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Brodmerkel MN, Thiede L, De Santis E, Uetrecht C, Caleman C, Marklund EG. Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Phys Chem Chem Phys 2024; 26:13094-13105. [PMID: 38628116 DOI: 10.1039/d3cp06344e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
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2
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Dhillon A, Persson BD, Volkov AN, Sülzen H, Kádek A, Pompach P, Kereïche S, Lepšík M, Danskog K, Uetrecht C, Arnberg N, Zoll S. Structural insights into the interaction between adenovirus C5 hexon and human lactoferrin. J Virol 2024; 98:e0157623. [PMID: 38323814 PMCID: PMC10949841 DOI: 10.1128/jvi.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development. IMPORTANCE Our study delves into the structural aspects of adenovirus (AdV) infections, specifically HAdV-C5 in the respiratory epithelium. It uncovers the molecular details of a novel pathway where human lactoferrin (hLF) interacts with the major capsid protein, hexon, facilitating viral entry, and bypassing traditional receptors such as CAR and integrins. The study's cryo-EM structures reveal how hLF engages hexon, primarily through its N-terminal lactoferricin (Lfcin) region and hexon's hypervariable region 1 (HVR-1). Mutational analyses identify critical Lfcin contacts and other regions within hLF vital for hexon binding. This structural insight sheds light on HAdV-C5's mechanism of utilizing soluble hLF/Lfcin for cellular entry, holding promise for gene therapy and vaccine development advancements in adenovirus research.
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Affiliation(s)
- Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alan Kádek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Petr Pompach
- Biotechnology and Biomedical Center of the Academy of Sciences and Charles University in Vestec, Vestec, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarina Danskog
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Charlotte Uetrecht
- Department of Health Sciences and Biomedicine, Faculty V: School of Life Sciences, CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY and Leibniz Institute of Virology, Hamburg, University of Siegen, Siegen, Germany
| | - Niklas Arnberg
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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3
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Sänger L, Williams HM, Yu D, Vogel D, Kosinski J, Rosenthal M, Uetrecht C. RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment. J Am Chem Soc 2023; 145:27958-27974. [PMID: 38104324 PMCID: PMC10755698 DOI: 10.1021/jacs.3c07325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Lassa virus is a negative-strand RNA virus with only four structural proteins that causes periodic outbreaks in West Africa. The nucleoprotein (NP) encapsidates the viral genome, forming ribonucleoprotein complexes (RNPs) together with the viral RNA and the L protein. RNPs must be continuously restructured during viral genome replication and transcription. The Z protein is important for membrane recruitment of RNPs, viral particle assembly, and budding and has also been shown to interact with the L protein. However, the interaction of NP, viral RNA, and Z is poorly understood. Here, we characterize the interactions between Lassa virus NP, Z, and RNA using structural mass spectrometry. We identify the presence of RNA as the driver for the disassembly of ring-like NP trimers, a storage form, into monomers to subsequently form higher order RNA-bound NP assemblies. We locate the interaction site of Z and NP and demonstrate that while NP binds Z independently of the presence of RNA, this interaction is pH-dependent. These data improve our understanding of RNP assembly, recruitment, and release in Lassa virus.
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Affiliation(s)
- Lennart Sänger
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Harry M. Williams
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
| | - Dingquan Yu
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
| | - Dominik Vogel
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
| | - Jan Kosinski
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- European
Molecular Biology Laboratory Notkestraße 85, 22607 Hamburg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Maria Rosenthal
- Bernhard
Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB
Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany
- Leibniz
Institute of Virology (LIV), Notkestraße 85, 22607 Hamburg, Germany
- Faculty
V: School of Life Sciences, University of
Siegen, Am Eichenhang 50, 57076 Siegen, Germany
- Deutsches
Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
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4
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Feng Y, Pogan R, Thiede L, Müller-Guhl J, Uetrecht C, Roos WH. Fucose Binding Cancels out Mechanical Differences between Distinct Human Noroviruses. Viruses 2023; 15:1482. [PMID: 37515170 PMCID: PMC10383637 DOI: 10.3390/v15071482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The majority of nonbacterial gastroenteritis in humans and livestock is caused by noroviruses. Like most RNA viruses, frequent mutations result in various norovirus variants. The strain-dependent binding profiles of noroviruses to fucose are supposed to facilitate norovirus infection. It remains unclear, however, what the molecular mechanism behind strain-dependent functioning is. In this study, by applying atomic force microscopy (AFM) nanoindentation technology, we studied norovirus-like particles (noroVLPs) of three distinct human norovirus variants. We found differences in viral mechanical properties even between the norovirus variants from the same genogroup. The noroVLPs were then subjected to fucose treatment. Surprisingly, after fucose treatment, the previously found considerable differences in viral mechanical properties among these variants were diminished. We attribute a dynamic switch of the norovirus P domain upon fucose binding to the reduced differences in viral mechanical properties across the tested norovirus variants. These findings shed light on the mechanisms used by norovirus capsids to adapt to environmental changes and, possibly, increase cell infection. Hereby, a new step towards connecting viral mechanical properties to viral prevalence is taken.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, 9747AG Groningen, The Netherlands
| | - Ronja Pogan
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Jürgen Müller-Guhl
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Partner Site Hamburg-Lübeck-Borstel-Riems, Bernhard Nocht Institute for Tropical Medicine and German Center for Infection Research (DZIF), 20359 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY) & Leibniz Institute of Virology (LIV), 22607 Hamburg, Germany
- Faculty V: School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, 9747AG Groningen, The Netherlands
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5
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Kierspel T, Kadek A, Barran P, Bellina B, Bijedic A, Brodmerkel MN, Commandeur J, Caleman C, Damjanović T, Dawod I, De Santis E, Lekkas A, Lorenzen K, Morillo LL, Mandl T, Marklund EG, Papanastasiou D, Ramakers LAI, Schweikhard L, Simke F, Sinelnikova A, Smyrnakis A, Timneanu N, Uetrecht C. Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC. Anal Bioanal Chem 2023:10.1007/s00216-023-04658-y. [PMID: 37014373 PMCID: PMC10329076 DOI: 10.1007/s00216-023-04658-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm-1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.
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Affiliation(s)
- Thomas Kierspel
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany.
| | - Alan Kadek
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany
- Institute of Microbiology of the Czech Academy of Sciences - BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Perdita Barran
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Adi Bijedic
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Jan Commandeur
- MS Vision, Televisieweg 40, 1322 AM, Almere, Netherlands
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, E22607, Hamburg, Germany
| | - Tomislav Damjanović
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Faculty V: School of Life Sciences, University of Siegen, Adolf-Reichwein-Str. 2a, 57076, Siegen, Germany
| | - Ibrahim Dawod
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Alexandros Lekkas
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | | | | | - Thomas Mandl
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
- University of Applied Sciences Technikum Wien, Höchstädtpl. 6, 1200, Vienna, Austria
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Dimitris Papanastasiou
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | - Lennart A I Ramakers
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Lutz Schweikhard
- Institut Für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489, Greifswald, Germany
| | - Florian Simke
- Institut Für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489, Greifswald, Germany
| | - Anna Sinelnikova
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Athanasios Smyrnakis
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany.
- Faculty V: School of Life Sciences, University of Siegen, Adolf-Reichwein-Str. 2a, 57076, Siegen, Germany.
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6
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Shukla S, Komarek J, Novakova Z, Nedvedova J, Ustinova K, Vankova P, Kadek A, Uetrecht C, Mertens H, Barinka C. In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach. FEBS J 2023; 290:821-836. [PMID: 36062318 DOI: 10.1111/febs.16616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 07/08/2022] [Accepted: 09/02/2022] [Indexed: 02/04/2023]
Abstract
Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains, and a holistic picture of the full-length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modelling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in-solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration-dependent manner, and its oligomerization is mediated via the positively charged N-terminal microtubule-binding domain. Our findings provide the first insights into the structure of full-length human HDAC6 and can be used as a basis for further research into structure function and physiological studies of this unique deacetylase.
