51
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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52
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The cryo-EM structure of the acid activatable pore-forming immune effector Macrophage-expressed gene 1. Nat Commun 2019; 10:4288. [PMID: 31537793 PMCID: PMC6753088 DOI: 10.1038/s41467-019-12279-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, however, its mode of action remains unknown. We use cryo-Electron Microscopy (cryo-EM) to determine the 2.4 Å structure of a hexadecameric assembly of MPEG1 that displays the expected features of a soluble prepore complex. We further discover that MPEG1 prepore-like assemblies can be induced to perforate membranes through acidification, such as would occur within maturing phagolysosomes. We next solve the 3.6 Å cryo-EM structure of MPEG1 in complex with liposomes. These data reveal that a multi-vesicular body of 12 kDa (MVB12)-associated β-prism (MABP) domain binds membranes such that the pore-forming machinery of MPEG1 is oriented away from the bound membrane. This unexpected mechanism of membrane interaction suggests that MPEG1 remains bound to the phagolysosome membrane while simultaneously forming pores in engulfed bacterial targets. Macrophage-expressed gene 1 (MPEG1) functions within the phagolysosome to damage engulfed microbes, presumably via forming pores in target membranes. In order to provide insights into the mechanism of MPEG1 function and membrane binding, the authors present structures of hexadecameric MPEG1 prepores both in solution and in complex with liposomes.
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53
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Doorduijn DJ, Rooijakkers SHM, Heesterbeek DAC. How the Membrane Attack Complex Damages the Bacterial Cell Envelope and Kills Gram‐Negative Bacteria. Bioessays 2019; 41:e1900074. [DOI: 10.1002/bies.201900074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/11/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Dennis J. Doorduijn
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
| | - Suzan H. M. Rooijakkers
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
| | - Dani A. C. Heesterbeek
- Medical Microbiology, University Medical Center UtrechtUtrecht University Heidelberglaan 100 3584 CX Utrecht The Netherlands
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54
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Abstract
Perforin is an indispensable effector protein of primary cytotoxic lymphocytes (CTL or NK cells) that typically defend the host against virus infection, or gene-modified (chimeric antigen receptor-CAR) anticancer T cells. Perforin's pore-forming activity is necessary for the delivery of proapoptotic serine proteases, granzymes, into the cytosol of infected or cancerous target cells. The complete loss of perforin function is detrimental for the function of cytotoxic lymphocytes, and leads to fatal immune dysregulation in infants and predisposes the carriers of hypomorphic perforin mutations to various chronic inflammatory sequelae and blood cancers. Here, we describe several optimized and validated functional assays using purified effector proteins and cytotoxic lymphocytes that enable detailed analysis of perforin-mediated target cell death pathways.
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55
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Stanley G, Akpinar B, Shen Q, Fisher PDE, Lusk CP, Lin C, Hoogenboom BW. Quantification of Biomolecular Dynamics Inside Real and Synthetic Nuclear Pore Complexes Using Time-Resolved Atomic Force Microscopy. ACS NANO 2019; 13:7949-7956. [PMID: 31241896 PMCID: PMC6660115 DOI: 10.1021/acsnano.9b02424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/26/2019] [Indexed: 05/30/2023]
Abstract
Over the past decades, atomic force microscopy (AFM) has emerged as an increasingly powerful tool to study the dynamics of biomolecules at nanometer length scales. However, the more stochastic the nature of such biomolecular dynamics, the harder it becomes to distinguish them from AFM measurement noise. Rapid, stochastic dynamics are inherent to biological systems comprising intrinsically disordered proteins. One role of such proteins is in the formation of the transport barrier of the nuclear pore complex (NPC): the selective gateway for macromolecular traffic entering or exiting the nucleus. Here, we use AFM to observe the dynamics of intrinsically disordered proteins from two systems: the transport barrier of native NPCs and the transport barrier of a mimetic NPC made using a DNA origami scaffold. Analyzing data recorded with 50-200 ms temporal resolution, we highlight the importance of drift correction and appropriate baseline measurements in such experiments. In addition, we describe an autocorrelation analysis to quantify time scales of observed dynamics and to assess their veracity-an analysis protocol that lends itself to the quantification of stochastic fluctuations in other biomolecular systems. The results reveal the surprisingly slow rate of stochastic, collective transitions inside mimetic NPCs, highlighting the importance of FG-nup cohesive interactions.
