1
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Gupta LK, Molla J, Prabhu AA. Story of Pore-Forming Proteins from Deadly Disease-Causing Agents to Modern Applications with Evolutionary Significance. Mol Biotechnol 2024; 66:1327-1356. [PMID: 37294530 DOI: 10.1007/s12033-023-00776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/21/2023] [Indexed: 06/10/2023]
Abstract
Animal venoms are a complex mixture of highly specialized toxic molecules. Among them, pore-forming proteins (PFPs) or toxins (PFTs) are one of the major disease-causing toxic elements. The ability of the PFPs in defense and toxicity through pore formation on the host cell surface makes them unique among the toxin proteins. These features made them attractive for academic and research purposes for years in the areas of microbiology as well as structural biology. All the PFPs share a common mechanism of action for the attack of host cells and pore formation in which the selected pore-forming motifs of the host cell membrane-bound protein molecules drive to the lipid bilayer of the cell membrane and eventually produces water-filled pores. But surprisingly their sequence similarity is very poor. Their existence can be seen both in a soluble state and also in transmembrane complexes in the cell membrane. PFPs are prevalent toxic factors that are predominately produced by all kingdoms of life such as virulence bacteria, nematodes, fungi, protozoan parasites, frogs, plants, and also from higher organisms. Nowadays, multiple approaches to applications of PFPs have been conducted by researchers both in basic as well as applied biological research. Although PFPs are very devastating for human health nowadays researchers have been successful in making these toxic proteins into therapeutics through the preparation of immunotoxins. We have discussed the structural, and functional mechanism of action, evolutionary significance through dendrogram, domain organization, and practical applications for various approaches. This review aims to emphasize the PFTs to summarize toxic proteins together for basic knowledge as well as to highlight the current challenges, and literature gap along with the perspective of promising biotechnological applications for their future research.
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Affiliation(s)
- Laxmi Kumari Gupta
- Bioprocess Development Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Johiruddin Molla
- Ghatal Rabindra Satabarsiki Mahavidyalaya Ghatal, Paschim Medinipur, Ghatal, West Bengal, 721212, India
| | - Ashish A Prabhu
- Bioprocess Development Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India.
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2
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Surm JM, Landau M, Columbus-Shenkar YY, Moran Y. Sea Anemone Membrane Attack Complex/Perforin Superfamily Demonstrates an Evolutionary Transitional State between Venomous and Developmental Functions. Mol Biol Evol 2024; 41:msae082. [PMID: 38676945 PMCID: PMC11090067 DOI: 10.1093/molbev/msae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Gene duplication is a major force driving evolutionary innovation. A classic example is generating new animal toxins via duplication of physiological protein-encoding genes and recruitment into venom. While this process drives the innovation of many animal venoms, reverse recruitment of toxins into nonvenomous cells remains unresolved. Using comparative genomics, we find members of the Membrane Attack Complex and Perforin Family (MAC) have been recruited into venom-injecting cells (cnidocytes), in soft and stony corals and sea anemones, suggesting that the ancestral MAC was a cnidocyte expressed toxin. Further investigation into the model sea anemone Nematostella vectensis reveals that three members have undergone Nematostella-specific duplications leading to their reverse recruitment into endomesodermal cells. Furthermore, simultaneous knockdown of all three endomesodermally expressed MACs leads to mis-development, supporting that these paralogs have nonvenomous function. By resolving the evolutionary history and function of MACs in Nematostella, we provide the first proof for reverse recruitment from venom to organismal development.
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Affiliation(s)
- Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Morani Landau
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yaara Y Columbus-Shenkar
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
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3
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Anderluh G. A label-free approach for measuring interactions of proteins with lipid membranes. CELL REPORTS METHODS 2023; 3:100649. [PMID: 37989086 PMCID: PMC10694574 DOI: 10.1016/j.crmeth.2023.100649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023]
Abstract
In this issue of Cell Reports Methods, Sadi et al. present a nuclear magnetic resonance approach for quantitative assessment of protein interactions with lipid membranes. It is sensitive, applicable to diverse membrane systems, covers a broad range of KDs, and does not require large amounts of material.