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Affiliation(s)
- Shivam Shukla
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.,Department of Physical Chemistry, Faculty of Natural Science, Charles University, Prague, Czech Republic
| | - Jan Komarek
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jana Nedvedova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Kseniya Ustinova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Pavla Vankova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Alan Kadek
- Leibniz Institute of Virology (LIV), Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany
| | - Charlotte Uetrecht
- Leibniz Institute of Virology (LIV), Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany.,Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,Department of Health Sciences and Biomedicine, School of Life Sciences, University of Siegen, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory (EMBL)-Hamburg Outstation, c/o DESY, Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
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7
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Soh TK, Pfefferle S, Wurr S, von Possel R, Oestereich L, Rieger T, Uetrecht C, Rosenthal M, Bosse JB. A validated protocol to UV-inactivate SARS-CoV-2 and herpesvirus-infected cells. PLoS One 2023; 18:e0274065. [PMID: 37163509 PMCID: PMC10171616 DOI: 10.1371/journal.pone.0274065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/19/2022] [Indexed: 05/12/2023] Open
Abstract
Downstream analysis of virus-infected cell samples, such as reverse transcription polymerase chain reaction (RT PCR) or mass spectrometry, often needs to be performed at lower biosafety levels than their actual cultivation, and thus the samples require inactivation before they can be transferred. Common inactivation methods involve chemical crosslinking with formaldehyde or denaturing samples with strong detergents, such as sodium dodecyl sulfate. However, these protocols destroy the protein quaternary structure and prevent the analysis of protein complexes, albeit through different chemical mechanisms. This often leads to studies being performed in over-expression or surrogate model systems. To address this problem, we generated a protocol that achieves the inactivation of infected cells through ultraviolet (UV) irradiation. UV irradiation damages viral genomes and crosslinks nucleic acids to proteins but leaves the overall structure of protein complexes mostly intact. Protein analysis can then be performed from intact cells without biosafety containment. While UV treatment protocols have been established to inactivate viral solutions, a protocol was missing to inactivate crude infected cell lysates, which heavily absorb light. In this work, we develop and validate a UV inactivation protocol for SARS-CoV-2, HSV-1, and HCMV-infected cells. A fluence of 10,000 mJ/cm2 with intermittent mixing was sufficient to completely inactivate infected cells, as demonstrated by the absence of viral replication even after three sequential passages of cells inoculated with the treated material. The herein described protocol should serve as a reference for inactivating cells infected with these or similar viruses and allow for the analysis of protein quaternary structure from bona fide infected cells.
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Affiliation(s)
- Timothy K Soh
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Susanne Pfefferle
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
- Virology and Hygiene, Institute for Medical Microbiology, University Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Stephanie Wurr
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
- DZIF German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Ronald von Possel
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
- Department of Tropical Medicine and Infectious Diseases, Center for Internal Medicine, University of Rostock, Rostock, Germany
| | - Lisa Oestereich
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
- DZIF German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Toni Rieger
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology, Hamburg, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Department of Health Sciences and Biomedicine, School of Life Sciences, University of Siegen, Germany
| | - Maria Rosenthal
- Centre for Structural Systems Biology, Hamburg, Germany
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
| | - Jens B Bosse
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Leibniz Institute of Virology (LIV), Hamburg, Germany
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8
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Creutznacher R, Maass T, Veselkova B, Ssebyatika G, Krey T, Empting M, Tautz N, Frank M, Kölbel K, Uetrecht C, Peters T. NMR Experiments Provide Insights into Ligand-Binding to the SARS-CoV-2 Spike Protein Receptor-Binding Domain. J Am Chem Soc 2022; 144:13060-13065. [PMID: 35830336 DOI: 10.1021/jacs.2c05603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used chemical shift perturbation (CSP) and saturation transfer difference (STD) NMR experiments to identify and characterize the binding of selected ligands to the receptor-binding domain (RBD) of the spike glycoprotein (S-protein) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We also subjected full-length S-protein to STD NMR experiments, allowing correlations with RBD-based results. CSPs reveal the binding sites for heparin and fondaparinux, and affinities were measured using CSP titrations. We then show that α-2,3-sialyllactose binds to the S-protein but not to the RBD. Finally, combined CSP and STD NMR experiments show that lifitegrast, a compound used for the treatment of dry eye, binds to the linoleic acid (LA) binding pocket with a dissociation constant in the μM range. This is an interesting finding, as lifitegrast lends itself well as a blueprint for medicinal chemistry, eventually furnishing novel entry inhibitors targeting the highly conserved LA binding site.
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Affiliation(s)
- Robert Creutznacher
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thorben Maass
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Barbora Veselkova
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - George Ssebyatika
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thomas Krey
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Antiviral & Antivirulence Drugs (AVID), Campus E8.1, 66123 Saarbrücken, Germany
| | - Norbert Tautz
- Center of Structural and Cell Biology in Medicine, Institute of Virology and Cell Biology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Martin Frank
- Biognos AB, Generatorsgatan 1, P.O. Box 8963, SE-402 74 Göteborg, Sweden
| | - Knut Kölbel
- CSSB Center for Structural Systems Biology, Leibniz Institute of Virology (LIV) & Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- CSSB Center for Structural Systems Biology, Leibniz Institute of Virology (LIV) & Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607 Hamburg, Germany.,School of Life Sciences, University of Siegen, 57076 Siegen, Germany
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
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9
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Creutznacher R, Maass T, Dülfer J, Feldmann C, Hartmann V, Lane MS, Knickmann J, Westermann LT, Thiede L, Smith TJ, Uetrecht C, Mallagaray A, Waudby CA, Taube S, Peters T. Distinct dissociation rates of murine and human norovirus P-domain dimers suggest a role of dimer stability in virus-host interactions. Commun Biol 2022; 5:563. [PMID: 35680964 PMCID: PMC9184547 DOI: 10.1038/s42003-022-03497-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/19/2022] [Indexed: 11/29/2022] Open
Abstract
Norovirus capsids are icosahedral particles composed of 90 dimers of the major capsid protein VP1. The C-terminus of the VP1 proteins forms a protruding (P)-domain, mediating receptor attachment, and providing a target for neutralizing antibodies. NMR and native mass spectrometry directly detect P-domain monomers in solution for murine (MNV) but not for human norovirus (HuNoV). We report that the binding of glycochenodeoxycholic acid (GCDCA) stabilizes MNV-1 P-domain dimers (P-dimers) and induces long-range NMR chemical shift perturbations (CSPs) within loops involved in antibody and receptor binding, likely reflecting corresponding conformational changes. Global line shape analysis of monomer and dimer cross-peaks in concentration-dependent methyl TROSY NMR spectra yields a dissociation rate constant koff of about 1 s−1 for MNV-1 P-dimers. For structurally closely related HuNoV GII.4 Saga P-dimers a value of about 10−6 s−1 is obtained from ion-exchange chromatography, suggesting essential differences in the role of GCDCA as a cofactor for MNV and HuNoV infection. NMR and native mass spectrometry reveal that the major capsid VP1 protein from murine and human norovirus exhibit distinct behaviors and are differentially regulated by the binding of glycochenodeoxycholic acid.
