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Reinke PYA, Schubert R, Oberthür D, Galchenkova M, Rahmani Mashhour A, Günther S, Chretien A, Round A, Seychell BC, Norton-Baker B, Kim C, Schmidt C, Koua FHM, Tolstikova A, Ewert W, Peña Murillo GE, Mills G, Kirkwood H, Brognaro H, Han H, Koliyadu J, Schulz J, Bielecki J, Lieske J, Maracke J, Knoska J, Lorenzen K, Brings L, Sikorski M, Kloos M, Vakili M, Vagovic P, Middendorf P, de Wijn R, Bean R, Letrun R, Han S, Falke S, Geng T, Sato T, Srinivasan V, Kim Y, Yefanov OM, Gelisio L, Beck T, Doré AS, Mancuso AP, Betzel C, Bajt S, Redecke L, Chapman HN, Meents A, Turk D, Hinrichs W, Lane TJ. SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds. Nat Commun 2024; 15:3827. [PMID: 38714735 PMCID: PMC11076503 DOI: 10.1038/s41467-024-48109-3] [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: 09/15/2023] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.
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Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Anaïs Chretien
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Brandon Charles Seychell
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Brenna Norton-Baker
- Max Plank Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92697-2025, USA
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Faisal H M Koua
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Gisel Esperanza Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mohammad Vakili
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Seonghyun Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- La Trobe Institute for Molecular Science, Department of Chemistry and Physics, La Trobe University, Melbourne, VIC, 3086, Australia
- Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE, Didcot, UK
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Universität zu Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dušan Turk
- Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins Jamova 39, 1000, Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK.
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2
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Kardoost A, Schönherr R, Deiter C, Redecke L, Lorenzen K, Schulz J, de Diego I. Convolutional neural network approach for the automated identification of in cellulo crystals. J Appl Crystallogr 2024; 57:266-275. [PMID: 38596734 PMCID: PMC11001417 DOI: 10.1107/s1600576724000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
In cellulo crystallization is a rare event in nature. Recent advances that have made use of heterologous overexpression can promote the intracellular formation of protein crystals, but new tools are required to detect and characterize these targets in the complex cell environment. The present work makes use of Mask R-CNN, a convolutional neural network (CNN)-based instance segmentation method, for the identification of either single or multi-shaped crystals growing in living insect cells, using conventional bright field images. The algorithm can be rapidly adapted to recognize different targets, with the aim of extracting relevant information to support a semi-automated screening pipeline, in order to aid the development of the intracellular protein crystallization approach.
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Affiliation(s)
- Amirhossein Kardoost
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Schleswig-Holstein, Germany
| | - Carsten Deiter
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Schleswig-Holstein, Germany
- Deutsches Elektronen-Synchrotron DESY, Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kristina Lorenzen
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Joachim Schulz
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
| | - Iñaki de Diego
- Sample Environment and Characterization Group, European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Schleswig-Holstein, Germany
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3
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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4
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Williamson LJ, Galchenkova M, Best HL, Bean RJ, Munke A, Awel S, Pena G, Knoska J, Schubert R, Dörner K, Park HW, Bideshi DK, Henkel A, Kremling V, Klopprogge B, Lloyd-Evans E, Young MT, Valerio J, Kloos M, Sikorski M, Mills G, Bielecki J, Kirkwood H, Kim C, de Wijn R, Lorenzen K, Xavier PL, Rahmani Mashhour A, Gelisio L, Yefanov O, Mancuso AP, Federici BA, Chapman HN, Crickmore N, Rizkallah PJ, Berry C, Oberthür D. Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX. Proc Natl Acad Sci U S A 2023; 120:e2203241120. [PMID: 38015839 PMCID: PMC10710082 DOI: 10.1073/pnas.2203241120] [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: 02/24/2022] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
The Lysinibacillus sphaericus proteins Tpp49Aa1 and Cry48Aa1 can together act as a toxin toward the mosquito Culex quinquefasciatus and have potential use in biocontrol. Given that proteins with sequence homology to the individual proteins can have activity alone against other insect species, the structure of Tpp49Aa1 was solved in order to understand this protein more fully and inform the design of improved biopesticides. Tpp49Aa1 is naturally expressed as a crystalline inclusion within the host bacterium, and MHz serial femtosecond crystallography using the novel nanofocus option at an X-ray free electron laser allowed rapid and high-quality data collection to determine the structure of Tpp49Aa1 at 1.62 Å resolution. This revealed the packing of Tpp49Aa1 within these natural nanocrystals as a homodimer with a large intermolecular interface. Complementary experiments conducted at varied pH also enabled investigation of the early structural events leading up to the dissolution of natural Tpp49Aa1 crystals-a crucial step in its mechanism of action. To better understand the cooperation between the two proteins, assays were performed on a range of different mosquito cell lines using both individual proteins and mixtures of the two. Finally, bioassays demonstrated Tpp49Aa1/Cry48Aa1 susceptibility of Anopheles stephensi, Aedes albopictus, and Culex tarsalis larvae-substantially increasing the potential use of this binary toxin in mosquito control.
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Affiliation(s)
| | - Marina Galchenkova
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Hannah L. Best
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | | | - Anna Munke
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Salah Awel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Gisel Pena
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Juraj Knoska
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | | | | | - Hyun-Woo Park
- Department of Biological Sciences, California Baptist University, Riverside, CA92504
| | - Dennis K. Bideshi
- Department of Biological Sciences, California Baptist University, Riverside, CA92504
| | - Alessandra Henkel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Viviane Kremling
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Emyr Lloyd-Evans
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Mark T. Young
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | | | - Marco Kloos
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | - Grant Mills
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | | | - Chan Kim
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | | | - Paul Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, 22761Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Luca Gelisio
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, 22869Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Brian A. Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Henry N. Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, 22761Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761Hamburg, Germany
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Falmer, BrightonBN1 9QG, United Kingdom
| | | | - Colin Berry
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Dominik Oberthür
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
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5
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Vakili M, Han H, Schmidt C, Wrona A, Kloos M, de Diego I, Dörner K, Geng T, Kim C, Koua FHM, Melo DVM, Rappas M, Round A, Round E, Sikorski M, Valerio J, Zhou T, Lorenzen K, Schulz J. Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography. J Appl Crystallogr 2023; 56:1038-1045. [PMID: 37555221 PMCID: PMC10405586 DOI: 10.1107/s1600576723004405] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/21/2023] [Indexed: 08/10/2023] Open
Abstract
Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.