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Affiliation(s)
- Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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4
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Pirc K, Albert I, Nürnberger T, Anderluh G. Disruption of plant plasma membrane by Nep1-like proteins in pathogen-plant interactions. THE NEW PHYTOLOGIST 2023; 237:746-750. [PMID: 36210522 PMCID: PMC10100409 DOI: 10.1111/nph.18524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Lipid membrane destruction by microbial pore-forming toxins (PFTs) is a ubiquitous mechanism of damage to animal cells, but is less prominent in plants. Nep1-like proteins (NLPs) secreted by phytopathogens that cause devastating crop diseases, such as potato late blight, represent the only family of microbial PFTs that effectively damage plant cells by disrupting the integrity of the plant plasma membrane. Recent research has elucidated the molecular mechanism of NLP-mediated membrane damage, which is unique among microbial PFTs and highly adapted to the plant membrane environment. In this review, we cover recent insight into how NLP cytolysins damage plant membranes and cause cell death.
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Affiliation(s)
- Katja Pirc
- Department of Molecular Biology and NanobiotechnologyNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia
| | - Isabell Albert
- Molecular Plant PhysiologyFAU Erlangen‐Nüremberg91058ErlangenGermany
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP)Eberhard‐Karls‐University Tübingen72076TübingenGermany
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006JohannesburgSouth Africa
| | - Gregor Anderluh
- Department of Molecular Biology and NanobiotechnologyNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia
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5
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Šolinc G, Švigelj T, Omersa N, Snoj T, Pirc K, Žnidaršič N, Yamaji-Hasegawa A, Kobayashi T, Anderluh G, Podobnik M. Pore-forming moss protein bryoporin is structurally and mechanistically related to actinoporins from evolutionarily distant cnidarians. J Biol Chem 2022; 298:102455. [PMID: 36063994 PMCID: PMC9526159 DOI: 10.1016/j.jbc.2022.102455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 10/26/2022] Open
Abstract
Pore-forming proteins perforate lipid membranes and consequently affect their integrity and cell fitness. Therefore, it is not surprising that many of these proteins from bacteria, fungi, or certain animals act as toxins. While pore-forming proteins have also been found in plants, there is little information on their molecular structure and mode of action. Bryoporin is a protein from the moss Physcomitrium patens, and its corresponding gene was found to be upregulated by various abiotic stresses, especially dehydration, as well as upon fungal infection. Based on the amino acid sequence, it was suggested that bryoporin was related to the actinoporin family of pore-forming proteins, originally discovered in sea anemones. Here, we provide the first detailed structural and functional analysis of this plant cytolysin. The crystal structure of the monomeric bryoporin is highly similar to those of actinoporins. Our cryo-EM analysis of its pores showed an actinoporin-like octameric structure, thereby revealing a close kinship of proteins from evolutionarily distant organisms. This was further confirmed by our observation of bryoporin's preferential binding to and formation of pores in membranes containing animal sphingolipids, such as sphingomyelin and ceramide phosphoethanolamine; however, its binding affinity was weaker than that of actinoporin equinatoxin II. We determined bryoporin did not bind to major sphingolipids found in fungi or plants, and its membrane-binding and pore-forming activity were enhanced by various sterols. Our results suggest that bryoporin could represent a part of the moss defense arsenal, acting as a pore-forming toxin against membranes of potential animal pathogens, parasites, or predators.
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Affiliation(s)
- Gašper Šolinc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Tomaž Švigelj
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Tina Snoj
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Nada Žnidaršič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, Slovenia
| | | | - Toshihide Kobayashi
- Lipid Biology Laboratory, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama 351-0198, Japan; UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia.