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10
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Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders AR, Linden N, Karner A, Preiner J, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Piehler J, Lanzerstorfer P, Springer S. Dissociation of β2m from MHC class I Triggers formation of Noncovalent, transient heavy chain dimers. J Cell Sci 2022; 135:274997. [PMID: 35393611 DOI: 10.1242/jcs.259498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
At the plasma membrane of mammalian cells, major histocompatibility complex class I molecules (MHC-I) present antigenic peptides to cytotoxic T cells. Following the loss of the peptide and the light chain beta-2 microglobulin (β2m), the resulting free heavy chains (FHCs) can associate into homotypic complexes in the plasma membrane. Here, we investigate the stoichiometry and dynamics of MHC-I FHCs assemblies by combining a micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single molecule co-tracking. We identify non-covalent MHC-I FHC dimers mediated by the α3 domain as the prevalent species at the plasma membrane, leading a moderate decrease in the diffusion coefficient. MHC-I FHC dimers show increased tendency to cluster into higher order oligomers as concluded from an increased immobile fraction with higher single molecule co-localization. In vitro studies with isolated proteins in conjunction with molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another FHC in a manner similar to the β2m light chain.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Sara Löchte
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Noemi Linden
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.,Centre for Structural Systems Biology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL, Schenefeld, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | | | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
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11
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Maass T, Westermann LT, Creutznacher R, Mallagaray A, Dülfer J, Uetrecht C, Peters T. Assignment of Ala, Ile, Leu proS, Met, and Val proS methyl groups of the protruding domain of murine norovirus capsid protein VP1 using methyl-methyl NOEs, site directed mutagenesis, and pseudocontact shifts. Biomol NMR Assign 2022; 16:97-107. [PMID: 35050443 PMCID: PMC9068638 DOI: 10.1007/s12104-022-10066-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/12/2022] [Indexed: 05/14/2023]
Abstract
The protruding domain (P-domain) of the murine norovirus (MNV) capsid protein VP1 is essential for infection. It mediates receptor binding and attachment of neutralizing antibodies. Protein NMR studies into interactions of the P-domain with ligands will yield insights not easily available from other biophysical techniques and will extend our understanding of MNV attachment to host cells. Such studies require at least partial NMR assignments. Here, we describe the assignment of about 70% of the Ala, Ile, LeuproS, Met, and ValproS methyl groups. An unfavorable distribution of methyl group resonance signals prevents complete assignment based exclusively on 4D HMQC-NOESY-HMQC experiments, yielding assignment of only 55 out of 100 methyl groups. Therefore, we created point mutants and measured pseudo contact shifts, extending and validating assignments based on methyl-methyl NOEs. Of note, the P-domains are present in two different forms caused by an approximate equal distribution of trans- and cis-configured proline residues in position 361.
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Affiliation(s)
- Thorben Maass
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Leon Torben Westermann
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Robert Creutznacher
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Alvaro Mallagaray
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
| | - Jasmin Dülfer
- Leibniz Institute for Experimental Virology (HPI), 20251, Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251, Hamburg, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen & Centre for Structural Systems Biology (CSSB), & Deutsches Elektronensynchrotron (DESY), 22607 Hamburg & European XFEL GmbH, 22869, Schenefeld, Germany
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany.
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12
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Konietzny A, Grendel J, Kadek A, Bucher M, Han Y, Hertrich N, Dekkers DHW, Demmers JAA, Grünewald K, Uetrecht C, Mikhaylova M. Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines. EMBO J 2022; 41:e106523. [PMID: 34935159 PMCID: PMC8844991 DOI: 10.15252/embj.2020106523] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/08/2021] [Accepted: 11/19/2021] [Indexed: 11/21/2022] Open
Abstract
Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in structural and molecular diversity of dendritic spines. Active spines with large calcium ion (Ca2+ ) transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into spines via the actin-based motor myosin V. An increase in synaptic strength correlates with stable anchoring of the ER, followed by the formation of an organelle referred to as the spine apparatus. Here, we show that myosin V binds the Ca2+ sensor caldendrin, a brain-specific homolog of the well-known myosin V interactor calmodulin. While calmodulin is an essential activator of myosin V motor function, we found that caldendrin acts as an inhibitor of processive myosin V movement. In mouse and rat hippocampal neurons, caldendrin regulates spine apparatus localization to a subset of dendritic spines through a myosin V-dependent pathway. We propose that caldendrin transforms myosin into a stationary F-actin tether that enables the localization of ER tubules and formation of the spine apparatus in dendritic spines.
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Affiliation(s)
- Anja Konietzny
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Jasper Grendel
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Alan Kadek
- Leibniz Institute for Experimental Virology (HPI)HamburgGermany
- European XFEL GmbHSchenefeldGermany
| | - Michael Bucher
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Yuhao Han
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
| | - Nathalie Hertrich
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | | | | | - Kay Grünewald
- Leibniz Institute for Experimental Virology (HPI)HamburgGermany
- Centre for Structural Systems BiologyHamburgGermany
- Department of ChemistryUniversity of HamburgHamburgGermany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI)HamburgGermany
- European XFEL GmbHSchenefeldGermany
- Centre for Structural Systems BiologyHamburgGermany
| | - Marina Mikhaylova
- RG OptobiologyInstitute of BiologyHumboldt Universität zu BerlinBerlinGermany
- Guest Group Neuronal Protein TransportCenter for Molecular NeurobiologyZMNHUniversity Medical Center Hamburg‐EppendorfHamburgGermany
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13
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaiza Fernández-García
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Helen M Ginn
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Brandon Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Henry Gieseler
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brenna Norton-Baker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sofiane Saouane
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anna Hänle
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Frank Schlünzen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nadine Werner
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hina Andaleeb
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Najeeb Ullah
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Sven Falke
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Vasundara Srinivasan
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Bruno Alves França
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Martin Schwinzer
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hévila Brognaro
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Cromarte Rogers
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo Melo
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joanna J Zaitseva-Doyle
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gisel E Peña-Murillo
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent Hennicke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | | | - Gleb Bourenkov
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David von Stetten
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Isabel Bento
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Ivars Karpics
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Stephan Niebling
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Günther
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Juliane Boger
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Diana C F Monteiro
- Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | | | - Jan Wollenhaupt
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Christian G Feiler
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eike-Christian Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henning Tidow
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Tobias Beck
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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14
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Springer S, Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders A, Linden N, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Lanzerstorfer P, Piehler J. Dissociation of β2m from cell surface MHC class I triggers formation of noncovalent, transient heavy chain dimers. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.104.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
Major histocompatibility complex class I molecules (MHC I) that lose the antigenic peptide and the light chain beta-2 microglobulin (β2m) to become free heavy chains at the cell surface are known to associate, forming oligomers on the plasma membrane that are insufficiently understood. Here, we investigate the homotypic interaction of MHC I free heavy chains by combining a printed antibody micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single molecule co-tracking in order to elucidate their molecular structure, abundance, and dynamics. We find that MHC I free heavy chain complexes are dimeric, transient, non-covalent, and mediated by the α3 domain. Free heavy chain interaction correlates with a decrease in the diffusion coefficient and an increase in the number of immobile molecules at the cell surface. Molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another free heavy chain in a manner similar to the β2m light chain. We propose distinct functions of the MHC I free heavy chain dimers in signaling and in endocytic sorting.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maria Garcia-Alai
- 5European Molecular Biology Laboratory, Hamburg Outstation, Germany
- 6Centre for Structural Systems Biology, Germany
| | - Charlotte Uetrecht
- 3Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Germany
- 7European XFEL, Germany
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15
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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16
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Dülfer J, Yan H, Brodmerkel MN, Creutznacher R, Mallagaray A, Peters T, Caleman C, Marklund EG, Uetrecht C. Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status. Molecules 2021; 26:molecules26082125. [PMID: 33917179 PMCID: PMC8067865 DOI: 10.3390/molecules26082125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. The structural aspects of glycan binding to fully deamidated GII.4 P dimers have been investigated before. However, considering the high specificity and half-life of N373D under physiological conditions, large fractions of partially deamidated virions with potentially altered dynamics in their P domains are likely to occur. Therefore, we also examined glycan binding to partially deamidated GII.4 Saga and GII.4 MI001 P dimers. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric subpopulation. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a complex role of deamidation in modulating glycan-mediated cell attachment in GII.4 strains.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
| | - Maxim N. Brodmerkel
- Department of Chemistry—BMC, Uppsala University, 75105 Uppsala, Sweden; (M.N.B.); (E.G.M.)
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75105 Uppsala, Sweden;
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Erik G. Marklund
- Department of Chemistry—BMC, Uppsala University, 75105 Uppsala, Sweden; (M.N.B.); (E.G.M.)