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Affiliation(s)
- George
J. Stanley
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Bernice Akpinar
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Patrick D. Ellis Fisher
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - C. Patrick Lusk
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Bart W. Hoogenboom
- London
Centre for Nanotechnology, University College
London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
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56
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Prager I, Watzl C. Mechanisms of natural killer cell-mediated cellular cytotoxicity. J Leukoc Biol 2019; 105:1319-1329. [PMID: 31107565 DOI: 10.1002/jlb.mr0718-269r] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/22/2019] [Accepted: 04/14/2019] [Indexed: 12/29/2022] Open
Abstract
Cellular cytotoxicity, the ability to kill other cells, is an important effector mechanism of the immune system to combat viral infections and cancer. Cytotoxic T cells and natural killer (NK) cells are the major mediators of this activity. Here, we summarize the cytotoxic mechanisms of NK cells. NK cells can kill virally infected of transformed cells via the directed release of lytic granules or by inducing death receptor-mediated apoptosis via the expression of Fas ligand or TRAIL. The biogenesis of perforin and granzymes, the major components of lytic granules, is a highly regulated process to prevent damage during the synthesis of these cytotoxic molecules. Additionally, NK cells have developed several strategies to protect themselves from the cytotoxic activity of granular content upon degranulation. While granule-mediated apoptosis is a fast process, death receptor-mediated cytotoxicity requires more time. Current data suggest that these 2 cytotoxic mechanisms are regulated during the serial killing activity of NK cells. As many modern approaches of cancer immunotherapy rely on cellular cytotoxicity for their effectiveness, unraveling these pathways will be important to further progress these therapeutic strategies.
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Affiliation(s)
- Isabel Prager
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
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57
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Parsons ES, Stanley GJ, Pyne ALB, Hodel AW, Nievergelt AP, Menny A, Yon AR, Rowley A, Richter RP, Fantner GE, Bubeck D, Hoogenboom BW. Single-molecule kinetics of pore assembly by the membrane attack complex. Nat Commun 2019; 10:2066. [PMID: 31061395 PMCID: PMC6502846 DOI: 10.1038/s41467-019-10058-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/12/2019] [Indexed: 12/24/2022] Open
Abstract
The membrane attack complex (MAC) is a hetero-oligomeric protein assembly that kills pathogens by perforating their cell envelopes. The MAC is formed by sequential assembly of soluble complement proteins C5b, C6, C7, C8 and C9, but little is known about the rate-limiting steps in this process. Here, we use rapid atomic force microscopy (AFM) imaging to show that MAC proteins oligomerize within the membrane, unlike structurally homologous bacterial pore-forming toxins. C5b-7 interacts with the lipid bilayer prior to recruiting C8. We discover that incorporation of the first C9 is the kinetic bottleneck of MAC formation, after which rapid C9 oligomerization completes the pore. This defines the kinetic basis for MAC assembly and provides insight into how human cells are protected from bystander damage by the cell surface receptor CD59, which is offered a maximum temporal window to halt the assembly at the point of C9 insertion.