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Affiliation(s)
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Iñaki de Diego
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
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6
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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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7
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Wang M, Thuenauer R, Schubert R, Gevorgyan S, Lorenzen K, Brognaro H, Betzel C. Formation kinetics and physicochemical properties of mesoscopic Alpha-Synuclein assemblies modulated by sodium chloride and a distinct pulsed electric field. Soft Matter 2023; 19:1363-1372. [PMID: 36723049 DOI: 10.1039/d2sm01615j] [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] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Alpha-Synuclein (ASN), a presynaptic protein, has been widely reported to form amyloid-rich hydrogel clusters through liquid-liquid phase separation (LLPS) and liquid-to-solid transition. However, in-depth investigations about the parameters that influence the assembling kinetics, structures, and physicochemical properties of intermediate ASN assemblies are still missing. Therefore, we monitored for the first time the assembling and ordering kinetics of ASN by polarized/depolarized light scattering (DLS/DDLS) under the effect of ionic strength and a pulsed electric field (EF), followed by characterizing the resultant ASN assemblies applying thermostability assays, fluorescence/autofluorescence assays, and TEM. The underlying molecular mechanism was discussed based on experimental evidence. Results showed that in the presence of 150-250 mM NaCl, monomeric ASN is highly soluble in a temperature range of 20-70 °C and could form dissoluble liquid dense clusters via LLPS in crowded environments, while the ionic strength of 50 mM NaCl could trigger conformational changes and attractive diffusion interactions of ASN monomers towards the formation of mesoscopic assemblies with ordered internal structures and high thermostabilities. We discovered that pulsed EFs and ionic strength can modulate effectively the thermostability and autofluorescence effect of mesoscopic ASN assemblies by tuning the molecular interaction and arrangement. Remarkably, a specie of thermostable ASN assemblies showing a maximum autofluorescence emission at approx. 700 nm was synthesized applying 250 mM NaCl and the distinct pulsed EF, which could be attributed to the increase of β-sheet structures and hydrogen-bond networks within ASN assemblies. In summary, the presented data provide novel insights for modulating the growth kinetics, structures, and physicochemical properties of bio-macromolecular mesoscopic assemblies.
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Affiliation(s)
- Mengying Wang
- University of Hamburg, Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, Notkestrasse 85, c/o DESY, Building 22a, 22607, Hamburg, Germany.
| | - Roland Thuenauer
- Technology Platform Light Microscopy, University of Hamburg, Mittelweg 177, 20148, Hamburg, Germany
- Center for Structural Systems Biology (CSSB), Notkestrasse 85, c/o DESY, Building 15, 22607, Hamburg, Germany
- Technology Platform Microscopy and Image Analysis (TP MIA), Leibniz Institute of Virology (LIV), Martinistrasse 52, 20251, Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Susanna Gevorgyan
- University of Hamburg, Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, Notkestrasse 85, c/o DESY, Building 22a, 22607, Hamburg, Germany.
| | | | - Hévila Brognaro
- University of Hamburg, Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, Notkestrasse 85, c/o DESY, Building 22a, 22607, Hamburg, Germany.
| | - Christian Betzel
- University of Hamburg, Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, Notkestrasse 85, c/o DESY, Building 22a, 22607, Hamburg, Germany.
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8
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Schmidt C, Dörner K, Schulz J, Lorenzen K. A metal-binding GFP-derivative reused as novel standard sample for serial crystallography approaches at FELs. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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9
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Han H, Brings L, Chretien A, De Diego I, Round E, Schmidt C, Schubert R, Schulz J, Lorenzen K. Protein crystallization and characterization for serial femtosecond crystallography at the European XFEL. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322089926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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10
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Gevorgyan S, Schubert R, Falke S, Lorenzen K, Trchounian K, Betzel C. Structural characterization and antibacterial activity of silver nanoparticles synthesized using a low-molecular-weight Royal Jelly extract. Sci Rep 2022; 12:14077. [PMID: 35982108 PMCID: PMC9388513 DOI: 10.1038/s41598-022-17929-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 04/18/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years silver nanoparticles (Ag NPs) gained increased and widespread applications in various fields of industry, technology, and medicine. This study describes the green synthesis of silver nanoparticles (Ag NPs) applying a low-molecular-weight fraction (LMF) of Royal Jelly, the nanoparticle characterization, and particularly their antibacterial activity. The optical properties of NPs, characterized by UV–Vis absorption spectroscopy, showed a peak at ~ 430 nm. The hydrodynamic radius and concentration were determined by complementary dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). The particle morphology was investigated using transmission electron microscopy (TEM), and the crystallinity of the silver was confirmed by X-ray diffraction (XRD). The antibacterial activities were evaluated utilizing Gram-negative and Gram-positive bacteria and colony counting assays. The growth inhibition curve method was applied to obtain information about the corresponding minimum inhibitory concentrations (MIC) and the minimum bactericidal concentrations (MBC) required. Obtained results showed that (i) the sizes of Ag NPs are increasing within the increase of silver ion precursor concentration, (ii) DLS, in agreement with NTA, showed that most particles have dimensions in the range of 50–100 nm; (iii) E. coli was more susceptible to all Ag NP samples compared to B. subtilis.
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Affiliation(s)
- Susanna Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia.,The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Notkestrasse 85, Build. 22A, 22607, Hamburg, Germany
| | - Robin Schubert
- European X-Ray Free Electron Laser GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Kristina Lorenzen
- European X-Ray Free Electron Laser GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Christian Betzel
- The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany. .,Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Notkestrasse 85, Build. 22A, 22607, Hamburg, Germany.