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
- European XFEL GmbH, 22869 Schenefeld, Germany
- Correspondence:
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17
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Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. Sci Adv 2021; 7:7/10/eabf1004. [PMID: 33658206 PMCID: PMC7929516 DOI: 10.1126/sciadv.abf1004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/19/2021] [Indexed: 05/02/2023]
Abstract
Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses, with SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing a pandemic in 2020. Coronaviral non-structural proteins (nsps) form the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complexes has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations, SARS-CoV-2 nsp7+8 consists primarily of heterotetramers. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model proposed.
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Affiliation(s)
- Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ganesh Bylapudi
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | - Martin Koehler
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | | | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
- European XFEL GmbH, Schenefeld, Germany
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Krichel B, Bylapudi G, Schmidt C, Blanchet C, Schubert R, Brings L, Koehler M, Zenobi R, Svergun D, Lorenzen K, Madhugiri R, Ziebuhr J, Uetrecht C. Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes. bioRxiv 2020:2020.09.30.320762. [PMID: 33024972 PMCID: PMC7536876 DOI: 10.1101/2020.09.30.320762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coronaviruses infect many different species including humans. The last two decades have seen three zoonotic coronaviruses with SARS-CoV-2 causing a pandemic in 2020. Coronaviral non-structural proteins (nsp) built up the replication-transcription complex (RTC). Nsp7 and nsp8 interact with and regulate the RNA-dependent RNA-polymerase and other enzymes in the RTC. However, the structural plasticity of nsp7+8 complex has been under debate. Here, we present the framework of nsp7+8 complex stoichiometry and topology based on a native mass spectrometry and complementary biophysical techniques of nsp7+8 complexes from seven coronaviruses in the genera Alpha- and Betacoronavirus including SARS-CoV-2. Their complexes cluster into three groups, which systematically form either heterotrimers or heterotetramers or both, exhibiting distinct topologies. Moreover, even at high protein concentrations mainly heterotetramers are observed for SARS-CoV-2 nsp7+8. From these results, the different assembly paths can be pinpointed to specific residues and an assembly model is proposed.
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Affiliation(s)
- Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ganesh Bylapudi
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | - Martin Koehler
- ETH Zurich D-CHAB Lab of Organic Chemistry, Zürich, Switzerland
| | - Renato Zenobi
- ETH Zurich D-CHAB Lab of Organic Chemistry, Zürich, Switzerland
| | - Dmitri Svergun
- EMBL Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | | | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- European XFEL GmbH, Schenefeld, Germany
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20
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Schulz EC, Henderson SR, Illarionov B, Crosskey T, Southall SM, Krichel B, Uetrecht C, Fischer M, Wilmanns M. The crystal structure of mycobacterial epoxide hydrolase A. Sci Rep 2020; 10:16539. [PMID: 33024154 PMCID: PMC7538969 DOI: 10.1038/s41598-020-73452-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/16/2020] [Indexed: 01/08/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the α/β-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH’s have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 Å resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to α/β-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis.
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Affiliation(s)
- Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausee 149, 22761, Hamburg, Germany. .,European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.
| | - Sara R Henderson
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Norwich Medical School, Rosalind Franklin Road, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Thomas Crosskey
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany
| | - Stacey M Southall
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,University of Hamburg Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
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21
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Heidemann J, Kölbel K, Konijnenberg A, Van Dyck J, Garcia-Alai M, Meijers R, Sobott F, Uetrecht C. Further insights from structural mass spectrometry into endocytosis adaptor protein assemblies. Int J Mass Spectrom 2020; 447:116240. [PMID: 33244295 PMCID: PMC7116418 DOI: 10.1016/j.ijms.2019.116240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
As a fundament in many biologically relevant processes, endocytosis in its different guises has been arousing interest for decades and still does so. This is true for the actual transport and its initiation alike. In clathrin-mediated endocytosis, a comparatively well understood endocytic pathway, a set of adaptor proteins bind specific lipids in the plasma membrane, subsequently assemble and thus form a crucial bridge from clathrin to actin for the ongoing process. These adaptor proteins are highly interesting themselves and the subject of this manuscript. Using many of the instruments that are available now in the mass spectrometry toolbox, we added some facets to the picture of how these minimal assemblies may look, how they form, and what influences the structure. Especially, lipids in the adaptor protein complexes result in reduced charging of a normal sized complex due to their specific binding position. The results further support our structural model of a double ring structure with interfacial lipids.
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Affiliation(s)
- Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Knut Kölbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Albert Konijnenberg
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
| | - Jeroen Van Dyck
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Frank Sobott
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
- Astbury Centre for Structural Molecular and Cellular Biology, School of Molecular and Cellular Biology, University of Leeds, LS3 9JT, United Kingdom
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Corresponding author. Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany.
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22
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Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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23
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Bernal I, Römermann J, Flacht L, Lunelli M, Uetrecht C, Kolbe M. Structural analysis of ligand-bound states of the Salmonella type III secretion system ATPase InvC. Protein Sci 2019; 28:1888-1901. [PMID: 31393998 PMCID: PMC6739812 DOI: 10.1002/pro.3704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
Abstract
Translocation of virulence effector proteins through the type III secretion system (T3SS) is essential for the virulence of many medically relevant Gram‐negative bacteria. The T3SS ATPases are conserved components that specifically recognize chaperone–effector complexes and energize effector secretion through the system. It is thought that functional T3SS ATPases assemble into a cylindrical structure maintained by their N‐terminal domains. Using size‐exclusion chromatography coupled to multi‐angle light scattering and native mass spectrometry, we show that in the absence of the N‐terminal oligomerization domain the Salmonella T3SS ATPase InvC can form monomers and dimers in solution. We also present for the first time a 2.05 å resolution crystal structure of InvC lacking the oligomerization domain (InvCΔ79) and map the amino acids suggested for ATPase intersubunit interaction, binding to other T3SS proteins and chaperone–effector recognition. Furthermore, we validate the InvC ATP‐binding site by co‐crystallization of InvCΔ79 with ATPγS (2.65 å) and ADP (2.80 å). Upon ATP‐analogue recognition, these structures reveal remodeling of the ATP‐binding site and conformational changes of two loops located outside of the catalytic site. Both loops face the central pore of the predicted InvC cylinder and are essential for the function of the T3SS ATPase. Our results present a fine functional and structural correlation of InvC and provide further details of the homo‐oligomerization process and ATP‐dependent conformational changes underlying the T3SS ATPase activity. PDB Code(s): 6RAE, 6RAD and 6SDX
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Affiliation(s)
- Ivonne Bernal
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany
| | - Jonas Römermann
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany
| | - Lara Flacht
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany.,Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Michele Lunelli
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany
| | - Michael Kolbe
- Department of Structural Infection Biology, Center for Structural Systems Biology (CSSB), Helmholtz-Center for Infection Research (HZI), Hamburg, Germany.,MIN-Faculty University Hamburg, Hamburg, Germany
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24
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Weiss VU, Pogan R, Zoratto S, Bond KM, Boulanger P, Jarrold MF, Lyktey N, Pahl D, Puffler N, Schelhaas M, Selivanovitch E, Uetrecht C, Allmaier G. Virus-like particle size and molecular weight/mass determination applying gas-phase electrophoresis (native nES GEMMA). Anal Bioanal Chem 2019; 411:5951-5962. [PMID: 31280479 PMCID: PMC6706367 DOI: 10.1007/s00216-019-01998-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 02/04/2023]
Abstract
(Bio-)nanoparticle analysis employing a nano-electrospray gas-phase electrophoretic mobility molecular analyzer (native nES GEMMA) also known as nES differential mobility analyzer (nES DMA) is based on surface-dry analyte separation at ambient pressure. Based on electrophoretic principles, single-charged nanoparticles are separated according to their electrophoretic mobility diameter (EMD) corresponding to the particle size for spherical analytes. Subsequently, it is possible to correlate the (bio-)nanoparticle EMDs to their molecular weight (MW) yielding a corresponding fitted curve for an investigated analyte class. Based on such a correlation, (bio-)nanoparticle MW determination via its EMD within one analyte class is possible. Turning our attention to icosahedral, non-enveloped virus-like particles (VLPs), proteinaceous shells, we set up an EMD/MW correlation. We employed native electrospray ionization mass spectrometry (native ESI MS) to obtain MW values of investigated analytes, where possible, after extensive purification. We experienced difficulties in native ESI MS with time-of-flight (ToF) detection to determine MW due to sample inherent characteristics, which was not the case for charge detection (CDMS). nES GEMMA exceeds CDMS in speed of analysis and is likewise less dependent on sample purity and homogeneity. Hence, gas-phase electrophoresis yields calculated MW values in good approximation even when charge resolution was not obtained in native ESI ToF MS. Therefore, both methods-native nES GEMMA-based MW determination via an analyte class inherent EMD/MW correlation and native ESI MS-in the end relate (bio-)nanoparticle MW values. However, they differ significantly in, e.g., ease of instrument operation, sample and analyte handling, or costs of instrumentation. Graphical abstract ![]()
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Affiliation(s)
- Victor U Weiss
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria.