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Affiliation(s)
- Edward S Parsons
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
| | - George J Stanley
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Adrian W Hodel
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Adrian P Nievergelt
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Anaïs Menny
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Alexander R Yon
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ashlea Rowley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ralf P Richter
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- School of Physics and Astronomy, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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58
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Krishnan R S, Satheesan R, Puthumadathil N, Kumar KS, Jayasree P, Mahendran KR. Autonomously Assembled Synthetic Transmembrane Peptide Pore. J Am Chem Soc 2019; 141:2949-2959. [DOI: 10.1021/jacs.8b09973] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Smrithi Krishnan R
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Remya Satheesan
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Neethu Puthumadathil
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - K. Santhosh Kumar
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Poornendhu Jayasree
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Kozhinjampara R. Mahendran
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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59
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Brander S, Jank T, Hugel T. AFM Imaging Suggests Receptor-Free Penetration of Lipid Bilayers by Toxins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:365-371. [PMID: 30565941 DOI: 10.1021/acs.langmuir.8b03146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A crucial step of exotoxin action is the attack on the membrane. Many exotoxins show an architecture following the AB model, where a binding subunit translocates an "action" subunit across a cell membrane. Atomic force microscopy is an ideal technique to study these systems because of its ability to provide structural as well as dynamic information at the same time. We report first images of toxins Photorhabdus luminescens TcdA1 and Clostridium difficile TcdB on a supported lipid bilayer. A significant amount of toxin binds to the bilayer at neutral pH in the absence of receptors. Lack of diffusion indicates that toxin particles penetrate the membrane. This observation is supported by fluorescence recovery after photobleaching measurements. We mimic endocytosis by acidification while imaging the particles over time; however, we see no large conformational change. We therefore conclude that the toxin particles we imaged in neutral conditions had already formed a pore and speculate that there is no "pre-pore" state in our imaging conditions (i.e., in the absence of receptor).
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60
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Heesterbeek DA, Bardoel BW, Parsons ES, Bennett I, Ruyken M, Doorduijn DJ, Gorham RD, Berends ET, Pyne AL, Hoogenboom BW, Rooijakkers SH. Bacterial killing by complement requires membrane attack complex formation via surface-bound C5 convertases. EMBO J 2019; 38:embj.201899852. [PMID: 30643019 PMCID: PMC6376327 DOI: 10.15252/embj.201899852] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/05/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
The immune system kills bacteria by the formation of lytic membrane attack complexes (MACs), triggered when complement enzymes cleave C5. At present, it is not understood how the MAC perturbs the composite cell envelope of Gram-negative bacteria. Here, we show that the role of C5 convertase enzymes in MAC assembly extends beyond the cleavage of C5 into the MAC precursor C5b. Although purified MAC complexes generated from preassembled C5b6 perforate artificial lipid membranes and mammalian cells, these components lack bactericidal activity. In order to permeabilize both the bacterial outer and inner membrane and thus kill a bacterium, MACs need to be assembled locally by the C5 convertase enzymes. Our data indicate that C5b6 rapidly loses the capacity to form bactericidal pores; therefore, bacterial killing requires both in situ conversion of C5 and immediate insertion of C5b67 into the membrane. Using flow cytometry and atomic force microscopy, we show that local assembly of C5b6 at the bacterial surface is required for the efficient insertion of MAC pores into bacterial membranes. These studies provide basic molecular insights into MAC assembly and bacterial killing by the immune system.
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Affiliation(s)
- Dani Ac Heesterbeek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bart W Bardoel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Edward S Parsons
- London Centre for Nanotechnology, University College London, London, UK
| | - Isabel Bennett
- London Centre for Nanotechnology, University College London, London, UK
| | - Maartje Ruyken
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dennis J Doorduijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ronald D Gorham
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Evelien Tm Berends
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alice Lb Pyne
- London Centre for Nanotechnology, University College London, London, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, UK.,Department of Physics and Astronomy, University College London, London, UK
| | - Suzan Hm Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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61
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Drücker P, Iacovache I, Bachler S, Zuber B, Babiychuk EB, Dittrich PS, Draeger A. Membrane deformation and layer-by-layer peeling of giant vesicles induced by the pore-forming toxin pneumolysin. Biomater Sci 2019; 7:3693-3705. [DOI: 10.1039/c9bm00134d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Membranes under attack by the pore-forming toxin pneumolysin reveal a hitherto unknown layer-by-layer peeling mechanism and disclose the multilamellar structure.