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11
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Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 2022; 5:805. [PMID: 35953531 PMCID: PMC9366811 DOI: 10.1038/s42003-022-03737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/15/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
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Affiliation(s)
- Vasundara Srinivasan
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Prince R Prabhu
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Thomas J Lane
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Helen Ginn
- Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Huijong Han
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sven Falke
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadine Werner
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Hina Andaleeb
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Najeeb Ullah
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Bruno Alves Franca
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Mengying Wang
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Angélica Luana C Barra
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Markus Perbandt
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Martin Schwinzer
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robin Schubert
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Erika Donizette Candido
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Danielle Bruna Leal Oliveira
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sofiane Saouane
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Johanna Hakanpää
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee114, 22525, Hamburg, Germany
| | - Maria Garcia Alai
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000, Ljubljana, Slovenia.,Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKEBIP), Jamova 39, 1 000, Ljubljana, Slovenia
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Alke Meents
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. .,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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12
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Ewert W, Günther S, Miglioli F, Falke S, Reinke PYA, Niebling S, Günther C, Han H, Srinivasan V, Brognaro H, Lieske J, Lorenzen K, Garcia-Alai MM, Betzel C, Carcelli M, Hinrichs W, Rogolino D, Meents A. Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Front Chem 2022; 10:832431. [PMID: 35480391 PMCID: PMC9038201 DOI: 10.3389/fchem.2022.832431] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
The papain-like protease (PLpro) of SARS-CoV-2 is essential for viral propagation and, additionally, dysregulation of the host innate immune system. Using a library of 40 potential metal-chelating compounds we performed an X-ray crystallographic screening against PLpro. As outcome we identified six compounds binding to the target protein. Here we describe the interaction of one hydrazone (H1) and five thiosemicarbazone (T1-T5) compounds with the two distinct natural substrate binding sites of PLpro for ubiquitin and ISG15. H1 binds to a polar groove at the S1 binding site by forming several hydrogen bonds with PLpro. T1-T5 bind into a deep pocket close to the polyubiquitin and ISG15 binding site S2. Their interactions are mainly mediated by multiple hydrogen bonds and further hydrophobic interactions. In particular compound H1 interferes with natural substrate binding by sterical hindrance and induces conformational changes in protein residues involved in substrate binding, while compounds T1-T5 could have a more indirect effect. Fluorescence based enzyme activity assay and complementary thermal stability analysis reveal only weak inhibition properties in the high micromolar range thereby indicating the need for compound optimization. Nevertheless, the unique binding properties involving strong hydrogen bonding and the various options for structural optimization make the compounds ideal lead structures. In combination with the inexpensive and undemanding synthesis, the reported hydrazone and thiosemicarbazones represent an attractive scaffold for further structure-based development of novel PLpro inhibitors by interrupting protein-protein interactions at the S1 and S2 site.
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Affiliation(s)
- Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Francesca Miglioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Patrick Y. A. Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, DESY, Hamburg, Germany
| | - Christian Günther
- European Molecular Biology Laboratory Hamburg, DESY, Hamburg, Germany
| | | | - Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | | | | | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, University Hamburg, Hamburg, Germany
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Winfried Hinrichs
- Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Dominga Rogolino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
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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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Gevorgyan S, Schubert R, Yeranosyan M, Gabrielyan L, Trchounian A, Lorenzen K, Trchounian K. Antibacterial activity of royal jelly-mediated green synthesized silver nanoparticles. AMB Express 2021; 11:51. [PMID: 33796941 PMCID: PMC8017077 DOI: 10.1186/s13568-021-01213-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
The application of green synthesis in nanotechnology is growing day by day. It's a safe and eco-friendly alternative to conventional methods. The current research aimed to study raw royal jelly's potential in the green synthesis of silver nanoparticles and their antibacterial activity. Royal jelly served as a reducing and oxidizing agent in the green synthesis technology of colloidal silver nanoparticles. The UV-Vis maximum absorption at ~ 430 nm and fluorescence emission peaks at ~ 487 nm confirmed the presence of Ag NPs. Morphology and structural properties of Ag NPs and the effect of ultrasound studies revealed: (i) the formation of polydispersed and spherical particles with different sizes; (ii) size reduction and homogeneity increase by ultrasound treatment. Antibacterial activity of different concentrations of green synthesized Ag NPs has been assessed on Gram-negative S. typhimurium and Gram-positive S. aureus, revealing higher sensitivity on Gram-negative bacteria.
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Affiliation(s)
- Susanna Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Robin Schubert
- European X-ray Free Electron Laser GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mkrtich Yeranosyan
- Institute of Chemical Physics, NAS RA, Paruir Sevak 5/2, 0014, Yerevan, Armenia
- Military Aviation University Named After Marshal A. Khamperyants, Arshakunyats 89, 0007, Yerevan, Armenia
| | - Lilit Gabrielyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Kristina Lorenzen
- European X-ray Free Electron Laser GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia.
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15
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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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16
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Han H, Round E, Schubert R, Gül Y, Makroczyová J, Meza D, Heuser P, Aepfelbacher M, Barák I, Betzel C, Fromme P, Kursula I, Nissen P, Tereschenko E, Schulz J, Uetrecht C, Ulicný J, Wilmanns M, Hajdu J, Lamzin VS, Lorenzen K. The XBI BioLab for life science experiments at the European XFEL. J Appl Crystallogr 2021; 54:7-21. [PMID: 33833637 PMCID: PMC7941304 DOI: 10.1107/s1600576720013989] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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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. 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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18
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Wang M, Falke S, Schubert R, Lorenzen K, Cheng QD, Exner C, Brognaro H, Mudogo CN, Betzel C. Pulsed electric fields induce modulation of protein liquid-liquid phase separation. Soft Matter 2020; 16:8547-8553. [PMID: 32909579 DOI: 10.1039/d0sm01478h] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The time-resolved dynamic assembly and the structures of protein liquid dense clusters (LDCs) were analyzed under pulsed electric fields (EFs) applying complementary polarized and depolarized dynamic light scattering (DLS/DDLS), optical microscopy, and transmission electron microscopy (TEM). We discovered that pulsed EFs substantially affected overall morphologies and spatial distributions of protein LDCs and microcrystals, and affected the phase diagrams of LDC formation, including enabling protein solutions to overcome the diffusive flux energy barrier to phase separate. Data obtained from DLS/DDLS and TEM showed that LDCs appeared as precursors of protein crystal nuclei, followed by the formation of ordered structures within LDCs applying a pulsed EF. Experimental results of circular dichroism spectroscopy provided evidence that the protein secondary structure content is changing under EFs, which may consequently modulate protein-protein interactions, and the morphology, dimensions, and internal structure of LDCs. Data and results obtained unveil options to modulate the phase diagram of crystallization, and physical morphologies of protein LDCs and microcrystals by irradiating sample suspensions with pulsed EFs.