| | - Ronja Pogan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Samuele Zoratto
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Kevin M Bond
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Nicholas Lyktey
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Dominik Pahl
- Institute of Cellular Virology, WWU Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Nicole Puffler
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Mario Schelhaas
- Institute of Cellular Virology, WWU Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
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25
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Uetrecht C, Lorenzen K, Kitel M, Heidemann J, Robinson Spencer JH, Schlüter H, Schulz J. Native mass spectrometry provides sufficient ion flux for XFEL single-particle imaging. J Synchrotron Radiat 2019; 26:653-659. [PMID: 31074428 PMCID: PMC6510201 DOI: 10.1107/s1600577519002686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/21/2019] [Indexed: 05/11/2023]
Abstract
The SPB/SFX instrument at the European XFEL provides unique conditions for single-particle imaging (SPI) experiments due to its high brilliance, nano-focus and unique pulse structure. Promising initial results provided by the international LCLS (Linac Coherent Light Source) SPI initiative highlight the potential of SPI. Current available injection methods generally have high sample consumption and do not provide any options for pulsing, selection or orientation of particles, which poses a problem for data evaluation. Aerosol-injector-based sample delivery is the current method of choice for SPI experiments, although, to a lesser extent, electrospray and electrospinning are used. Single particles scatter only a limited number of photons providing a single orientation for data evaluation, hence large datasets are required from particles in multiple orientations in order to reconstruct a structure. Here, a feasibility study demonstrates that nano-electrospray ionization, usually employed in biomolecular mass spectrometry, provides enough ion flux for SPI experiments. A novel instrument setup at the SPB/SFX instrument is proposed, which has the benefit of extremely low background while delivering mass over charge and conformation-selected ions for SPI.
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Affiliation(s)
- Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
- Correspondence e-mail:
| | | | - Matthäus Kitel
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, Hamburg 20251, Germany
| | - Jesse Huron Robinson Spencer
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
- Institute for Clinical Chemistry, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
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26
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Kesgin-Schaefer S, Heidemann J, Puchert A, Koelbel K, Yorke BA, Huse N, Pearson AR, Uetrecht C, Tidow H. Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway. FEBS J 2019; 286:2329-2340. [PMID: 30817081 DOI: 10.1111/febs.14797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 01/23/2023]
Abstract
Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 Å resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.
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Affiliation(s)
- Stephanie Kesgin-Schaefer
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Anke Puchert
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Knut Koelbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Briony A Yorke
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Nils Huse
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Arwen R Pearson
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Physics, Center for Free-Electron Laser Science, Institute for Nanostructure and Solid State Physics, University of Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL GmbH, Schenefeld, Germany
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
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27
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Zaitsev-Doyle JJ, Puchert A, Pfeifer Y, Yan H, Yorke BA, Müller-Werkmeister HM, Uetrecht C, Rehbein J, Huse N, Pearson AR, Sans M. Synthesis and characterisation of α-carboxynitrobenzyl photocaged l-aspartates for applications in time-resolved structural biology. RSC Adv 2019; 9:8695-8699. [PMID: 35518684 PMCID: PMC9061760 DOI: 10.1039/c9ra00968j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 01/17/2023] Open
Abstract
We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l-aspartates for application in time-resolved structural biology. The resulting compounds were characterised in terms of UV/Vis absorption properties, aqueous solubility and stability, and photocleavage rates (τ = μs to ms) and quantum yields (φ = 0.05 to 0.14). We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l-aspartates for application in time-resolved structural biology.![]()
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Affiliation(s)
- John J. Zaitsev-Doyle
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
| | - Anke Puchert
- Department of Physics and Centre for Hybrid Nanostructures
- University of Hamburg
- 22761 Hamburg
- Germany
| | - Yannik Pfeifer
- University of Potsdam
- Institute of Chemistry, Physical Chemistry
- 14476 Potsdam
- Germany
| | - Hao Yan
- Heinrich Pette Institute
- Leibniz Institute for Experimental Virology
- 20251 Hamburg
- Germany
| | | | | | - Charlotte Uetrecht
- Heinrich Pette Institute
- Leibniz Institute for Experimental Virology
- 20251 Hamburg
- Germany
- European XFEL GmbH
| | - Julia Rehbein
- Fachbereich für Chemie und Pharmazie
- Universität Regensburg
- 93053 Regensburg
- Germany
| | - Nils Huse
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
- Department of Physics and Centre for Hybrid Nanostructures
- University of Hamburg
| | - Arwen R. Pearson
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
| | - Marta Sans
- The Hamburg Center for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics
- 22761 Hamburg
- Germany
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28
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Holm T, Kopicki JD, Busch C, Olschewski S, Rosenthal M, Uetrecht C, Günther S, Reindl S. Biochemical and structural studies reveal differences and commonalities among cap-snatching endonucleases from segmented negative-strand RNA viruses. J Biol Chem 2018; 293:19686-19698. [PMID: 30348898 PMCID: PMC6314124 DOI: 10.1074/jbc.ra118.004373] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/20/2018] [Indexed: 12/22/2022] Open
Abstract
Viruses rely on many host cell processes, including the cellular transcription machinery. Segmented negative-strand RNA viruses (sNSV) in particular cannot synthesize the 5'-cap structure for their mRNA but cleave off cellular caps and use the resulting oligonucleotides as primers for their transcription. This cap-snatching mechanism, involving a viral cap-binding site and RNA endonuclease, is both virus-specific and essential for viral proliferation and therefore represents an attractive drug target. Here, we present biochemical and structural results on the putative cap-snatching endonuclease of Crimean-Congo hemorrhagic fever virus (CCHFV), a highly pathogenic bunyavirus belonging to the Nairoviridae family, and of two additional nairoviruses, Erve virus (EREV) and Nairobi sheep disease virus (NSDV). Our findings are presented in the context of other cap-snatching endonucleases, such as the enzymatically active endonuclease from Rift Valley fever virus (RVFV), from Arenaviridae and Bunyavirales, belonging to the His- and His+ endonucleases, respectively, according to the absence or presence of a metal ion-coordinating histidine in the active site. Mutational and metal-binding experiments revealed the presence of only acidic metal-coordinating residues in the active site of the CCHFV domain and a unique active-site conformation that was intermediate between those of His+ and His- endonucleases. On the basis of small-angle X-ray scattering (SAXS) and homology modeling results, we propose a protein topology for the CCHFV domain that, despite its larger size, has a structure overall similar to those of related endonucleases. These results suggest structural and functional conservation of the cap-snatching mechanism among sNSVs.
