization, their synergy enhances bundling and spatial arrangement of microtubules. We further show that different Tau condensates efficiently induce pathological Tau aggregates in cells, including accumulations at the nuclear envelope that correlate with nucleocytoplasmic transport deficits. Fluorescent lifetime imaging reveals different molecular packing densities of Tau in cellular accumulations and a condensate‐like density for nuclear‐envelope Tau. These findings suggest that a complex interplay between interaction partners, post‐translational modifications, and molecular crowding regulates the formation and function of Tau condensates. Conditions leading to prolonged existence of Tau condensates may induce the formation of seeding‐competent Tau and lead to distinct cellular Tau accumulations.
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Affiliation(s)
- Janine Hochmair
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Christian Exner
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Maximilian Franck
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | | | - Lisa Diez
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Hévila Brognaro
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | | | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics (MOLGEN), Berlin, Germany
| | - Helena Radbruch
- Institute for Neuropathology, Charité Berlin, Berlin, Germany
| | - Senthil Kaniyappan
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Sven Falke
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Christian Betzel
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
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9
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Tsukimoto J, Takeuchi Y, Horii Y, Iniwa T, Fukushi Y, Nishioka SI, Itoh K. In Cellulo Crystallization of Human Neuraminidase 1 and Biological Roles of N-Glycans. ACS APPLIED BIO MATERIALS 2022; 5:205-213. [DOI: 10.1021/acsabm.1c01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Tsukimoto
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Yoshie Takeuchi
- Department of Medicinal Biotechnology, Faculty of Pharmacy, Tokushima University, Tokushima 770-8505, Japan
| | - Yuto Horii
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Toshiki Iniwa
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Yuri Fukushi
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - So-ichiro Nishioka
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
| | - Kohji Itoh
- Department of Medicinal Biotechnology, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan
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10
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Correlation between Renal Artery Anatomy and Hypertension: A Retrospective Analysis of 3000 Patients. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2021:9957361. [PMID: 35003315 PMCID: PMC8731270 DOI: 10.1155/2021/9957361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/04/2021] [Accepted: 12/13/2021] [Indexed: 11/24/2022]
Abstract
Objective To assess the correlation between renal artery anatomy and blood pressure in Undiagnosed Hypertension and Diagnosed Hypertension. Methods The renal artery CT scanning imaging data and laboratory data of 3000 inpatients and outpatients were collected retrospectively in 4 centers of China. Morphometric parameters were assessed using the quantitative vascular analysis (unit: mM). Results 687 cases (23.2%) had accessory renal arteries unilaterally, and 216 cases (7.3%) had bilateral accessory renal arteries, including left kidney 825 (27.9%) and right kidney 798 (27.0%). The presence of accessory renal arteries and renal artery branches was higher in the diagnosed hypertension group as compared with the undiagnosed hypertension group (MARB, pp < 0.001; ARA, p < 0.001; others, p < 0.001). Consequently, multivariate regression analysis showed that age (OR = 2.519 (95% CI: 0.990–6.411, p < 0.001)), dyslipidemia (OR = 1.187 (95% CI: 0.960–1.454, p = 0.007)), renal hilum Outside the main renal artery branch (MRAB) (OR = 2.069 (95% CI: 1.614–2.524, p = 0.002)), and accessory renal artery (ARA) (OR = 2.071 (95% CI: 1.614–2.634, p = 0.001)) were risk factors of hypertension. In addition, higher renin activity was associated with ARA patients (2.19 ± 2.91 vs. 1.75 ± 2.85, p < 0.001). Conclusions When comparing renal arteries side by side, the anatomical length of the renal arteries is significantly different. In addition, the prevalence of accessory renal arteries and renal artery branches is higher in the hypertension group. The auxiliary renal artery and the main renal artery branch outside the renal portal are independent factors of hypertension. Renal sympathetic nerve activity is affected by renin activity and is related to the accessory renal artery.