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6
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Kumar H, Jimah JR, Misal SA, Salinas ND, Fried M, Schlesinger PH, Tolia NH. Implications of conformational flexibility, lipid binding, and regulatory domains in cell traversal-protein CelTOS for apicomplexan migration. J Biol Chem 2022; 298:102241. [PMID: 35809642 PMCID: PMC9400078 DOI: 10.1016/j.jbc.2022.102241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
Malaria and other apicomplexan-caused diseases affect millions of humans, agricultural animals, and pets. Cell traversal is a common feature used by multiple apicomplexan parasites to migrate through host cells and can be exploited to develop therapeutics against these deadly parasites. Here, we provide insights into the mechanism of the Cell-traversal protein for ookinetes and sporozoites (CelTOS), a conserved cell-traversal protein in apicomplexan parasites and malaria vaccine candidate. CelTOS has previously been shown to form pores in cell membranes to enable traversal of parasites through cells. We establish roles for the distinct protein regions of Plasmodium vivax CelTOS and examine the mechanism of pore formation. We further demonstrate that CelTOS dimer dissociation is required for pore formation, as disulfide bridging between monomers inhibits pore formation, and this inhibition is rescued by disulfide-bridge reduction. We also show that a helix-destabilizing amino acid, Pro127, allows CelTOS to undergo significant conformational changes to assemble into pores. The flexible C terminus of CelTOS is a negative regulator that limits pore formation. Finally, we highlight that lipid binding is a prerequisite for pore assembly as mutation of a phospholipids-binding site in CelTOS resulted in loss of lipid binding and abrogated pore formation. These findings identify critical regions in CelTOS and will aid in understanding the egress mechanism of malaria and other apicomplexan parasites as well as have implications for studying the function of other essential pore-forming proteins.
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Affiliation(s)
- Hirdesh Kumar
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - John R Jimah
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Santosh A Misal
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Nichole D Salinas
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Michal Fried
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland
| | - Paul H Schlesinger
- Department of Cell Biology and Physiology, Washington, University School of Medicine, Saint Louis, United States
| | - Niraj H Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, National Institutes of Health Bethesda, Maryland.
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7
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Pirc K, Clifton LA, Yilmaz N, Saltalamacchia A, Mally M, Snoj T, Žnidaršič N, Srnko M, Borišek J, Parkkila P, Albert I, Podobnik M, Numata K, Nürnberger T, Viitala T, Derganc J, Magistrato A, Lakey JH, Anderluh G. An oomycete NLP cytolysin forms transient small pores in lipid membranes. SCIENCE ADVANCES 2022; 8:eabj9406. [PMID: 35275729 PMCID: PMC8916740 DOI: 10.1126/sciadv.abj9406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/21/2022] [Indexed: 05/31/2023]
Abstract
Microbial plant pathogens secrete a range of effector proteins that damage host plants and consequently constrain global food production. Necrosis and ethylene-inducing peptide 1-like proteins (NLPs) are produced by numerous phytopathogenic microbes that cause important crop diseases. Many NLPs are cytolytic, causing cell death and tissue necrosis by disrupting the plant plasma membrane. Here, we reveal the unique molecular mechanism underlying the membrane damage induced by the cytotoxic model NLP. This membrane disruption is a multistep process that includes electrostatic-driven, plant-specific lipid recognition, shallow membrane binding, protein aggregation, and transient pore formation. The NLP-induced damage is not caused by membrane reorganization or large-scale defects but by small membrane ruptures. This distinct mechanism of lipid membrane disruption is highly adapted to effectively damage plant cells.