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Affiliation(s)
- Tobias Holm
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Janine-Denise Kopicki
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany, and
| | - Carola Busch
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Silke Olschewski
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Maria Rosenthal
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Charlotte Uetrecht
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany, and
- the European XFEL GmbH, 22869 Schenefeld, Germany
| | - Stephan Günther
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Sophia Reindl
- From the Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20359 Hamburg, Germany,
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29
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Bücher KS, Yan H, Creutznacher R, Ruoff K, Mallagaray A, Grafmüller A, Dirks JS, Kilic T, Weickert S, Rubailo A, Drescher M, Schmidt S, Hansman G, Peters T, Uetrecht C, Hartmann L. Fucose-Functionalized Precision Glycomacromolecules Targeting Human Norovirus Capsid Protein. Biomacromolecules 2018; 19:3714-3724. [PMID: 30071731 DOI: 10.1021/acs.biomac.8b00829] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Norovirus infection is the major cause of nonbacterial gastroenteritis in humans and has been the subject of numerous studies investigating the virus's biophysical properties and biochemical function with the aim of deriving novel and highly potent entry inhibitors to prevent infection. Recently, it has been shown that the protruding P domain dimer (P-dimer) of a GII.10 Norovirus strain exhibits two new binding sites for l-fucose in addition to the canonical binding sites. Thus, these sites provide a novel target for the design of multivalent fucose ligands as entry inhibitors of norovirus infections. In this current study, a first generation of multivalent fucose-functionalized glycomacromolecules was synthesized and applied as model structures to investigate the potential targeting of fucose binding sites in human norovirus P-dimer. Following previously established solid phase polymer synthesis, eight precision glycomacromolecules varying in number and position of fucose ligands along an oligo(amidoamine) backbone were obtained and then used in a series of binding studies applying native MS, NMR, and X-ray crystallography. We observed only one fucose per glycomacromolecule binding to one P-dimer resulting in similar binding affinities for all fucose-functionalized glycomacromolecules, which based on our current findings we attribute to the overall size of macromolecular ligands and possibly to steric hindrance.
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Affiliation(s)
- Katharina Susanne Bücher
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Kerstin Ruoff
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Andrea Grafmüller
- Max-Planck-Institute of Colloids and Interfaces , Department of Theory and Bio-Systems , Potsdam , Germany
| | - Jan Sebastian Dirks
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Turgay Kilic
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Sabrina Weickert
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Anna Rubailo
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Malte Drescher
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Stephan Schmidt
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Grant Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.,European XFEL GmbH , Schenefeld , Germany
| | - Laura Hartmann
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
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30
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Pogan R, Dülfer J, Uetrecht C. Norovirus assembly and stability. Curr Opin Virol 2018; 31:59-65. [DOI: 10.1016/j.coviro.2018.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/05/2018] [Accepted: 05/11/2018] [Indexed: 02/06/2023]
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Wegener H, Mallagaray Á, Schöne T, Peters T, Lockhauserbäumer J, Yan H, Uetrecht C, Hansman GS, Taube S. Human norovirus GII.4(MI001) P dimer binds fucosylated and sialylated carbohydrates. Glycobiology 2018; 27:1027-1037. [PMID: 28973640 DOI: 10.1093/glycob/cwx078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
Human noroviruses (HuNoV), members of the family Caliciviridae, are the major cause of acute viral gastroenteritis worldwide. Successful infection is linked to the ability of the protruding (P) domain of the viral capsid to bind histo-blood group antigens (HBGA). Binding to gangliosides plays a major role for many nonhuman calici- and noroviruses. Increasing evidence points to a broader role of sialylated carbohydrates such as gangliosides in norovirus infection. Here, we compare HBGA and ganglioside binding of a GII.4 HuNoV variant (MI001), previously shown to be infectious in a HuNoV mouse model. Saturation transfer difference nuclear magnetic resonance spectroscopy, native mass spectrometry (MS) and surface plasmon resonance spectroscopy were used to characterize binding epitopes, affinities, stoichiometry and dynamics, focusing on 3'-sialyllactose, the GM3 ganglioside saccharide and B antigen. Binding was observed for 3'-sialyllactose and various HBGAs following a multistep binding process. Intrinsic affinities (Kd) of fucose, 3'-sialyllactose and B antigen were determined for the individual binding steps. Stronger affinities were observed for B antigen over 3'-sialyllactose and fucose, which bound in the mM range. Binding stoichiometry was analyzed by native MS showing the presence of four B antigens or two 3'-sialyllactose in the complex. Epitope mapping of 3'-sialyllactose revealed direct interaction of α2,3-linked sialic acid with the P domain. The ability of HuNoV to engage multiple carbohydrates emphasizes the multivalent nature of norovirus glycan-specificity. Our findings reveal direct binding of a GII.4 HuNoV P dimer to α2,3-linked sialic acid and support a broader role of ganglioside binding in norovirus infection.
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Affiliation(s)
- Henrik Wegener
- University of Lübeck, Institute of Virology and Cell Biology,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Álvaro Mallagaray
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Tobias Schöne
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thomas Peters
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Julia Lockhauserbäumer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology,Martinistrasse 52, 20251 Hamburg, Germany
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology,Martinistrasse 52, 20251 Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant S Hansman
- German Cancer Research Center (DKFZ), CHS Foundation at the University of Heidelberg, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Stefan Taube
- University of Lübeck, Institute of Virology and Cell Biology,Ratzeburger Allee 160, 23562 Lübeck, Germany
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Pogan R, Schneider C, Reimer R, Hansman G, Uetrecht C. Norovirus-like VP1 particles exhibit isolate dependent stability profiles. J Phys Condens Matter 2018; 30:064006. [PMID: 29282349 PMCID: PMC7104913 DOI: 10.1088/1361-648x/aaa43b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 05/08/2023]
Abstract
Noroviruses are the main cause of viral gastroenteritis with new variants emerging frequently. There are three norovirus genogroups infecting humans. These genogroups are divided based on the sequence of their major capsid protein, which is able to form virus-like particles (VLPs) when expressed recombinantly. VLPs of the prototypical GI.1 Norwalk virus are known to disassemble into specific capsid protein oligomers upon alkaline treatment. Here, native mass spectrometry and electron microscopy on variants of GI.1 and of GII.17 were performed, revealing differences in terms of stability between these groups. Beyond that, these experiments indicate differences even between variants within a genotype. The capsid stability was monitored in different ammonium acetate solutions varying both in ionic strength and pH. The investigated GI.1 West Chester isolate showed comparable disassembly profiles to the previously studied GI.1 Norwalk virus isolate. However, differences were observed with the West Chester being more sensitive to alkaline pH. In stark contrast to that, capsids of the variant belonging to the currently prevalent genogroup GII were stable in all tested conditions. Both variants formed smaller capsid particles already at neutral pH. Certain amino acid substitutions in the S domain of West Chester relative to the Norwalk virus potentially result in the formation of these T = 1 capsids.
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Affiliation(s)
- Ronja Pogan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Carola Schneider
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Rudolph Reimer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Grant Hansman
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- European XFEL, Schenefeld, Germany
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33
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Garcia-Alai MM, Heidemann J, Skruzny M, Gieras A, Mertens HDT, Svergun DI, Kaksonen M, Uetrecht C, Meijers R. Epsin and Sla2 form assemblies through phospholipid interfaces. Nat Commun 2018; 9:328. [PMID: 29362354 PMCID: PMC5780493 DOI: 10.1038/s41467-017-02443-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/30/2017] [Indexed: 01/22/2023] Open
Abstract
In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions with specific lipids on the plasma membrane. However, the precise mechanism of adapter protein assembly at the cell membrane is still unknown. Here, we show that the membrane–proximal domains ENTH of epsin and ANTH of Sla2 form complexes through phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how ENTH and ANTH domains form assemblies by sharing PIP2 molecules. Furthermore, crystal structures of epsin Ent2 ENTH domain from S. cerevisiae in complex with PIP2 and Sla2 ANTH domain from C. thermophilum illustrate how allosteric phospholipid binding occurs. A comparison with human ENTH and ANTH domains reveal only the human ENTH domain can form a stable hexameric core in presence of PIP2, which could explain functional differences between fungal and human epsins. We propose a general phospholipid-driven multifaceted assembly mechanism tolerating different adapter protein compositions to induce endocytosis. Adapter proteins assist clathrin coated pit assembly. Here, the authors combine native mass spectrometry, crystallography and SAXS measurements and show that the membrane–proximal domains of the adaptor proteins epsin and Sla2 form complexes mediated through phosphatidylinositol 4,5-bisphosphate interfaces leading to assembly formation.