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Affiliation(s)
- Mengying Wang
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Sven Falke
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Qing-di Cheng
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Christian Exner
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Célestin Nzanzu Mudogo
- Department of Basic Sciences, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
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19
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Schubert R, Han H, Meza D, Round E, Schulz J, Lorenzen K. Biological user support at the European XFEL. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319088120] [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: 11/10/2022] Open
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20
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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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21
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Xiong S, Lorenzen K, Couzens AL, Templeton CM, Rajendran D, Mao DYL, Juang YC, Chiovitti D, Kurinov I, Guettler S, Gingras AC, Sicheri F. Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Structure 2018; 26:1101-1115.e6. [PMID: 29983373 PMCID: PMC6087429 DOI: 10.1016/j.str.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 12/19/2017] [Revised: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 11/27/2022]
Abstract
The human NDR family kinases control diverse aspects of cell growth, and are regulated through phosphorylation and association with scaffolds such as MOB1. Here, we report the crystal structure of the human NDR1 kinase domain in its non-phosphorylated state, revealing a fully resolved atypically long activation segment that blocks substrate binding and stabilizes a non-productive position of helix αC. Consistent with an auto-inhibitory function, mutations within the activation segment of NDR1 dramatically enhance in vitro kinase activity. Interestingly, NDR1 catalytic activity is further potentiated by MOB1 binding, suggesting that regulation through modulation of the activation segment and by MOB1 binding are mechanistically distinct. Lastly, deleting the auto-inhibitory activation segment of NDR1 causes a marked increase in the association with upstream Hippo pathway components and the Furry scaffold. These findings provide a point of departure for future efforts to explore the cellular functions and the mechanism of NDR1.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cloning, Molecular
- Crystallography, X-Ray
- Epithelial Cells/cytology
- Epithelial Cells/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Hepatocyte Growth Factor/chemistry
- Hepatocyte Growth Factor/genetics
- Hepatocyte Growth Factor/metabolism
- Humans
- Kinetics
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Serine-Threonine Kinases/chemistry
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine-Threonine Kinase 3
- Signal Transduction
- Substrate Specificity
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Affiliation(s)
- Shawn Xiong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Catherine M Templeton
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Daniel Y L Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Yu-Chi Juang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - David Chiovitti
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Advanced Photon Source, Bldg. 436E, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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22
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Choinski K, Rocca JP, Torabi J, Lorenzen K, Yongue C, Herbert ME, Block T, Chokechanachaisakul A, Kamal L, Kinkhabwala M, Graham JA. The Pancreas Can Take the Cold: Lower Waitlist Times Through Importation. Transplant Proc 2017; 49:2305-2309. [PMID: 29198666 DOI: 10.1016/j.transproceed.2017.10.006] [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: 10/18/2022]
Abstract
BACKGROUND Our center has used a strategy of pancreas importation owing to long regional waitlist times. Here we assess the clinical outcomes and financial considerations of this strategy. METHODS This was a retrospective observational cohort study of patients who received a pancreas transplant at Montefiore Medical Center (MMC) from 2014 to 2017 (n = 28). Clinical parameters, including hemoglobin A1c and complications, were analyzed. The cohort was compared with United Network for Organ Sharing (UNOS) Region 9 with the use of the UNOS/Organ Procurement and Transplantation Network database. Cost analysis of length of stay (LOS), standard acquisition (SAC) fees, and transportation was performed with the use of internal financial data. RESULTS Pancreas importation resulted in significantly shorter simultaneous pancreas kidney transplant waitlist times compared with Region 9: 518 days vs 1001 days (P = .038). In addition, postoperative complications and 1-year HbA1c did not differ between groups: local 6.30% vs import 6.17% (P = .87). Patients receiving local pancreata stayed an average of 9.2 days compared with 11 days for the import group (P = .36). As such, pancreas importation was associated with higher mean charges ($445,968) compared with local pancreas recipients ($325,470). CONCLUSIONS Long waitlist times in Region 9 have encouraged our center's adoption of pancreas importation to address the needs of our patient population. This practice has resulted in a reduction of waitlist times by an average of 483 days. Understandably, centers have long been wary of importation owing to perceived risk in clinical outcomes. In our single-center experience, we have demonstrated equivalent postoperative glucose control and graft survival. Importantly, there does appear to be increased costs associated with importation, which are mainly driven by LOS. Curiously, importation from regions with lower SAC fees has the potential to offset costs related to transportation expenses. Notwithstanding these findings, pancreas importation does have the potential to lessen the financial societal burden through reduction in waitlist times.
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Affiliation(s)
- K Choinski
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - J P Rocca
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - J Torabi
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - K Lorenzen
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York
| | - C Yongue
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - M E Herbert
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York
| | - T Block
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York
| | - A Chokechanachaisakul
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - L Kamal
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - M Kinkhabwala
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York
| | - J A Graham
- Montefiore-Einstein Center for Transplantation, Montefiore Medical Center, Bronx, New York; Albert Einstein College of Medicine, Bronx, New York.
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23
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Zeqiraj E, Tian L, Piggott CA, Pillon MC, Duffy NM, Ceccarelli DF, Keszei AFA, Lorenzen K, Kurinov I, Orlicky S, Gish GD, Heck AJR, Guarné A, Greenberg RA, Sicheri F. Higher-Order Assembly of BRCC36-KIAA0157 Is Required for DUB Activity and Biological Function. Mol Cell 2015; 59:970-83. [PMID: 26344097 PMCID: PMC4579573 DOI: 10.1016/j.molcel.2015.07.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 11/30/2014] [Revised: 06/01/2015] [Accepted: 07/27/2015] [Indexed: 12/11/2022]
Abstract
BRCC36 is a Zn2+ dependent deubiquitinating enzyme (DUB) that hydrolyzes lysine-63-linked ubiquitin chains as part of distinct macromolecular complexes that participate in either interferon signaling or DNA-damage recognition. The MPN+ domain protein BRCC36 associates with pseudo-DUB MPN− proteins KIAA0157 or Abraxas, which are essential for BRCC36 enzymatic activity. To understand the basis for BRCC36 regulation, we have solved the structure of an active BRCC36-KIAA0157 heterodimer and an inactive BRCC36 homodimer. Structural and functional characterizations show how BRCC36 is switched to an active conformation by contacts with KIAA0157. Higher order association of BRCC36 and KIAA0157 into a dimer of heterodimers (super dimers) was required for DUB activity and interaction with targeting proteins SHMT2 and RAP80. These data provide the first explanation of how an inactive pseudo DUB allosterically activates a cognate DUB partner, and implicates super dimerization as a new regulatory mechanism underlying BRCC36 DUB activity, subcellular localization, and biological function.
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Affiliation(s)
- Elton Zeqiraj
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Lei Tian
- Departments of Cancer Biology and Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
| | - Christopher A Piggott
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Monica C Pillon
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Nicole M Duffy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Alexander F A Keszei
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada; Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, IL 60439, USA
| | - Stephen Orlicky
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Gerald D Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Roger A Greenberg
- Departments of Cancer Biology and Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, ON M5G 1X5, Canada; Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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24
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Camp EV, Lorenzen K, Ahrens RNM, Allen MS. Stock enhancement to address multiple recreational fisheries objectives: an integrated model applied to red drum Sciaenops ocellatus in Florida. J Fish Biol 2014; 85:1868-1889. [PMID: 25469950 DOI: 10.1111/jfb.12548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/23/2014] [Indexed: 06/04/2023]
Abstract
An integrated socioecological model was developed to evaluate the potential for stock enhancement with hatchery fishes to achieve socioeconomic and conservation objectives in recreational fisheries. As a case study, this model was applied to the red drum Sciaenops ocellatus recreational fishery in the Tampa Bay estuary, Florida, U.S.A. The results suggest that stocking of juvenile fish larger than the size at which the strongest density dependence in mortality occurs can help increase angler satisfaction and total fishing effort (socioeconomic objectives) but are likely to result in decreases to the abundance of wild fishes (a conservation objective). Stocking of small juveniles that are susceptible to density-dependent mortality after release does not achieve socioeconomic objectives (or only at excessive cost) but still leads to a reduction of wild fish abundance. The intensity and type of socioeconomic gains depended on assumptions of dynamic angler-effort responses and importance of catch-related satisfaction, with greatest gains possible if aggregate effort is responsive to increases in abundance and satisfaction that are greatly related to catch rates. These results emphasize the view of stock enhancement, not as a panacea but rather as a management tool with inherent costs that is best applied to recreational fisheries under certain conditions.