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Affiliation(s)
- Patrick Drücker
- Department of Biosystems Science and Engineering
- ETH Zurich
- 4058 Basel
- Switzerland
- Department of Cell Biology
| | - Ioan Iacovache
- Laboratory of Experimental Morphology
- Institute of Anatomy
- University of Bern
- 3000 Bern 9
- Switzerland
| | - Simon Bachler
- Department of Biosystems Science and Engineering
- ETH Zurich
- 4058 Basel
- Switzerland
| | - Benoît Zuber
- Laboratory of Experimental Morphology
- Institute of Anatomy
- University of Bern
- 3000 Bern 9
- Switzerland
| | - Eduard B. Babiychuk
- Department of Cell Biology
- Institute of Anatomy
- University of Bern
- 3000 Bern 9
- Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering
- ETH Zurich
- 4058 Basel
- Switzerland
| | - Annette Draeger
- Department of Cell Biology
- Institute of Anatomy
- University of Bern
- 3000 Bern 9
- Switzerland
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62
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Menny A, Serna M, Boyd CM, Gardner S, Joseph AP, Morgan BP, Topf M, Brooks NJ, Bubeck D. CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers. Nat Commun 2018; 9:5316. [PMID: 30552328 PMCID: PMC6294249 DOI: 10.1038/s41467-018-07653-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/12/2018] [Indexed: 01/08/2023] Open
Abstract
The membrane attack complex (MAC) is one of the immune system's first responders. Complement proteins assemble on target membranes to form pores that lyse pathogens and impact tissue homeostasis of self-cells. How MAC disrupts the membrane barrier remains unclear. Here we use electron cryo-microscopy and flicker spectroscopy to show that MAC interacts with lipid bilayers in two distinct ways. Whereas C6 and C7 associate with the outer leaflet and reduce the energy for membrane bending, C8 and C9 traverse the bilayer increasing membrane rigidity. CryoEM reconstructions reveal plasticity of the MAC pore and demonstrate how C5b6 acts as a platform, directing assembly of a giant β-barrel whose structure is supported by a glycan scaffold. Our work provides a structural basis for understanding how β-pore forming proteins breach the membrane and reveals a mechanism for how MAC kills pathogens and regulates cell functions.
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Affiliation(s)
- Anaïs Menny
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Marina Serna
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
- Spanish National Cancer Research Centre, CNIO, Melchor Fernández Almagro, 3.28029, Madrid, Spain
| | - Courtney M Boyd
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Agnel Praveen Joseph
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot, OX11 0FA, UK
| | - B Paul Morgan
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Nicholas J Brooks
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK.
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63
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Evans CT, Payton O, Picco L, Allen MJ. Algal Viruses: The (Atomic) Shape of Things to Come. Viruses 2018; 10:E490. [PMID: 30213102 PMCID: PMC6165301 DOI: 10.3390/v10090490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 01/15/2023] Open
Abstract
Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.
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Affiliation(s)
- Christopher T Evans
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Oliver Payton
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Loren Picco
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Michael J Allen
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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64
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Christie MP, Johnstone BA, Tweten RK, Parker MW, Morton CJ. Cholesterol-dependent cytolysins: from water-soluble state to membrane pore. Biophys Rev 2018; 10:1337-1348. [PMID: 30117093 DOI: 10.1007/s12551-018-0448-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/07/2018] [Indexed: 12/22/2022] Open
Abstract
The cholesterol-dependent cytolysins (CDCs) are a family of bacterial toxins that are important virulence factors for a number of pathogenic Gram-positive bacterial species. CDCs are secreted as soluble, stable monomeric proteins that bind specifically to cholesterol-rich cell membranes, where they assemble into well-defined ring-shaped complexes of around 40 monomers. The complex then undergoes a concerted structural change, driving a large pore through the membrane, potentially lysing the target cell. Understanding the details of this process as the protein transitions from a discrete monomer to a complex, membrane-spanning protein machine is an ongoing challenge. While many of the details have been revealed, there are still questions that remain unanswered. In this review, we present an overview of some of the key features of the structure and function of the CDCs, including the structure of the secreted monomers, the process of interaction with target membranes, and the transition from bound monomers to complete pores. Future directions in CDC research and the potential of CDCs as research tools will also be discussed.