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Affiliation(s)
- Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Luke A. Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, Oxford OX11 OQX, UK
| | - Neval Yilmaz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | | | - Mojca Mally
- Institute of Biophysics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tina Snoj
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Nada Žnidaršič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marija Srnko
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Jure Borišek
- Theory Department, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Petteri Parkkila
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Isabell Albert
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
- Molecular Plant Physiology, FAU Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Tapani Viitala
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Jure Derganc
- Institute of Biophysics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Chair of Microprocess Engineering and Technology—COMPETE, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Alessandra Magistrato
- International School for Advanced Studies (SISSA/ISAS), 34136 Trieste, Italy
- National Research Council Institute of Material (CNR-IOM), 34136 Trieste, Italy
| | - Jeremy H. Lakey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
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8
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Donato M, Soto C, Lanio ME, Itri R, Álvarez C. The pore-forming activity of sticholysin I is enhanced by the presence of a phospholipid hydroperoxide in membrane. Toxicon 2021; 204:44-55. [PMID: 34736955 DOI: 10.1016/j.toxicon.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/23/2021] [Accepted: 10/29/2021] [Indexed: 11/19/2022]
Abstract
Sticholysin I (StI) is a pore-forming toxin (PFT) belonging to the actinoporin protein family characterized by high permeabilizing activity in membranes. StI readily associates with sphingomyelin (SM)-containing membranes originating pores that can lead to cell death. Binding and pore-formation are critically dependent on the physicochemical properties of membrane. 1-palmitoyl-2-oleoylphosphatidylcholine hydroperoxide (POPC-OOH) is an oxidized phospholipid (OxPL) containing an -OOH moiety in the unsaturated hydrocarbon chain which orientates towards the bilayer interface. This orientation causes an increase in the lipid molecular area, lateral expansion and decrease in bilayer thickness, elastic and bending modulus, as well as modification of lipid packing. Taking advantage of membrane structural changes promoted by POPC-OOH, we investigated its influence on the permeabilizing ability of StI. Here we report the action of StI on Giant Unilamellar Vesicles (GUVs) made of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and SM containing increasing amount of POPC-OOH to assess vesicle permeability changes when compared to OxPL-lacking membranes. Inclusion of POPC-OOH in membranes did not promote spontaneous vesicle leaking but resulted in increased membrane permeability due to StI action. StI activity did not modify the fluid-gel phase coexistence boundaries neither in POPC:SM or POPC-OOH:SM membranes. However, the StI insertion mechanism in membrane seems to differ between POPC:SM and POPC-OOH:SM mixtures as suggested by changes in the time course of monolayer surface tension measurements, even though a preferable binding of the toxin to OxPL-containing systems could not be here demonstrated. In summary, modifications in the membrane imposed by lipid hydroperoxidation favor StI permeabilizing activity.
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Affiliation(s)
- Maressa Donato
- Instituto de Física, Universidade de São Paulo (USP), São Paulo, SP, Brazil; Center for Laser and Applications, Nuclear and Energy Research Institute, São Paulo, Brazil
| | - Carmen Soto
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, CP, 10400, La Habana, Cuba
| | - María Eliana Lanio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, CP, 10400, La Habana, Cuba
| | - Rosangela Itri
- Instituto de Física, Universidade de São Paulo (USP), São Paulo, SP, Brazil.
| | - Carlos Álvarez
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, CP, 10400, La Habana, Cuba.
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Alvarez C, Soto C, Cabezas S, Alvarado-Mesén J, Laborde R, Pazos F, Ros U, Hernández AM, Lanio ME. Panorama of the Intracellular Molecular Concert Orchestrated by Actinoporins, Pore-Forming Toxins from Sea Anemones. Toxins (Basel) 2021; 13:toxins13080567. [PMID: 34437438 PMCID: PMC8402351 DOI: 10.3390/toxins13080567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/25/2022] Open
Abstract
Actinoporins (APs) are soluble pore-forming proteins secreted by sea anemones that experience conformational changes originating in pores in the membranes that can lead to cell death. The processes involved in the binding and pore-formation of members of this protein family have been deeply examined in recent years; however, the intracellular responses to APs are only beginning to be understood. Unlike pore formers of bacterial origin, whose intracellular impact has been studied in more detail, currently, we only have knowledge of a few poorly integrated elements of the APs’ intracellular action. In this review, we present and discuss an updated landscape of the studies aimed at understanding the intracellular pathways triggered in response to APs attack with particular reference to sticholysin II, the most active isoform produced by the Caribbean Sea anemone Stichodactyla helianthus. To achieve this, we first describe the major alterations these cytolysins elicit on simpler cells, such as non-nucleated mammalian erythrocytes, and then onto more complex eukaryotic cells, including tumor cells. This understanding has provided the basis for the development of novel applications of sticholysins such as the construction of immunotoxins directed against undesirable cells, such as tumor cells, and the design of a cancer vaccine platform. These are among the most interesting potential uses for the members of this toxin family that have been carried out in our laboratory.