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11
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Lahey-Rudolph JM, Schönherr R, Barthelmess M, Fischer P, Seuring C, Wagner A, Meents A, Redecke L. Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals. IUCRJ 2021; 8:665-677. [PMID: 34258014 PMCID: PMC8256716 DOI: 10.1107/s2052252521005297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/18/2021] [Indexed: 05/05/2023]
Abstract
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
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Affiliation(s)
- J. Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Carolin Seuring
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22671 Hamburg, Germany
| | - Armin Wagner
- Diamond Light Source, Diamond House DH2-52, Chilton, Didcot OX11 0DE, United Kingdom
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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Tetreau G, Andreeva EA, Banneville AS, De Zitter E, Colletier JP. Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins? Toxins (Basel) 2021; 13:toxins13070441. [PMID: 34206749 PMCID: PMC8309801 DOI: 10.3390/toxins13070441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
The development of finely tuned and reliable crystallization processes to obtain crystalline formulations of proteins has received growing interest from different scientific fields, including toxinology and structural biology, as well as from industry, notably for biotechnological and medical applications. As a natural crystal-making bacterium, Bacillus thuringiensis (Bt) has evolved through millions of years to produce hundreds of highly structurally diverse pesticidal proteins as micrometer-sized crystals. The long-term stability of Bt protein crystals in aqueous environments and their specific and controlled dissolution are characteristics that are particularly sought after. In this article, we explore whether the crystallization machinery of Bt can be hijacked as a means to produce (micro)crystalline formulations of proteins for three different applications: (i) to develop new bioinsecticidal formulations based on rationally improved crystalline toxins, (ii) to functionalize crystals with specific characteristics for biotechnological and medical applications, and (iii) to produce microcrystals of custom proteins for structural biology. By developing the needs of these different fields to figure out if and how Bt could meet each specific requirement, we discuss the already published and/or patented attempts and provide guidelines for future investigations in some underexplored yet promising domains.
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13
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Chang CC, Keppeke GD, Antos CL, Peng M, Andrade LEC, Sung LY, Liu JL. CTPS forms the cytoophidium in zebrafish. Exp Cell Res 2021; 405:112684. [PMID: 34129847 DOI: 10.1016/j.yexcr.2021.112684] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/26/2022]
Abstract
Cytidine triphosphate synthase (CTPS) catalyzes the rate-limiting step of de novo CTP biosynthesis. An intracellular structure of CTPS, the cytoophidium, has been found in many organisms including prokaryotes and eukaryotes. Formation of the cytoophidium has been suggested to regulate the activity and stability of CTPS and may participate in certain physiological events. Herein, we demonstrate that both CTPS1a and CTPS1b in zebrafish are able to form the cytoophidium in cultured cells. A point mutation, H355A, abrogates cytoophidium assembly of zebrafish CTPS1a and CTPS1b. In addition, we show the presence of CTPS cytoophidia in multiple tissues of larval and adult fish under normal conditions, while treatment with a CTPS inhibitor 6-diazo-5-oxo-l-norleucine (DON) can induce more cytoophidia in some tissues. Our findings reveal that forming the CTPS cytoophidium is a natural phenomenon of zebrafish and provide valuable information for future research on the physiological importance of this intracellular structure in vertebrates.
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Affiliation(s)
- Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gerson Dierley Keppeke
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Christopher L Antos
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Min Peng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP 04023-062, Brazil
| | - Li-Ying Sung
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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14
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Hasegawa H, Wei KY, Thomas M, Li P, Kinderman F, Franey H, Liu L, Jacobsen F. Light chain subunit of a poorly soluble human IgG2λ crystallizes in physiological pH environment both in cellulo and in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119078. [PMID: 34118277 DOI: 10.1016/j.bbamcr.2021.119078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
Prominent inclusion bodies can develop in the endoplasmic reticulum (ER) when overexpressed antibodies possess intrinsically high condensation propensities. These observations suggest that antibodies deemed to show notable solubility problems may reveal such characteristics preemptively in the form of ER-associated inclusion bodies during antibody overexpression. To define the relationships between solubility problems and inclusion body phenotypes, we investigated the biosynthesis of a model human IgG2λ that shows severe opalescence in an acidic formulation buffer yet retains high solubility at physiological pH. Consistent with the pH-dependent solubility characteristics, the model antibody did not induce notable inclusion body in the physiological pH environment of the ER lumen. However, when individual subunit chains of the antibody were expressed separately, the light chain (LC) spontaneously induced notable crystal-like inclusion bodies in the ER. The LC crystallization event was readily reproducible in vitro by simply concentrating the purified LC protein at physiological pH. Two independent structural determinants for the LC crystallization were identified through rational mutagenesis approach by monitoring the effect of amino acid substitutions on intracellular LC crystallogenesis. The effect of mutations on crystallization was also recapitulated in vitro using purified LC proteins. Importantly, when introduced directly into the model antibody, a mutation that prevents the LC crystallization remediated the antibody's solubility problem without compromising the secretory output or antigen binding. These results illustrate that the ER can serve as a "physiological test tube" that not only reports secretory cargo's high condensation propensity at physiological pH, but also provides an orthogonal method that guides antibody engineering strategy.