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Affiliation(s)
- E V Camp
- School of Forest Resources and Conservation, Fisheries and Aquatic Sciences Program, University of Florida, 7922 NW 71st Street, Gainesville, FL 32605, U.S.A
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25
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Garlock TM, Monk CT, Lorenzen K, Matthews MD, St Mary CM. Effects of hatchery rearing on Florida largemouth bass Micropterus floridanus resource allocation and performance under semi-natural conditions. J Fish Biol 2014; 85:1830-1842. [PMID: 25257181 DOI: 10.1111/jfb.12514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/24/2014] [Indexed: 06/03/2023]
Abstract
This study examined the growth, activity, metabolism and post-release survival of three groups of Florida largemouth bass Micropterus floridanus: wild-caught fish, hatchery fish reared according to standard practice (hatchery standard) and hatchery fish reared under reduced and unpredictable food provisioning (hatchery manipulated). Hatchery-standard fish differed from wild-caught fish in all measured variables, including survival in semi-natural ponds. Hatchery-standard and hatchery-manipulated fish showed higher activity levels, faster growth and lower standard metabolic rates than wild-caught fish in the hatchery. Fish reared under the manipulated feeding regime showed increased metabolic rates and increased post-release growth, similar to wild-caught fish. Their activity levels and post-release survival, however, remained similar to those of hatchery-standard fish. Activity was negatively correlated with post-release survival and failure of the feed manipulation to reduce activity may have contributed to its failure to improve post-release survival. Activity and post-release survival may be influenced by characteristics of the rearing environment other than the feeding regime, such as stock density or water flow rates.
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Affiliation(s)
- T M Garlock
- Fisheries and Aquatic Sciences Program, School of Forest Resources and Conservation, University of Florida, P. O. Box 110410, Gainesville, FL 32611, U.S.A
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Lorenzen K. Understanding and managing enhancements: why fisheries scientists should care. J Fish Biol 2014; 85:1807-29. [PMID: 25469948 DOI: 10.1111/jfb.12573] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/03/2014] [Indexed: 05/07/2023]
Abstract
Fisheries enhancements are a set of management approaches involving the use of aquaculture technologies to enhance or restore fisheries in natural ecosystems. Enhancements are widely used in inland and coastal fisheries, but have received limited attention from fisheries scientists. This paper sets out 10 reasons why fisheries scientists should care about understanding and managing enhancements. (1) Enhancements happen, driven mostly by resource users and managers rather than scientists. (2) Enhancements create complex fisheries systems that encompass and integrate everything fisheries stakeholders can practically manage. (3) Enhancements emerge in fisheries where the scope for technical and governance control is high, and they synergistically reinforce both. (4) Successful enhancements expand management options and achievable outcomes. (5) Many enhancements fail or do ecological harm but persist regardless. (6) Effective science engagement is crucial to developing beneficial enhancements and preventing harmful ones. (7) Good scientific guidance is available to aid development or reform of enhancements but is not widely applied. (8) Enhancement research advances, integrates and unifies the fisheries sciences. (9) Enhancements provide unique opportunities for learning about natural fish populations and fisheries. (10) Needs, opportunities and incentives for enhancements are bound to increase.
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Affiliation(s)
- K Lorenzen
- Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, 7922 NW 71st St., Gainesville, FL, 32653, U.S.A
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Edwards CTT, Hillary RM, Levontin P, Blanchard JL, Lorenzen K. Fisheries Assessment and Management: A Synthesis of Common Approaches with Special Reference to Deepwater and Data-Poor Stocks. ACTA ACUST UNITED AC 2012. [DOI: 10.1080/10641262.2012.683210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Blattner C, Jennebach S, Herzog F, Mayer A, Cheung AC, Witte G, Lorenzen K, Hopfner KP, Heck AJ, Aebersold R, Cramer P. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev 2011; 25:2093-105. [PMID: 21940764 PMCID: PMC3197207 DOI: 10.1101/gad.17363311] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [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: 07/04/2011] [Accepted: 08/24/2011] [Indexed: 01/24/2023]
Abstract
Cell growth is regulated during RNA polymerase (Pol) I transcription initiation by the conserved factor Rrn3/TIF-IA in yeast/humans. Here we provide a structure-function analysis of Rrn3 based on a combination of structural biology with in vivo and in vitro functional assays. The Rrn3 crystal structure reveals a unique HEAT repeat fold and a surface serine patch. Phosphorylation of this patch represses human Pol I transcription, and a phospho-mimetic patch mutation prevents Rrn3 binding to Pol I in vitro and reduces cell growth and Pol I gene occupancy in vivo. Cross-linking indicates that Rrn3 binds Pol I between its subcomplexes, AC40/19 and A14/43, which faces the serine patch. The corresponding region of Pol II binds the Mediator head that cooperates with transcription factor (TF) IIB. Consistent with this, the Rrn3-binding factor Rrn7 is predicted to be a TFIIB homolog. This reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth, and indicates a general architecture of eukaryotic transcription initiation complexes.
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Affiliation(s)
- Claudia Blattner
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Stefan Jennebach
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Franz Herzog
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland
| | - Andreas Mayer
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Alan C.M. Cheung
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Gregor Witte
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Kristina Lorenzen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | - Patrick Cramer
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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Abstract
Native mass spectrometry (native MS) gives information about the composition, topological arrangements, dynamics, and structural properties of protein complexes. The mass range is principally unlimited and highly dynamic, allowing the detection of small subunits and large complexes within the same measurement. The amount of protein needed for an analysis is, compared to most other structural biology methods, very low. This unit provides an introduction to native MS. It starts with an explanation of the basic method and details on how to measure intact proteins and protein complexes, and continues with the study of dynamics and complex stability in the gas phase. The final section discusses the most recent extension to the native MS field, ion mobility, which allows the direct assessment of the structural properties of the complexes of interest.