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Affiliation(s)
- Carlos Alvarez
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
- Correspondence:
| | - Carmen Soto
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
| | - Sheila Cabezas
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
| | - Javier Alvarado-Mesén
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
- Escuela de Ciencias Biológicas, Universidad Nacional, Heredia 40101, Costa Rica
| | - Rady Laborde
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
| | - Fabiola Pazos
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
| | - Uris Ros
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-strasse 26, 50931 Cologne, Germany
| | - Ana María Hernández
- Immunobiology Division, Molecular Immunology Institute, Center of Molecular Immunology (CIM), Playa, Havana CP 11600, Cuba;
| | - María Eliana Lanio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana (UH) and Laboratorio UH-Centro de Inmunología Molecular, Havana CP 11600, Cuba; (C.S.); (S.C.); (J.A.-M.); (R.L.); (F.P.); (U.R.); (M.E.L.)
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10
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Palacios-Ortega J, García-Linares S, Rivera-de-Torre E, Heras-Márquez D, Gavilanes JG, Slotte JP, Martínez-Del-Pozo Á. Structural foundations of sticholysin functionality. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140696. [PMID: 34246789 DOI: 10.1016/j.bbapap.2021.140696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023]
Abstract
Actinoporins constitute a family of α pore-forming toxins produced by sea anemones. The soluble fold of these proteins consists of a β-sandwich flanked by two α-helices. Actinoporins exert their activity by specifically recognizing sphingomyelin at their target membranes. Once there, they penetrate the membrane with their N-terminal α-helices, a process that leads to the formation of cation-selective pores. These pores kill the target cells by provoking an osmotic shock on them. In this review, we examine the role and relevance of the structural features of actinoporins, down to the residue level. We look at the specific amino acids that play significant roles in the function of actinoporins and their fold. Particular emphasis is given to those residues that display a high degree of conservation across the actinoporin sequences known to date. In light of the latest findings in the field, the membrane requirements for pore formation, the effect of lipid composition, and the process of pore formation are also discussed.
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Affiliation(s)
- Juan Palacios-Ortega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
| | - Sara García-Linares
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - Esperanza Rivera-de-Torre
- Department of Biochemistry and Biotechnology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Diego Heras-Márquez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - José G Gavilanes
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Álvaro Martínez-Del-Pozo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
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11
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Rostovtseva TK, Bezrukov SM, Hoogerheide DP. Regulation of Mitochondrial Respiration by VDAC Is Enhanced by Membrane-Bound Inhibitors with Disordered Polyanionic C-Terminal Domains. Int J Mol Sci 2021; 22:7358. [PMID: 34298976 PMCID: PMC8306229 DOI: 10.3390/ijms22147358] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the primary regulating pathway of water-soluble metabolites and ions across the mitochondrial outer membrane. When reconstituted into lipid membranes, VDAC responds to sufficiently large transmembrane potentials by transitioning to gated states in which ATP/ADP flux is reduced and calcium flux is increased. Two otherwise unrelated cytosolic proteins, tubulin, and α-synuclein (αSyn), dock with VDAC by a novel mechanism in which the transmembrane potential draws their disordered, polyanionic C-terminal domains into and through the VDAC channel, thus physically blocking the pore. For both tubulin and αSyn, the blocked state is observed at much lower transmembrane potentials than VDAC gated states, such that in the presence of these cytosolic docking proteins, VDAC's sensitivity to transmembrane potential is dramatically increased. Remarkably, the features of the VDAC gated states relevant for bioenergetics-reduced metabolite flux and increased calcium flux-are preserved in the blocked state induced by either docking protein. The ability of tubulin and αSyn to modulate mitochondrial potential and ATP production in vivo is now supported by many studies. The common physical origin of the interactions of both tubulin and αSyn with VDAC leads to a general model of a VDAC inhibitor, facilitates predictions of the effect of post-translational modifications of known inhibitors, and points the way toward the development of novel therapeutics targeting VDAC.