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Affiliation(s)
- Haruki Hasegawa
- Department of Therapeutic Discovery, Amgen Inc., South San Francisco, CA 94080, USA.
| | - Kathy Y Wei
- Department of Therapeutic Discovery, Amgen Inc., South San Francisco, CA 94080, USA
| | - Melissa Thomas
- Department of Therapeutic Discovery, Amgen Inc., South San Francisco, CA 94080, USA
| | - Peng Li
- Department of Therapeutic Discovery, Amgen Inc., South San Francisco, CA 94080, USA
| | - Francis Kinderman
- Department of Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Heather Franey
- Department of Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Ling Liu
- Department of Therapeutic Discovery, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Frederick Jacobsen
- Department of Therapeutic Discovery, Amgen Inc., Thousand Oaks, CA 91320, USA
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15
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Lahey-Rudolph JM, Schönherr R, Jeffries CM, Blanchet CE, Boger J, Ferreira Ramos AS, Riekehr WM, Triandafillidis DP, Valmas A, Margiolaki I, Svergun D, Redecke L. Rapid screening of in cellulo grown protein crystals via a small-angle X-ray scattering/X-ray powder diffraction synergistic approach. J Appl Crystallogr 2020; 53:1169-1180. [PMID: 33117106 PMCID: PMC7534541 DOI: 10.1107/s1600576720010687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
Crystallization of recombinant proteins in living cells is an exciting new approach for structural biology that provides an alternative to the time-consuming optimization of protein purification and extensive crystal screening steps. Exploiting the potential of this approach requires a more detailed understanding of the cellular processes involved and versatile screening strategies for crystals in a cell culture. Particularly if the target protein forms crystalline structures of unknown morphology only in a small fraction of cells, their detection by applying standard visualization techniques can be time consuming and difficult owing to the environmental challenges imposed by the living cells. In this study, a high-brilliance and low-background bioSAXS beamline is employed for rapid and sensitive detection of protein microcrystals grown within insect cells. On the basis of the presence of Bragg peaks in the recorded small-angle X-ray scattering profiles, it is possible to assess within seconds whether a cell culture contains microcrystals, even in a small percentage of cells. Since such information cannot be obtained by other established detection methods in this time frame, this screening approach has the potential to overcome one of the bottlenecks of intracellular crystal detection. Moreover, the association of the Bragg peak positions in the scattering curves with the unit-cell composition of the protein crystals raises the possibility of investigating the impact of environmental conditions on the crystal structure of the intracellular protein crystals. This information provides valuable insights helping to further understand the in cellulo crystallization process.
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Affiliation(s)
- Janine Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Clément E. Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
| | | | - Winnie Maria Riekehr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
| | | | - Alexandros Valmas
- Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Patras GR-26500, Greece
| | - Irene Margiolaki
- Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, Patras GR-26500, Greece
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
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16
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Tang Y, Saul J, Nagaratnam N, Martin-Garcia JM, Fromme P, Qiu J, LaBaer J. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Sci Rep 2020; 10:13323. [PMID: 32770037 PMCID: PMC7414197 DOI: 10.1038/s41598-020-70163-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Baculovirus mediated-insect cell expression systems have been widely used for producing heterogeneous proteins. However, to date, there is still the lack of an easy-to-manipulate system that enables the high-throughput protein characterization in insect cells by taking advantage of large existing Gateway clone libraries. To resolve this limitation, we have constructed a suite of Gateway-compatible pIEx-derived baculovirus expression vectors that allow the rapid and cost-effective construction of expression clones for mass parallel protein expression in insect cells. This vector collection also supports the attachment of a variety of fusion tags to target proteins to meet the needs for different research applications. We first demonstrated the utility of these vectors for protein expression and purification using a set of 40 target proteins of various sizes, cellular localizations and host organisms. We then established a scalable pipeline coupled with the SONICC and TEM techniques to screen for microcrystal formation within living insect cells. Using this pipeline, we successfully identified microcrystals for ~ 16% of the tested protein set, which can be potentially used for structure elucidation by X-ray crystallography. In summary, we have established a versatile pipeline enabling parallel gene cloning, protein expression and purification, and in vivo microcrystal screening for structural studies.