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Affiliation(s)
- Maria M Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Michal Skruzny
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Anna Gieras
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.,University Medical Center Hamburg - Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marko Kaksonen
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany. .,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
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Hantke MF, Hasse D, Ekeberg T, John K, Svenda M, Loh D, Martin AV, Timneanu N, Larsson DSD, van der Schot G, Carlsson GH, Ingelman M, Andreasson J, Westphal D, Iwan B, Uetrecht C, Bielecki J, Liang M, Stellato F, DePonte DP, Bari S, Hartmann R, Kimmel N, Kirian RA, Seibert MM, Mühlig K, Schorb S, Ferguson K, Bostedt C, Carron S, Bozek JD, Rolles D, Rudenko A, Foucar L, Epp SW, Chapman HN, Barty A, Andersson I, Hajdu J, Maia FRNC. A data set from flash X-ray imaging of carboxysomes. Sci Data 2016; 3:160061. [PMID: 27479842 DOI: 10.1038/nphoton.2014.270] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/01/2016] [Indexed: 05/26/2023] Open
Abstract
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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Affiliation(s)
- Max F Hantke
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Dirk Hasse
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Katja John
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Nicusor Timneanu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, Uppsala SE- 751 20, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gijs van der Schot
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gunilla H Carlsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Margareta Ingelman
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Jakob Andreasson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague 18221, Czech Republic
| | - Daniel Westphal
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Bianca Iwan
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Charlotte Uetrecht
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Johan Bielecki
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sadia Bari
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, Hamburg 22607, Germany
| | | | - Nils Kimmel
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, Garching 85741, Germany
| | - Richard A Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - M Marvin Seibert
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Kerstin Mühlig
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Sebastian Schorb
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Artem Rudenko
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Inger Andersson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
| | - Filipe R N C Maia
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U. Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 2016; 13:973-987. [PMID: 27471797 DOI: 10.1080/15476286.2016.1212151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA:protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R.
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Affiliation(s)
- Kristina Szameit
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Katharina Berg
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Sven Kruspe
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Erica Valentini
- b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | - Eileen Magbanua
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
| | - Marcel Kwiatkowski
- c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany
| | | | - Boris Krichel
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Kira Schamoni
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Charlotte Uetrecht
- e Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.,f European XFEL GmbH , Hamburg , Germany
| | - Dmitri I Svergun
- b European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | - Hartmut Schlüter
- c University Medical Center Hamburg-Eppendorf , Department of Clinical Chemistry , Hamburg , Germany
| | - Martin Zacharias
- d Physics Department , Technical University Munich , Garching , Germany
| | - Ulrich Hahn
- a Institute for Biochemistry and Molecular Biology, Department of Chemistry , University of Hamburg , Hamburg , Germany
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36
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Snijder J, Kononova O, Barbu IM, Uetrecht C, Rurup WF, Burnley RJ, Koay MST, Cornelissen JJLM, Roos WH, Barsegov V, Wuite GJL, Heck AJR. Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin. Biomacromolecules 2016; 17:2522-9. [DOI: 10.1021/acs.biomac.6b00469] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Natuur-
en Sterrenkunde and LaserLab, Vrije Universiteit, De Boelelaan 1081, Amsterdam, The Netherlands
| | - Olga Kononova
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
- Moscow Institute
of Physics
and Technology, Moscow Region, Russia 141700
| | - Ioana M. Barbu
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Charlotte Uetrecht
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - W. Frederik Rurup
- Department
of Biomolecular Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Rebecca J. Burnley
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Melissa S. T. Koay
- Department
of Biomolecular Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Department
of Biomolecular Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wouter H. Roos
- Natuur-
en Sterrenkunde and LaserLab, Vrije Universiteit, De Boelelaan 1081, Amsterdam, The Netherlands
- Moleculaire
Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Valeri Barsegov
- Department
of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
- Moscow Institute
of Physics
and Technology, Moscow Region, Russia 141700
| | - Gijs J. L. Wuite
- Natuur-
en Sterrenkunde and LaserLab, Vrije Universiteit, De Boelelaan 1081, Amsterdam, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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37
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Dunne M, Leicht S, Krichel B, Mertens HDT, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R. Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product. J Biol Chem 2016; 291:4882-93. [PMID: 26683375 PMCID: PMC4777826 DOI: 10.1074/jbc.m115.671172] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/16/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages produce endolysins, which lyse the bacterial host cell to release newly produced virions. The timing of lysis is regulated and is thought to involve the activation of a molecular switch. We present a crystal structure of the activated endolysin CTP1L that targets Clostridium tyrobutyricum, consisting of a complex between the full-length protein and an N-terminally truncated C-terminal cell wall binding domain (CBD). The truncated CBD is produced through an internal translation start site within the endolysin gene. Mutants affecting the internal translation site change the oligomeric state of the endolysin and reduce lytic activity. The activity can be modulated by reconstitution of the full-length endolysin-CBD complex with free CBD. The same oligomerization mechanism applies to the CD27L endolysin that targets Clostridium difficile and the CS74L endolysin that targets Clostridium sporogenes. When the CTP1L endolysin gene is introduced into the commensal bacterium Lactococcus lactis, the truncated CBD is also produced, showing that the alternative start codon can be used in other bacterial species. The identification of a translational switch affecting oligomerization presented here has implications for the design of effective endolysins for the treatment of bacterial infections.
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Affiliation(s)
- Matthew Dunne
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Leicht
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Boris Krichel
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Haydyn D T Mertens
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Thompson
- the Synchrotron Soleil, L'Orme des Merisiers, BP 48, Saint Aubin, 91192 Gif sur Yvette, France
| | - Jeroen Krijgsveld
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Dmitri I Svergun
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Natalia Gómez-Torres
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Sonia Garde
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Charlotte Uetrecht
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany, the European XFEL GmbH, Notkestrasse 85, 22607 Hamburg, Germany, and
| | - Arjan Narbad
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Melinda J Mayer
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Rob Meijers
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany,
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Mallagaray A, Lockhauserbäumer J, Hansman G, Uetrecht C, Peters T. Attachment of norovirus to histo blood group antigens: a cooperative multistep process. Angew Chem Int Ed Engl 2015; 54:12014-9. [PMID: 26329854 DOI: 10.1002/anie.201505672] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/11/2022]
Abstract
Human noroviruses recognize histo blood group antigens (HBGAs) as cellular attachment factors. Recently, it has been discovered that norovirus infection can be significantly enhanced by HBGA binding. Yet the attachment process and how it promotes host-cell entry is only poorly understood. The binding of a norovirus protruding (P) domain of a predominant GII.4 Saga strain to HBGAs at atomic resolution was studied. So far, independent and equivalent multiple binding sites were held responsible for attachment. Using NMR experiments we show that norovirus-HBGA binding is a cooperative multi-step process, and native mass spectrometry reveals four instead of two HBGA binding sites per P-dimer. An accompanying crystallographic study has disclosed four instead of two L-fucose binding sites per P-dimer of a related GII.10 strain1 further supporting our findings. We have uncovered a novel paradigm for norovirus-HBGA recognition that will inspire further studies into norovirus-host interactions.
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Affiliation(s)
- Alvaro Mallagaray
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck (Germany)
| | - Julia Lockhauserbäumer
- Dynamics of Viral Structures, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg (Germany).,Sample Environment Group, European XFEL GmbH, Notkestrasse 85, 22607 Hamburg (Germany)
| | - Grant Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, 69120 Heidelberg (Germany).,Department of Infectious Diseases and Virology, University of Heidelberg, 69120 Heidelberg (Germany)
| | - Charlotte Uetrecht
- Dynamics of Viral Structures, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg (Germany).,Sample Environment Group, European XFEL GmbH, Notkestrasse 85, 22607 Hamburg (Germany)
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck (Germany).