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Affiliation(s)
- Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
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12
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Klompen AML, Kayal E, Collins AG, Cartwright P. Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa). Genome Biol Evol 2021; 13:6248095. [PMID: 33892512 PMCID: PMC8214413 DOI: 10.1093/gbe/evab081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
Many jellyfish species are known to cause a painful sting, but box jellyfish (class Cubozoa) are a well-known danger to humans due to exceptionally potent venoms. Cubozoan toxicity has been attributed to the presence and abundance of cnidarian-specific pore-forming toxins called jellyfish toxins (JFTs), which are highly hemolytic and cardiotoxic. However, JFTs have also been found in other cnidarians outside of Cubozoa, and no comprehensive analysis of their phylogenetic distribution has been conducted to date. Here, we present a thorough annotation of JFTs from 147 cnidarian transcriptomes and document 111 novel putative JFTs from over 20 species within Medusozoa. Phylogenetic analyses show that JFTs form two distinct clades, which we call JFT-1 and JFT-2. JFT-1 includes all known potent cubozoan toxins, as well as hydrozoan and scyphozoan representatives, some of which were derived from medically relevant species. JFT-2 contains primarily uncharacterized JFTs. Although our analyses detected broad purifying selection across JFTs, we found that a subset of cubozoan JFT-1 sequences are influenced by gene-wide episodic positive selection compared with homologous toxins from other taxonomic groups. This suggests that duplication followed by neofunctionalization or subfunctionalization as a potential mechanism for the highly potent venom in cubozoans. Additionally, published RNA-seq data from several medusozoan species indicate that JFTs are differentially expressed, spatially and temporally, between functionally distinct tissues. Overall, our findings suggest a complex evolutionary history of JFTs involving duplication and selection that may have led to functional diversification, including variability in toxin potency and specificity.
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Affiliation(s)
- Anna M L Klompen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
| | - Ehsan Kayal
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Allen G Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,National Systematics Laboratory of NOAA's Fisheries Service, Silver Spring, Maryland, USA
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
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13
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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14
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Žerovnik E. Viroporins vs. Other Pore-Forming Proteins: What Lessons Can We Take? Front Chem 2021; 9:626059. [PMID: 33681145 PMCID: PMC7930612 DOI: 10.3389/fchem.2021.626059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Pore-forming proteins (PFPs) exist in virtually all domains of life, and by disrupting cellular membranes, depending on the pore size, they cause ion dis-balance, small substances, or even protein efflux/influx, influencing cell’s signaling routes and fate. Such pore-forming proteins exist from bacteria to viruses and also shape host defense systems, including innate immunity. There is strong evidence that amyloid toxicity is also caused by prefibrillar oligomers making “amyloid pores” into cellular membranes. For most of the PFPs, a 2-step mechanism of protein-membrane interaction takes place on the “lipid rafts,” membrane microdomains rich in gangliosides and cholesterol. In this mini-review paper, common traits of different PFPs are looked at. Possible ways for therapy of channelopathies and/or modulating immunity relevant to the new threat of SARS-CoV-2 infections could be learnt from such comparisons.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
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15
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Aden S, Snoj T, Anderluh G. The use of giant unilamellar vesicles to study functional properties of pore-forming toxins. Methods Enzymol 2021; 649:219-251. [PMID: 33712188 DOI: 10.1016/bs.mie.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pore-forming toxins (PFTs) act upon lipid membranes and appropriate model systems are of great importance in researching these proteins. Giant unilamellar vesicles (GUVs) are an excellent model membrane system to study interactions between lipids and proteins. Their main advantage is the size comparable to cells, which means that GUVs can be observed directly under the light microscope. Many PFTs properties can be studied by using GUVs, such as binding specificity, membrane reorganization upon protein binding and oligomerization, pore properties and mechanism of pore formation. GUVs also represent a good model for biotechnological approaches, e.g., in applications in synthetic biology and medicine. Each research area has its own demands for GUVs properties, so several different approaches for GUVs preparations have been developed and will be discussed in this chapter.