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Geiger SR, Lorenzen K, Schreieck A, Hanecker P, Kostrewa D, Heck AJ, Cramer P. RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex. Mol Cell 2010; 39:583-94. [DOI: 10.1016/j.molcel.2010.07.028] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/15/2010] [Accepted: 06/29/2010] [Indexed: 01/09/2023]
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Koschubs T, Lorenzen K, Baumli S, Sandström S, Heck AJR, Cramer P. Preparation and topology of the Mediator middle module. Nucleic Acids Res 2010; 38:3186-95. [PMID: 20123732 PMCID: PMC2879511 DOI: 10.1093/nar/gkq029] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 11/18/2022] Open
Abstract
Mediator is the central coactivator complex required for regulated transcription by RNA polymerase (Pol) II. Mediator consists of 25 subunits arranged in the head, middle, tail and kinase modules. Structural and functional studies of Mediator are limited by the availability of protocols for the preparation of recombinant modules. Here, we describe protocols for obtaining pure endogenous and recombinant complete Mediator middle module from Saccharomyces cerevisiae that consists of seven subunits: Med1, 4, 7, 9, 10, 21 and 31. Native mass spectrometry reveals that all subunits are present in equimolar stoichiometry. Ion-mobility mass spectrometry, limited proteolysis, light scattering and small-angle X-ray scattering all indicate a high degree of intrinsic flexibility and an elongated shape of the middle module. Protein-protein interaction assays combined with previously published data suggest that the Med7 and Med4 subunits serve as a binding platform to form the three heterodimeric subcomplexes, Med7N/21, Med7C/31 and Med4/9. The subunits, Med1 and Med10, which bridge to the Mediator tail module, bind to both Med7 and Med4.
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Affiliation(s)
- Tobias Koschubs
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Kristina Lorenzen
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sonja Baumli
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Saana Sandström
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Albert J. R. Heck
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick Cramer
- Gene Center Munich and Center for Integrated Protein Science Munich (CIPSM), Department of Biochemistry, Ludwig-Maximilians-Universität (LMU) München, Feodor-Lynen-Str. 25, 81377 Munich, Germany, Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, Netherlands and Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Wu H, Sun L, Blombach F, Brouns SJJ, Snijders APL, Lorenzen K, van den Heuvel RHH, Heck AJR, Fu S, Li X, Zhang XC, Rao Z, van der Oost J. Structure of the ribosome associating GTPase HflX. Proteins 2010; 78:705-13. [PMID: 19787775 DOI: 10.1002/prot.22599] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The HflX-family is a widely distributed but poorly characterized family of translation factor-related guanosine triphosphatases (GTPases) that interact with the large ribosomal subunit. This study describes the crystal structure of HflX from Sulfolobus solfataricus solved to 2.0-A resolution in apo- and GDP-bound forms. The enzyme displays a two-domain architecture with a novel "HflX domain" at the N-terminus, and a classical G-domain at the C-terminus. The HflX domain is composed of a four-stranded parallel beta-sheet flanked by two alpha-helices on either side, and an anti-parallel coiled coil of two long alpha-helices that lead to the G-domain. The cleft between the two domains accommodates the nucleotide binding site as well as the switch II region, which mediates interactions between the two domains. Conformational changes of the switch regions are therefore anticipated to reposition the HflX-domain upon GTP-binding. Slow GTPase activity has been confirmed, with an HflX domain deletion mutant exhibiting a 24-fold enhanced turnover rate, suggesting a regulatory role for the HflX domain. The conserved positively charged surface patches of the HflX-domain may mediate interaction with the large ribosomal subunit. The present study provides a structural basis to uncover the functional role of this GTPases family whose function is largely unknown.
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Affiliation(s)
- Hao Wu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR. Ion mobility mass spectrometry of proteins and proteinassemblies. Chem Soc Rev 2010; 39:1633-55. [DOI: 10.1039/b914002f] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Rosenberg N, Bech P, Lorenzen K, Mellergård M, Rasmussen S, Rafaelsen OJ, Rosenberg R. Personality Disorder in Panic Disorder Patients. ACTA ACUST UNITED AC 2009. [DOI: 10.3109/08039488609096508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Mohammed S, Lorenzen K, Kerkhoven R, Breukelen BV, Vannini A, Cramer P, Heck AJR. Multiplexed Proteomics Mapping of Yeast RNA Polymerase II and III Allows Near-Complete Sequence Coverage and Reveals Several Novel Phosphorylation Sites. Anal Chem 2008; 80:3584-92. [DOI: 10.1021/ac7024283] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Kristina Lorenzen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Robert Kerkhoven
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Alessandro Vannini
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Patrick Cramer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Gene Center Munich and Center for Integrated Protein Science CiPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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Lorenzen K, Olia AS, Uetrecht C, Cingolani G, Heck AJR. Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly. J Mol Biol 2008; 379:385-96. [PMID: 18448123 DOI: 10.1016/j.jmb.2008.02.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [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: 10/29/2007] [Revised: 02/08/2008] [Accepted: 02/11/2008] [Indexed: 11/16/2022]
Abstract
Large oligomeric portal assemblies have a central role in the life-cycles of bacteriophages and herpesviruses. The stoichiometry of in vitro assembled portal proteins has been a subject of debate for several years. The intrinsic polymorphic oligomerization of ectopically expressed portal proteins makes it possible to form rings of diverse stoichiometry (e.g., 11-mer, 12-mer, 13-mer, etc.) in solution. In this study, we have investigated the stoichiometry of the in vitro-assembled portal protein of bacteriophage P22 and characterized its association with the tail factor gp4. Using native mass spectrometry, we show for the first time that the reconstituted portal protein (assembled in vitro using a modified purification and assembly protocol) is exclusively dodecameric. Under the conditions used here, 12 copies of tail factor gp4 bind to the portal ring, in a cooperative fashion, to form a 12:12 complex of 1.050 MDa. We applied tandem mass spectrometry to the complete assembly and found an unusual dimeric dissociation pattern of gp4, suggesting a dimeric sub-organization of gp4 when assembled with the portal ring. Furthermore, native and ion mobility mass spectrometry reveal a major conformational change in the portal upon binding of gp4. We propose that the gp4-induced conformational change in the portal ring initiates a cascade of events assisting in the stabilization of newly filled P22 particles, which marks the end of phage morphogenesis.