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von der Heyde A, Lockhauserbäumer J, Uetrecht C, Elleuche S. A hydrolase-based reporter system to uncover the protein splicing performance of an archaeal intein. Appl Microbiol Biotechnol 2015; 99:7613-24. [PMID: 26026939 DOI: 10.1007/s00253-015-6689-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/06/2015] [Accepted: 05/17/2015] [Indexed: 11/30/2022]
Abstract
Extein amino acid residues around the splice site junctions affect the functionality of inteins. To identify an optimal sequence context for efficient protein splicing of an intein from the thermoacidophilic archaeon Picrophilus torridus, single extein amino acid residues at the splice site junctions were continuously deleted. The construction of a set of different truncated extein variants showed that this intein tolerates multiple amino acid variations near the excision sites and exhibits full activity when -1 and +1 extein amino acid residues are conserved in an artificial GST-intein-HIS fusion construct. Moreover, splicing of the recombinant intein took place at temperatures between 4 and 42 °C with high efficiency, when produced in Escherichia coli. Therefore, structural model predictions were used to identify optimal insertion sites for the intein to be embedded within a hemicellulase from the psychrophilic bacterium Pseudoalteromonas arctica. The P. torridus intein inserted before amino acid residue Thr75 of the reporter enzyme retained catalytic activity. Moreover, the catalytic activity of the xylan-degrading hydrolase could be easily monitored in routine plate assays and in liquid test measurements at room temperature when produced in recombinant form in E. coli. This tool allows the indirect detection of the intein's catalytic activity to be used in screenings.
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Affiliation(s)
- Amélie von der Heyde
- Hamburg University of Technology (TUHH), Institute of Technical Microbiology, Kasernenstr. 12, 21073, Hamburg, Germany
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40
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Skruzny M, Desfosses A, Prinz S, Dodonova S, Gieras A, Uetrecht C, Jakobi A, Abella M, Hagen W, Schulz J, Meijers R, Rybin V, Briggs J, Sachse C, Kaksonen M. An Organized Co-assembly of Clathrin Adaptors Is Essential for Endocytosis. Dev Cell 2015; 33:150-62. [DOI: 10.1016/j.devcel.2015.02.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/29/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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41
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Uetrecht C, Barbu IM, Shoemaker GK, van Duijn E, Heck AJR. Erratum: Interrogating viral capsid assembly with ion mobility–mass spectrometry. Nat Chem 2014. [DOI: 10.1038/nchem.2025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Tseng YH, Uetrecht C, Yang SC, Barendregt A, Heck AJR, Peng WP. Game-Theory-Based Search Engine to Automate the Mass Assignment in Complex Native Electrospray Mass Spectra. Anal Chem 2013; 85:11275-83. [DOI: 10.1021/ac401940e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yao-Hsin Tseng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Charlotte Uetrecht
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Sample
Environment Group, European XFEL GmbH, Notkestraße 85, 22607 Hamburg, Germany
| | - Shih-Chieh Yang
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Arjan Barendregt
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Wen-Ping Peng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
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Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, Agirre J, Guérin DMA, Wuite GJL, Heck AJR, Roos WH. Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 2013; 5:502-9. [DOI: 10.1038/nchem.1627] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
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44
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Broeker NK, Gohlke U, Müller JJ, Uetrecht C, Heinemann U, Seckler R, Barbirz S. Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity. Glycobiology 2012; 23:59-68. [PMID: 22923442 DOI: 10.1093/glycob/cws126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.
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Baclayon M, Shoemaker GK, Uetrecht C, Crawford SE, Estes MK, Prasad BVV, Heck AJR, Wuite GJL, Roos WH. Prestress strengthens the shell of Norwalk virus nanoparticles. Nano Lett 2011; 11:4865-9. [PMID: 21967663 PMCID: PMC4059365 DOI: 10.1021/nl202699r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We investigated the influence of the protruding domain of Norwalk virus-like particles (NVLP) on its overall structural and mechanical stability. Deletion of the protruding domain yields smooth mutant particles and our AFM nanoindentation measurements show a surprisingly altered indentation response of these particles. Notably, the brittle behavior of the NVLP as compared to the plastic behavior of the mutant reveals that the protruding domain drastically changes the capsid's material properties. We conclude that the protruding domain introduces prestress, thereby increasing the stiffness of the NVLP and effectively stabilizing the viral nanoparticles. Our results exemplify the variety of methods that nature has explored to improve the mechanical properties of viral capsids, which in turn provides new insights for developing rationally designed, self-assembled nanodevices.
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Affiliation(s)
- Marian Baclayon
- Natuur- en Sterrenkunde and LaserLab, VU University, 1081 HV Amsterdam, The Netherlands
| | - Glen K. Shoemaker
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gijs J. L. Wuite
- Natuur- en Sterrenkunde and LaserLab, VU University, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- Natuur- en Sterrenkunde and LaserLab, VU University, 1081 HV Amsterdam, The Netherlands
- Corresponding Author Tel: +31 20 59 87838.
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Abstract
Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.
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Affiliation(s)
- Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
- Present address: Molecular Biophysics, Uppsala University, Uppsala (Sweden)
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
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47
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Uetrecht C, Heck AJR. Moderne biomolekulare Massenspektrometrie und ihre Bedeutung für die Erforschung der Struktur, der Dynamik und des Aufbaus von Viren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Brasch M, de la Escosura A, Ma Y, Uetrecht C, Heck AJR, Torres T, Cornelissen JJLM. Encapsulation of phthalocyanine supramolecular stacks into virus-like particles. J Am Chem Soc 2011; 133:6878-81. [PMID: 21506537 DOI: 10.1021/ja110752u] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report herein the encapsulation of a water-soluble phthalocyanine (Pc) into virus-like particles (VLPs) of two different sizes, depending on the conditions. At neutral pH, the cooperative encapsulation/templated assembly of the particles induces the formation of Pc stacks instead of Pc dimers, due to an increased confinement concentration. The Pc-containing VLPs may potentially be used as photosensitizer/vehicle systems for biomedical applications such as photodynamic therapy.
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Affiliation(s)
- Melanie Brasch
- Laboratory for Biomolecular Nanotechnology, MESA+ Institute, University of Twente, P.O. Box 207, 7500 AE Enschede, The Netherlands
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Affiliation(s)
- Yao-Hsin Tseng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Netherlands Proteomics Centre
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Netherlands Proteomics Centre
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
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50
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Roos WH, Gibbons MM, Arkhipov A, Uetrecht C, Watts NR, Wingfield PT, Steven AC, Heck AJR, Schulten K, Klug WS, Wuite GJL. Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophys J 2010; 99:1175-81. [PMID: 20713001 DOI: 10.1016/j.bpj.2010.05.033] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/07/2010] [Accepted: 05/20/2010] [Indexed: 01/01/2023] Open
Abstract
The current rapid growth in the use of nanosized particles is fueled in part by our increased understanding of their physical properties and ability to manipulate them, which is essential for achieving optimal functionality. Here we report detailed quantitative measurements of the mechanical response of nanosized protein shells (viral capsids) to large-scale physical deformations and compare them with theoretical descriptions from continuum elastic modeling and molecular dynamics (MD). Specifically, we used nanoindentation by atomic force microscopy to investigate the complex elastic behavior of Hepatitis B virus capsids. These capsids are hollow, approximately 30 nm in diameter, and conform to icosahedral (5-3-2) symmetry. First we show that their indentation behavior, which is symmetry-axis-dependent, cannot be reproduced by a simple model based on Föppl-von Kármán thin-shell elasticity with the fivefold vertices acting as prestressed disclinations. However, we can properly describe the measured nonlinear elastic and orientation-dependent force response with a three-dimensional, topographically detailed, finite-element model. Next, we show that coarse-grained MD simulations also yield good agreement with our nanoindentation measurements, even without any fitting of force-field parameters in the MD model. This study demonstrates that the material properties of viral nanoparticles can be correctly described by both modeling approaches. At the same time, we show that even for large deformations, it suffices to approximate the mechanical behavior of nanosized viral shells with a continuum approach, and ignore specific molecular interactions. This experimental validation of continuum elastic theory provides an example of a situation in which rules of macroscopic physics can apply to nanoscale molecular assemblies.
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Affiliation(s)
- W H Roos
- Natuur- en Sterrenkunde, Vrije Universiteit, Amsterdam, The Netherlands
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