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Affiliation(s)
- Yanyang Tang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Justin Saul
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
| | - Joshua LaBaer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
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17
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Li TL, Cui B. Production and Isolation of Magnetic Protein Crystals in HEK293T Cells. Bio Protoc 2020; 10:e3684. [PMID: 33659355 DOI: 10.21769/bioprotoc.3684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 11/02/2022] Open
Abstract
Advances in protein engineering have enabled the production of self-assembled protein crystals within living cells. Our recent publication demonstrates the production of ftn-PAK4, which is a ferritin-containing crystal that can mineralize iron and become magnetic when isolated. We have developed an optimized protocol for the production and isolation of PAK4-based crystals. The crystals are first grown in low-passage HEK293T cells, released using a lysis buffer containing NP-40 and DNase, and collected under careful centrifugation conditions. Our protocol maximizes the purity and yield of crystals and is quick and straightforward.
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Affiliation(s)
- Thomas L Li
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California, USA
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18
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Nagaratnam N, Tang Y, Botha S, Saul J, Li C, Hu H, Zaare S, Hunter M, Lowry D, Weierstall U, Zatsepin N, Spence JCH, Qiu J, LaBaer J, Fromme P, Martin-Garcia JM. Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs. Acta Crystallogr F Struct Biol Commun 2020; 76:278-289. [PMID: 32510469 PMCID: PMC7278499 DOI: 10.1107/s2053230x20006172] [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: 03/23/2020] [Accepted: 05/06/2020] [Indexed: 11/10/2022] Open
Abstract
μNS is a 70 kDa major nonstructural protein of avian reoviruses, which cause significant economic losses in the poultry industry. They replicate inside viral factories in host cells, and the μNS protein has been suggested to be the minimal viral factor required for factory formation. Thus, determining the structure of μNS is of great importance for understanding its role in viral infection. In the study presented here, a fragment consisting of residues 448-605 of μNS was expressed as an EGFP fusion protein in Sf9 insect cells. EGFP-μNS(448-605) crystallization in Sf9 cells was monitored and verified by several imaging techniques. Cells infected with the EGFP-μNS(448-605) baculovirus formed rod-shaped microcrystals (5-15 µm in length) which were reconstituted in high-viscosity media (LCP and agarose) and investigated by serial femtosecond X-ray diffraction using viscous jets at an X-ray free-electron laser (XFEL). The crystals diffracted to 4.5 Å resolution. A total of 4227 diffraction snapshots were successfully indexed into a hexagonal lattice with unit-cell parameters a = 109.29, b = 110.29, c = 324.97 Å. The final data set was merged and refined to 7.0 Å resolution. Preliminary electron-density maps were obtained. While more diffraction data are required to solve the structure of μNS(448-605), the current experimental strategy, which couples high-viscosity crystal delivery at an XFEL with in cellulo crystallization, paves the way towards structure determination of the μNS protein.
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Affiliation(s)
- Nirupa Nagaratnam
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yanyang Tang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Justin Saul
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Hunter
- Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - David Lowry
- Eyring Materials Center, Arizona State University, Tempe, AZ 85287, USA
| | - Uwe Weierstall
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia
| | - John C. H. Spence
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua LaBaer
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jose M. Martin-Garcia
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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19
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Nass K, Redecke L, Perbandt M, Yefanov O, Klinge M, Koopmann R, Stellato F, Gabdulkhakov A, Schönherr R, Rehders D, Lahey-Rudolph JM, Aquila A, Barty A, Basu S, Doak RB, Duden R, Frank M, Fromme R, Kassemeyer S, Katona G, Kirian R, Liu H, Majoul I, Martin-Garcia JM, Messerschmidt M, Shoeman RL, Weierstall U, Westenhoff S, White TA, Williams GJ, Yoon CH, Zatsepin N, Fromme P, Duszenko M, Chapman HN, Betzel C. In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors. Nat Commun 2020; 11:620. [PMID: 32001697 PMCID: PMC6992785 DOI: 10.1038/s41467-020-14484-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023] Open
Abstract
Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds. Trypanosoma brucei inosine-5′-monophosphate dehydrogenase (IMPDH) is an enzyme in the guanine nucleotide biosynthesis pathway and of interest as a drug target. Here the authors present the 2.8 Å room temperature structure of TbIMPDH determined by utilizing X-ray free-electron laser radiation and crystals that were grown in insect cells and find that ATP and GMP are bound at the canonical sites of the Bateman domains.