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Affiliation(s)
- Kristina Lorenzen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Lorenzen K, Vannini A, Cramer P, Heck AJR. Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture. Structure 2007; 15:1237-45. [PMID: 17937913 DOI: 10.1016/j.str.2007.07.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 07/09/2007] [Accepted: 07/31/2007] [Indexed: 12/01/2022]
Abstract
RNA polymerases (Pol) II and III synthesize eukaryotic mRNAs and tRNAs, respectively. The crystal structure of the 12 subunit Pol II is known, but only limited structural information is available for the 17 subunit Pol III. Using mass spectrometry (MS), we correlated masses of Pol II complexes with the Pol II structure. Analysis of Pol III showed that the complete enzyme contains a single copy of each subunit and revealed a 15 subunit form lacking the Pol III-specific subcomplex C53/37. DMSO treatment dissociated the C17/25 heterodimer of Pol III, confirming a peripheral location as its counterpart in Pol II. Tandem MS revealed the Pol III-specific subunits C82 and C34 dissociating as a heterodimer. C11 was retained, arguing against a stable trimeric subcomplex, C53/37/11. These data suggest that Pol III consists of a 10 subunit Pol II-like core; the peripheral heterodimers C17/25, C53/37, and C82/34; and subunit C31, which bridges between C82/34, C17/25, and the core.
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Affiliation(s)
- Kristina Lorenzen
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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van den Heuvel RHH, van Duijn E, Mazon H, Synowsky SA, Lorenzen K, Versluis C, Brouns SJJ, Langridge D, van der Oost J, Hoyes J, Heck AJR. Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry. Anal Chem 2007; 78:7473-83. [PMID: 17073415 DOI: 10.1021/ac061039a] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We modified and optimized a first generation quadrupole time-of-flight (Q-TOF) 1 to perform tandem mass spectrometry on macromolecular protein complexes. The modified instrument allows isolation and subsequent dissociation of high-mass protein complexes through collisions with argon molecules. The modifications of the Q-TOF 1 include the introduction of (1) a flow-restricting sleeve around the first hexapole ion bridge, (2) a low-frequency ion-selecting quadrupole, (3) a high-pressure hexapole collision cell, (4) high-transmission grids in the multicomponent ion lenses, and (5) a low repetition rate pusher. Using these modifications, we demonstrate the experimental isolation of ions up to 12 800 mass-to-charge units and detection of product ions up to 38 150 Da, enabling the investigation of the gas-phase stability, protein complex topology, and quaternary structure of protein complexes. Some of the data reveal a so-far unprecedented new mechanism in gas-phase dissociation of protein oligomers whereby a tetramer complex dissociates into two dimers. These data add to the current debate whether gas-phase structures of protein complexes do retain some of the structural features of the corresponding species in solution. The presented low-cost modifications on a Q-TOF 1 instrument are of interest to everyone working in the fields of macromolecular mass spectrometry and more generic structural biology.
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Affiliation(s)
- Robert H H van den Heuvel
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Reisen WK, Eldridge BE, Scott TW, Gutierrez A, Takahashi R, Lorenzen K, DeBenedictis J, Boyce K, Swartzell R. Comparison of dry ice-baited centers for disease control and New Jersey light traps for measuring mosquito abundance in California. J Am Mosq Control Assoc 2002; 18:158-163. [PMID: 12322936] [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] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mosquito catch in New Jersy light traps (NJLTs) has been declining in recent years, compromising the sensitivity of the California mosquito monitoring program. Centers for Disease Control traps (CDCTs) operated without light and augmented with dry ice have been considered for replacement or augmentation. To provide information on comparative sensitivity and ability to measure abundance over time and space, catch of mosquitoes in NJLTs was compared to catch in CDCTs operated concurrently at 8-10 sites within the Coachella Valley, Kern, San Joaquin County, and Sacramento-Yolo Mosquito and Vector Control Districts. The CDCTs always collected more female mosquitoes than did NJLTs; however, differences in sensitivity varied markedly over time and space precluding the calculation of a universal conversion factor. Regressions of the catch of female Culex tarsalis in CDCTs as a function of catch in NJLTs within districts indicated that the slopes varied markedly, again precluding the derivation of a universal function. Therefore, we recommend that mosquito surveillance programs replace or supplement NJLTs with systematically operated CDCTs to enhance sampling sensitivity for females of most mosquito species. However, both trap types should be operated concurrently at several sites within each district to derive regression functions to convert historical relative abundance data from NJLTs to equivalent counts in CDCTs for retrospective analyses.
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Affiliation(s)
- W K Reisen
- Center for Vectorborne Diseases, School of Veterinary Medicine, University of California, Davis 95616, USA
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Brüning T, Abel J, Koch B, Lorenzen K, Harth V, Donat S, Sachinidis A, Vetter H, Bolt HM, Ko Y. Real-time PCR-analysis of the cytochrome P450 1B1 codon 432-polymorphism. Arch Toxicol 1999; 73:427-30. [PMID: 10650913 DOI: 10.1007/s002040050631] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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: 11/30/2022]
Abstract
The aim of the present study was to develop and validate a rapid assay for genotyping of CYP1B1 codon 432-polymorphism. The described method is a single tube assay and combines both rapid-cycle polymerase chain reaction (PCR) with real-time monitoring by amplification and generation of the melting profiles of an allele-specific fluorescent probe. With this method 300 samples were analysed from healthy, unrelated Germans. Genotype frequency determined for the mutated allele CYP1B1*2 was 0.40. The results show that genotyping of CYP1B1 codon 432-polymorphism with a real-time fluorescence PCR method is a rapid and reliable assay for the analysis of large numbers of samples.
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Affiliation(s)
- T Brüning
- Institut für Arbeitsphysiologie an der Universität Dortmund, Germany
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42
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Abstract
The three protoilludanes radulone A (1), radulone B (2) and radudiol (3), the illudalane radulactone (4) and the illudane radulol (5) were isolated from the extracts of the culture fluids of the basidiomycete Radulomyces confluens. The structures of the five new compounds were determined by spectroscopic techniques. Radulone A (1) is a potent inhibitor of human and bovine platelet aggregation stimulated by different agonists, inhibiting preferentially the aggregation of human platelets induced by ADP with an IC50 value of 2 microM. In addition 1 exhibits cytotoxic and antimicrobial activities. The other four compounds exhibited weak antimicrobial and cytotoxic activity.
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Affiliation(s)
- K Fabian
- Lehrbereich Biotechnologie der Universität, Kaiserslautern, Germany
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43
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Abstract
Among the sources of bioactive metabolites, less intensively investigated organisms like the higher fungi seem to hold an excellent promise for new structures with interesting biological activities. In the last decades interesting compounds of different biogenetic origin with antibacterial, antifungal, phytotoxic, nematocidal, cytostatic, antiviral, and other pharmacological activities were isolated from basidiomycetes. In the following review we will concentrate on metabolites isolated from submerged cultures.