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Affiliation(s)
- Michelle P Christie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bronte A Johnstone
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rodney K Tweten
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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65
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The first transmembrane region of complement component-9 acts as a brake on its self-assembly. Nat Commun 2018; 9:3266. [PMID: 30111885 PMCID: PMC6093860 DOI: 10.1038/s41467-018-05717-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/09/2018] [Indexed: 11/09/2022] Open
Abstract
Complement component 9 (C9) functions as the pore-forming component of the Membrane Attack Complex (MAC). During MAC assembly, multiple copies of C9 are sequentially recruited to membrane associated C5b8 to form a pore. Here we determined the 2.2 Å crystal structure of monomeric murine C9 and the 3.9 Å resolution cryo EM structure of C9 in a polymeric assembly. Comparison with other MAC proteins reveals that the first transmembrane region (TMH1) in monomeric C9 is uniquely positioned and functions to inhibit its self-assembly in the absence of C5b8. We further show that following C9 recruitment to C5b8, a conformational change in TMH1 permits unidirectional and sequential binding of additional C9 monomers to the growing MAC. This mechanism of pore formation contrasts with related proteins, such as perforin and the cholesterol dependent cytolysins, where it is believed that pre-pore assembly occurs prior to the simultaneous release of the transmembrane regions.
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66
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Mulvihill E, Sborgi L, Mari SA, Pfreundschuh M, Hiller S, Müller DJ. Mechanism of membrane pore formation by human gasdermin-D. EMBO J 2018; 37:embj.201798321. [PMID: 29898893 PMCID: PMC6043855 DOI: 10.15252/embj.201798321] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022] Open
Abstract
Gasdermin‐D (GSDMD), a member of the gasdermin protein family, mediates pyroptosis in human and murine cells. Cleaved by inflammatory caspases, GSDMD inserts its N‐terminal domain (GSDMDNterm) into cellular membranes and assembles large oligomeric complexes permeabilizing the membrane. So far, the mechanisms of GSDMDNterm insertion, oligomerization, and pore formation are poorly understood. Here, we apply high‐resolution (≤ 2 nm) atomic force microscopy (AFM) to describe how GSDMDNterm inserts and assembles in membranes. We observe GSDMDNterm inserting into a variety of lipid compositions, among which phosphatidylinositide (PI(4,5)P2) increases and cholesterol reduces insertion. Once inserted, GSDMDNterm assembles arc‐, slit‐, and ring‐shaped oligomers, each of which being able to form transmembrane pores. This assembly and pore formation process is independent on whether GSDMD has been cleaved by caspase‐1, caspase‐4, or caspase‐5. Using time‐lapse AFM, we monitor how GSDMDNterm assembles into arc‐shaped oligomers that can transform into larger slit‐shaped and finally into stable ring‐shaped oligomers. Our observations translate into a mechanistic model of GSDMDNterm transmembrane pore assembly, which is likely shared within the gasdermin protein family.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | - Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
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Ni T, Williams SI, Rezelj S, Anderluh G, Harlos K, Stansfeld PJ, Gilbert RJC. Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin-like protein 1. SCIENCE ADVANCES 2018; 4:eaaq0762. [PMID: 29750191 PMCID: PMC5943054 DOI: 10.1126/sciadv.aaq0762] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/09/2018] [Indexed: 05/30/2023]
Abstract
Toxoplasma and Plasmodium are the parasitic agents of toxoplasmosis and malaria, respectively, and use perforin-like proteins (PLPs) to invade host organisms and complete their life cycles. The Toxoplasma gondii PLP1 (TgPLP1) is required for efficient exit from parasitophorous vacuoles in which proliferation occurs. We report structures of the membrane attack complex/perforin (MACPF) and Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains of TgPLP1. The MACPF domain forms hexameric assemblies, with ring and helix geometries, and the APCβ domain has a novel β-prism fold joined to the MACPF domain by a short linker. Molecular dynamics simulations suggest that the helical MACPF oligomer preserves a biologically important interface, whereas the APCβ domain binds preferentially through a hydrophobic loop to membrane phosphatidylethanolamine, enhanced by the additional presence of inositol phosphate lipids. This mode of membrane binding is supported by site-directed mutagenesis data from a liposome-based assay. Together, these structural and biophysical findings provide insights into the molecular mechanism of membrane targeting by TgPLP1.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sophie I. Williams