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Affiliation(s)
- Karol Nass
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Paul Scherrer Institute (PSI), Forschungstrasse 111, 5232, Villigen, PSI, Switzerland
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,German Centre for Infection Research, University of Lübeck, 23562, Lübeck, Germany.,Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestr. 85, 22607, Hamburg, Germany
| | - M Perbandt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany
| | - O Yefanov
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - M Klinge
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,BioAgilytix Europe GmbH, Lademannbogen 10, 22339, Hamburg, Germany
| | - R Koopmann
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str.4, 72076, Tübingen, Germany
| | - F Stellato
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Dipartimento di Fisica, Università di Roma Tor Vergata and INFN, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - A Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region, Russia, 142290
| | - R Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestr. 85, 22607, Hamburg, Germany
| | - D Rehders
- Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,BODE Chemie GmbH, Melanchthonstraße 27, 22525, Hamburg, Germany
| | - J M Lahey-Rudolph
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - A Aquila
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - A Barty
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - S Basu
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA.,European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, Grenoble, France
| | - R B Doak
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - R Duden
- Institute of Biology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - M Frank
- Biology and Biotechnology Division, Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - R Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - S Kassemeyer
- Max-Planck-Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - R Kirian
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - H Liu
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,Complex Systems Division, Beijing Computational Science Research Center, 100193, Beijing, China
| | - I Majoul
- Institute of Biology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - J M Martin-Garcia
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ, 85287, USA
| | - M Messerschmidt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.,Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ, 85287, USA
| | - R L Shoeman
- Max-Planck-Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - U Weierstall
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA
| | - S Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - T A White
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - G J Williams
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.,Brookhaven National Laboratory (BNL), PO Box 5000, Upton, NY, 11973-5000, USA
| | - C H Yoon
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - N Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, 85411, USA.,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia
| | - P Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287-160, USA
| | - M Duszenko
- Institute of Neurophysiology, University of Tübingen, Keplerstr. 15, 72074, Tübingen, Germany
| | - H N Chapman
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - C Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, at Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.
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20
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Mudogo CN, Falke S, Brognaro H, Duszenko M, Betzel C. Protein phase separation and determinants of in cell crystallization. Traffic 2019; 21:220-230. [DOI: 10.1111/tra.12711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Celestin N. Mudogo
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Department of Basic Sciences, School of MedicineUniversity of Kinshasa Kinshasa Democratic Republic of Congo
| | - Sven Falke
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
| | - Hévila Brognaro
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Centre for Free‐Electron‐Laser Science Hamburg Germany
| | - Michael Duszenko
- Institute of Neurophysiology, University of Tübingen Tübingen Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
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21
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Simultaneous induction of distinct protein phase separation events in multiple subcellular compartments of a single cell. Exp Cell Res 2019; 379:92-109. [DOI: 10.1016/j.yexcr.2019.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023]
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22
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Schönherr R, Rudolph JM, Redecke L. Protein crystallization in living cells. Biol Chem 2019; 399:751-772. [PMID: 29894295 DOI: 10.1515/hsz-2018-0158] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
Abstract
Protein crystallization in living cells has been observed surprisingly often as a native assembly process during the past decades, and emerging evidence indicates that this phenomenon is also accessible for recombinant proteins. But only recently the advent of high-brilliance synchrotron sources, X-ray free-electron lasers, and improved serial data collection strategies has allowed the use of these micrometer-sized crystals for structural biology. Thus, in cellulo crystallization could offer exciting new possibilities for proteins that do not crystallize applying conventional approaches. In this review, we comprehensively summarize the current knowledge of intracellular protein crystallization. This includes an overview of the cellular functions, the physical properties, and, if known, the mode of regulation of native in cellulo crystal formation, complemented with a discussion of the reported crystallization events of recombinant proteins and the current method developments to successfully collect X-ray diffraction data from in cellulo crystals. Although the intracellular protein self-assembly mechanisms are still poorly understood, regulatory differences between native in cellulo crystallization linked to a specific function and accidently crystallizing proteins, either disease associated or recombinantly introduced, become evident. These insights are important to systematically exploit living cells as protein crystallization chambers in the future.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Janine Mia Rudolph
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
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23
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Nguyen TK, Ueno T. Engineering of protein assemblies within cells. Curr Opin Struct Biol 2018; 51:1-8. [PMID: 29316472 DOI: 10.1016/j.sbi.2017.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Accepted: 12/18/2017] [Indexed: 12/27/2022]
Abstract
Recent achievements in development of protein assembles within cells have extended biosupramolecular composites into a new era with versatile applications in the fields of biomaterial and biotechnology. Using methods with biological and physicochemical routes has made this era of research more interesting and challenging. Further advances in protein engineering have facilitated efficient fabrication of supramolecular complexes within living cells. Here, we provide a review of recent efforts to engineer protein assemblies within cells and describe the promising properties of these assemblies.