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Affiliation(s)
- K. Lorenzen
- Department of Biotechnology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - T. Anke
- Department of Biotechnology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
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44
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Eldridge BF, Gimnig JE, Lorenzen K, Nixon KC, Reeves WC. The distribution of species of the Aedes increpitus complex in the western United States. J Am Mosq Control Assoc 1998; 14:173-177. [PMID: 9673918] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Maps of the California and Oregon distribution of members of the Aedes increpitus complex (Aedes clivis Lanzaro and Eldridge, Aedes increpitus Dyar, and Aedes washinoi Lanzaro and Eldridge) are presented that are based on collections reported by Lanzaro and Eldridge (1992) and new collections from various sites, many in the Central Valley of California. Analysis of individually reared specimens by polyacrylamide gel electrophoresis and conventional morphological methods confirmed the diagnostic value of isozymes for these species and of larval head hairs for distinguishing Ae. clivis from other members of the complex. Other larval characters and pupal hairs did not appear to have diagnostic value. An additional site was discovered where apparent hybrids between Ae. washinoi and Ae. increpitus occur, and a single possible hybrid between Ae. washinoi and Ae. clivis was found at a site where these species had previously been reported to occur sympatrically.
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Affiliation(s)
- B F Eldridge
- Department of Entomology, University of California, Davis 95616, USA
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45
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Abstract
11-Hydroxy-4-methyl-2,4,6-dodecatrienoic acid was isolated from fermentations of the Mucor species, strain KL 94-92 aq. The compound exhibits cytotoxic activity and the structural elucidation, as well as the biological properties of the new compound, are described.
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46
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Lorenzen K, Anke T, Konetschny-Rapp S, Scheuer W. 5-hydroxy-3-vinyl-2(5H)-furanone--a new inhibitor of human synovial phospholipase A2 and platelet aggregation from fermentations of a Calyptella species (basidiomycetes). Z NATURFORSCH C 1995; 50:403-9. [PMID: 7546033] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
5-Hydroxy-3-vinyl-2(5H)-furanone, a potent and selective inhibitor of human synovial phospholipase A2 was isolated from fermentations of a Calyptella species. Its structure as identified by spectroscopic methods is identical to PA 147, an antibiotic previously isolated from a streptomycete. 5-hydroxy-3-vinyl-2(5H)-furanone inhibits the aggregation of human and bovine platelets stimulated by different inducers and exhibits weak antimicrobial activities.
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Affiliation(s)
- K Lorenzen
- LB Biotechnologie der Universität, Kaiserslautern, Bundesrepublik Deutschland
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47
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Erkel G, Lorenzen K, Anke T, Velten R, Gimenez A, Steglich W. Kuehneromycins A and B, two new biological active compounds from a Tasmanian Kuehneromyces sp. (Strophariaceae, Basidiomycetes). Z NATURFORSCH C 1995; 50:1-9. [PMID: 7535532 DOI: 10.1515/znc-1995-1-202] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [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: 01/25/2023]
Abstract
In a search for new inhibitors of RNA-directed DNA-polymerases kuehneromycin A (1) was isolated from fermentations of a Tasmanian Kuehneromyces species. Its structure was elucidated by spectroscopic methods. Kuehneromycin A (1) is a non-competitive inhibitor of avian myeloblastosis virus (Ki 200 microM) and moloney murine leukemia virus (Ki 40 microM) reverse transcriptases. The second compound, kuehneromycin B (2) is a strong inhibitor of platelet aggregation stimulated with different inducers. In addition, both compounds exhibit cytotoxic and antimicrobial activities.
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Affiliation(s)
- G Erkel
- Lehrbereich Biotechnologie der Universität, Bundesrepublik, Deutschland
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48
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Lorenzen K, Anke T, Anders U, Hindermayr H, Hansske F. 14-epidihydrocochlioquinone B and 14-epicochlioquinone B, antibiotics from fermentations of the ascomycete Neobulgaria pura: structure elucidation and effects on platelet aggregation. Z NATURFORSCH C 1994; 49:312-20. [PMID: 8060456 DOI: 10.1515/znc-1994-5-606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 01/28/2023]
Abstract
14-Epicochlioquinone B (1) and 14-epidihydrocochlioquinone B (2) were isolated from submerged cultures of Neobulgaria pura (Pers. ex Fr.) Petrak. 14-Epicochlioquinone B is a potent inhibitor of human and bovine platelet aggregation stimulated by different inducers. 14-Epidihydrocochlioquinone B does not inhibit the aggregation of platelets. In addition, both 1 and 2 exhibited cytotoxic and antimicrobial activities.
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Affiliation(s)
- K Lorenzen
- LB Biotechnologie der Universität, Kaiserslautern, Bundesrepublik Deutschland
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49
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Abstract
Two inhibitors of platelet aggregation were isolated from fermentations of Panus sp. 9096. One inhibitor proved to be identical to naematolon (2), an antibiotic previously isolated by S. Backens et al. from several Hypholoma species. The other metabolite, panudial (1), is a new nordrimane (cis-annelation of the bicyclus) lacking the carbon atom in position 10 of the drimane skeleton. Panudial is a potent inhibitor of bovine and human platelet aggregation stimulated by different inducers.
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Affiliation(s)
- K Lorenzen
- LB Biotechnologie der Universität, Kaiserslautern, Bundesrepublik Deutschland
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50
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Linderkamp O, Betke K, Fendel H, Klemm J, Lorenzen K, Riegel KP. Tc-99m-labeled red blood cells for the measurement of red cell mass in newborn infants: concise communication. J Nucl Med 1980; 21:637-40. [PMID: 7391836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In vitro and in vivo investigations were performed to examine the binding of Tc-99m to neonatal red blood cells (RBC). Labeling efficiency was about 90%, and unbound Tc-99m less than 3% after one washing, in premature and full-term newborns and in children. Thus presence of high percentages of fetal hemoglobin (Hb F) did not influence the labeling of RBCs with Tc-99m. RBCs of 11 newborns were hemolysed and the distribution of Tc-99m on RBC components was analyzed. Although Hb F percentage averaged (60.0 +/- 8.1)% (s.d.), only (11.9 +/- 3.7)% of Tc-99m was bound by Hb F, whereas (45.0 +/- 6.1)% was associated with Hb A. RBC membranes bound (13.7 +/- 4.3)% and (29.3 +/- 4.0)% were found unbound in hemolysates. These results indicate that Tc-99m preferentially binds to beta chains. In vivo equilibration of Tc-99m RBCs and of albumin labeled with Evans blue was investigated in five newborn infants. Tc-99m RBCs were stable in each case during the first hour after injection. Elution of Tc-99m from RBCs was (3.4 +/- 1.5)% per hour. Body-to-venous hematocrit ratio averaged 0.86 +/- 0.03.
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