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Saša Rezelj
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robert J. C. Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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68
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Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS NANO 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
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Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
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69
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Brennan AJ, Law RHP, Conroy PJ, Noori T, Lukoyanova N, Saibil H, Yagita H, Ciccone A, Verschoor S, Whisstock JC, Trapani JA, Voskoboinik I. Perforin proteostasis is regulated through its C2 domain: supra-physiological cell death mediated by T431D-perforin. Cell Death Differ 2018; 25:1517-1529. [PMID: 29416110 DOI: 10.1038/s41418-018-0057-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 11/20/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022] Open
Abstract
The pore forming, Ca2+-dependent protein, perforin, is essential for the function of cytotoxic lymphocytes, which are at the frontline of immune defence against pathogens and cancer. Perforin is a glycoprotein stored in the secretory granules prior to release into the immune synapse. Congenital perforin deficiency causes fatal immune dysregulation, and is associated with various haematological malignancies. At least 50% of pathological missense mutations in perforin result in protein misfolding and retention in the endoplasmic reticulum. However, the regulation of perforin proteostasis remains unexplored. Using a variety of biochemical assays that assess protein stability and acquisition of complex glycosylation, we demonstrated that the binding of Ca2+ to the C2 domain stabilises perforin and regulates its export from the endoplasmic reticulum to the secretory granules. As perforin is a thermo-labile protein, we hypothesised that by altering its C2 domain it may be possible to improve protein stability. On the basis of the X-ray crystal structure of the perforin C2 domain, we designed a mutation (T431D) in the Ca2+ binding loop. Mutant perforin displayed markedly enhanced thermal stability and lytic function, despite its trafficking from the endoplasmic reticulum remaining unchanged. Furthermore, by introducing the T431D mutation into A90V perforin, a pathogenic mutation, which results in protein misfolding, we corrected the A90V folding defect and completely restored perforin's cytotoxic function. These results revealed an unexpected role for the Ca2+-dependent C2 domain in maintaining perforin proteostasis and demonstrated the possibility of designing perforin with supra-physiological cytotoxic function through stabilisation of the C2 domain.
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Affiliation(s)
- Amelia J Brennan
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | - Ruby H P Law
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC, Australia.,The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Paul J Conroy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC, Australia.,The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Tahereh Noori
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Natalya Lukoyanova
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Helen Saibil
- Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Hideo Yagita
- Department of Immunology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Annette Ciccone
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sandra Verschoor
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC, Australia.,The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Joseph A Trapani
- Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Ilia Voskoboinik
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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70
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Watanabe H, Gubbiotti A, Chinappi M, Takai N, Tanaka K, Tsumoto K, Kawano R. Analysis of Pore Formation and Protein Translocation Using Large Biological Nanopores. Anal Chem 2017; 89:11269-11277. [DOI: 10.1021/acs.analchem.7b01550] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hirokazu Watanabe
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Alberto Gubbiotti
- Department
of Mechanical and Aerospace Engineering, Sapienza University of Rome, Via Eudossiana 18, Rome 00184, Italy
| | - Mauro Chinappi
- Department
of Industrial Engineering, University of Rome Tor Vergata, Via
del Politecnico 1, Rome 00133, Italy
| | - Natsumi Takai
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Tanaka
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryuji Kawano
- Department
of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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