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Affiliation(s)
- Tien K Nguyen
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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24
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Boudes M, Garriga D, Coulibaly F. Microcrystallography of Protein Crystals and In Cellulo Diffraction. J Vis Exp 2017. [PMID: 28784967 DOI: 10.3791/55793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 µm in their largest dimension, which used to represent a challenge. We present two alternative workflows for the structure determination of protein microcrystals by X-ray crystallography with a particular focus on crystals grown in vivo. The microcrystals are either extracted from cells by sonication and purified by differential centrifugation, or analyzed in cellulo after cell sorting by flow cytometry of crystal-containing cells. Optionally, purified crystals or crystal-containing cells are soaked in heavy atom solutions for experimental phasing. These samples are then prepared for diffraction experiments in a similar way by application onto a micromesh support and flash cooling in liquid nitrogen. We briefly describe and compare serial diffraction experiments of isolated microcrystals and crystal-containing cells using a microfocus synchrotron beamline to produce datasets suitable for phasing, model building and refinement. These workflows are exemplified with crystals of the Bombyx mori cypovirus 1 (BmCPV1) polyhedrin produced by infection of insect cells with a recombinant baculovirus. In this case study, in cellulo analysis is more efficient than analysis of purified crystals and yields a structure in ~8 days from expression to refinement.
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Affiliation(s)
- Marion Boudes
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University
| | - Damià Garriga
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University
| | - Fasséli Coulibaly
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University;
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25
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Nürnberger S, Rentenberger C, Thiel K, Schädl B, Grunwald I, Ponomarev I, Marlovits S, Meyer C, Barnewitz D. Giant crystals inside mitochondria of equine chondrocytes. Histochem Cell Biol 2016; 147:635-649. [PMID: 28013370 PMCID: PMC5400799 DOI: 10.1007/s00418-016-1516-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 01/20/2023]
Abstract
The present study reports for the first time the presence of giant crystals in mitochondria of equine chondrocytes. These structures show dark contrast in TEM images as well as a granular substructure of regularly aligned 1-2 nm small units. Different zone axes of the crystalline structure were analysed by means of Fourier transformation of lattice-resolution TEM images proving the crystalline nature of the structure. Elemental analysis reveals a high content of nitrogen referring to protein. The outer shape of the crystals is geometrical with an up to hexagonal profile in cross sections. It is elongated, spanning a length of several micrometres through the whole cell. In some chondrocytes, several crystals were found, sometimes combined in a single mitochondrion. Crystals were preferentially aligned along the long axis of the cells, thus appearing in the same orientation as the chondrocytes in the tissue. Although no similar structures have been found in the cartilage of any other species investigated, they have been found in cartilage repair tissue formed within a mechanically stimulated equine chondrocyte construct. Crystals were mainly located in superficial regions of cartilage, especially in joint regions of well-developed superficial layers, more often in yearlings than in adult horses. These results indicate that intramitochondrial crystals are related to the high mechanical stress in the horse joint and potentially also to the increased metabolic activity of immature individuals.
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Affiliation(s)
- S Nürnberger
- Department of Trauma Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria. .,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstrasse 13, 1200, Vienna, Austria. .,University Clinic of Dentistry, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria. .,Austrian Cluster for Tissue Regeneration, Vienna, Austria.
| | - C Rentenberger
- Physics of Nanostructured Materials, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - K Thiel
- Department of Adhesive Bonding Technology and Surfaces, Fraunhofer Institute for Manufacturing Technology and Advanced Materials, Wiener Strasse 12, 28359 Bremen, Germany
| | - B Schädl
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstrasse 13, 1200, Vienna, Austria.,University Clinic of Dentistry, Medical University of Vienna, Sensengasse 2a, 1090, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - I Grunwald
- Department of Adhesive Bonding Technology and Surfaces, Fraunhofer Institute for Manufacturing Technology and Advanced Materials, Wiener Strasse 12, 28359 Bremen, Germany
| | - I Ponomarev
- Research Centre for Medical Technics and Biotechnology, Geranienweg 7, 99947, Bad Langensalza, Germany
| | - St Marlovits
- Department of Trauma Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Ch Meyer
- Clinic and Polyclinic for Traumatology, University of Giessen, Rudolf-Buchheim-Straße 7, 35385, Giessen, Germany.,Orthopaedic and Trauma Surgery, Klinikum Saarbrücken, Winterberg 1, 66119, Saarbrücken, Germany
| | - D Barnewitz
- Research Centre for Medical Technics and Biotechnology, Geranienweg 7, 99947, Bad Langensalza, Germany
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26
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Boudes M, Garriga D, Fryga A, Caradoc-Davies T, Coulibaly F. A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction. Acta Crystallogr D Struct Biol 2016; 72:576-85. [PMID: 27050136 PMCID: PMC4822565 DOI: 10.1107/s2059798316002369] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/08/2016] [Indexed: 11/10/2022] Open
Abstract
While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by flow cytometry and directly analysed by X-ray diffraction is presented and applied to in vivo-grown crystals of the recombinant CPV1 polyhedrin. When compared with the analysis of purified crystals, in cellulo diffraction produces data of better quality and a gain of ∼0.35 Å in resolution for comparable beamtime usage. Importantly, crystals within cells are readily derivatized with gold and iodine compounds through the cellular membrane. Using the multiple isomorphous replacement method, a near-complete model was autobuilt from 2.7 Å resolution data. Thus, in favourable cases, an in cellulo pipeline can replace the complete workflow of structure determination without compromising the quality of the resulting model. In addition to its efficiency, this approach maintains the protein in a cellular context throughout the analysis, which reduces the risk of disrupting transient or labile interactions in protein-protein or protein-ligand complexes.
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Affiliation(s)
- Marion Boudes
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Damià Garriga
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew Fryga
- Faculty of Medicine, Nursing and Health Sciences, FlowCore, Monash University, Melbourne, VIC 3800, Australia
| | | | - Fasséli Coulibaly
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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27
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Gavira JA. Current trends in protein crystallization. Arch Biochem Biophys 2015; 602:3-11. [PMID: 26747744 DOI: 10.1016/j.abb.2015.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/16/2015] [Accepted: 12/22/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. SYNOPSIS Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda. de las Palmeras, 4. 18100 Armilla, Granada, Spain
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28
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Schönherr R, Klinge M, Rudolph JM, Fita K, Rehders D, Lübber F, Schneegans S, Majoul IV, Duszenko M, Betzel C, Brandariz-Nuñez A, Martinez-Costas J, Duden R, Redecke L. Real-time investigation of dynamic protein crystallization in living cells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041712. [PMID: 26798811 PMCID: PMC4711630 DOI: 10.1063/1.4921591] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/05/2015] [Indexed: 05/21/2023]
Abstract
X-ray crystallography requires sufficiently large crystals to obtain structural insights at atomic resolution, routinely obtained in vitro by time-consuming screening. Recently, successful data collection was reported from protein microcrystals grown within living cells using highly brilliant free-electron laser and third-generation synchrotron radiation. Here, we analyzed in vivo crystal growth of firefly luciferase and Green Fluorescent Protein-tagged reovirus μNS by live-cell imaging, showing that dimensions of living cells did not limit crystal size. The crystallization process is highly dynamic and occurs in different cellular compartments. In vivo protein crystallization offers exciting new possibilities for proteins that do not form crystals in vitro.
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Affiliation(s)
- R Schönherr
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - M Klinge
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | | | - K Fita
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - D Rehders
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | | | | | - I V Majoul
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - M Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen , Hoppe-Seyler-Straβe 4, 72076 Tübingen, Germany
| | - C Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg , c/o DESY, Notkestr. 85, 22603 Hamburg, Germany
| | - A Brandariz-Nuñez
- Department of Biochemistry and Molecular Biology, Centro de Investigación en Química Biológica y Materiales Moleculares (CIQUS), University Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - J Martinez-Costas
- Department of Biochemistry and Molecular Biology, Centro de Investigación en Química Biológica y Materiales Moleculares (CIQUS), University Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - R Duden
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - L Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
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