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Affiliation(s)
- Saša Aden
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tina Snoj
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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16
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Caaveiro JMM, Tsumoto K. Molecular basis for the activation of actinoporins by lipids. Methods Enzymol 2021; 649:277-306. [PMID: 33712190 DOI: 10.1016/bs.mie.2021.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoporins are a family of homologous pore forming proteins from sea anemones. They are one of the few families of eukaryotic toxins that have been characterized in depth. Actinoporins are activated by lipids in the context of bilayers, especially in cell and in model membranes containing the lipid sphingomyelin. These proteins must undergo conformational changes induced upon interaction with lipids in the membrane, where they form cytotoxic pores causing cell death and lethality. Herein we review a list of procedures and techniques to study this family of toxins, with the goal of elucidating the physicochemical, thermodynamic and structural basis for their activation by lipids. The emerging picture indicates that actinoporins undergo a stepwise process that includes binding to the membrane, oligomerization, and pore formation, in this order. The key transformation from the inactive oligomer to the active pore is catalyzed by sphingomyelin, explaining the key role of this lipid in the function of actinoporins.
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Affiliation(s)
- Jose M M Caaveiro
- Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka-shi, Fukuoka, Japan.
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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17
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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18
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Sathyanarayana P, Visweswariah SS, Ayappa KG. Mechanistic Insights into Pore Formation by an α-Pore Forming Toxin: Protein and Lipid Bilayer Interactions of Cytolysin A. Acc Chem Res 2021; 54:120-131. [PMID: 33291882 DOI: 10.1021/acs.accounts.0c00551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pore forming toxins (PFTs) are the largest class of bacterial toxins playing a central role in bacterial pathogenesis. They are proteins specifically designed to form nanochannels in the membranes of target cells, ultimately resulting in cell death and establishing infection. PFTs are broadly classified as α- and β-PFTs, depending on secondary structures that form the transmembrane channel. A unique feature about this class of proteins is the drastic conformational changes and complex oligomerization pathways that occur upon exposure to the plasma membrane. A molecular understanding of pore formation has implications in designing novel intervention strategies to combat rising antimicrobial resistance, targeted-cancer therapy, as well as designing nanopores for specialized technologies. Central to unraveling the pore formation pathway is the availability of high resolution crystal structures. In this regard, β-toxins are better understood, when compared with α-toxins whose pore forming mechanisms are complicated by an incomplete knowledge of the driving forces for amphiphatic membrane-inserted helices to organize into functional pores. With the publication of the first crystal structure for an α-toxin, cytolysin A (ClyA), in 2009 we embarked on an extensive multiscale study to unravel its pore forming mechanism. This Account represents the collective mechanistic knowledge gained in our laboratories using a variety of experimental and theoretical techniques which include large scale molecular dynamics (MD) simulations, kinetic modeling studies, single-molecule fluorescence imaging, and super-resolution spectroscopy. We reported MD simulations of the ClyA protomer, oligomeric intermediates, and full pore complex in a lipid bilayer and mapped the conformational transitions that accompany membrane binding. Using single-molecule fluorescence imaging, the conformational transition was experimentally verified by analysis of various diffusion states of membrane bound ClyA. Importantly, we have uncovered a hitherto unknown putative cholesterol binding motif in the membrane-inserted helix of ClyA. Distinct binding pockets for cholesterol formed by adjacent membrane-inserted helices are revealed in MD simulations. Cholesterol appears to play a dual role by stabilizing both the membrane-inserted protomer as well as oligomeric intermediates. Molecular dynamics simulations and kinetic modeling studies suggest that the membrane-inserted arcs oligomerize reversibly to form the predominant transmembrane oligomeric intermediates during pore formation. We posit that this mechanistic understanding of the complex action of α-PFTs has implications in unraveling pore assembly across the wider family of bacterial toxins. With emerging antimicrobial resistance, alternate therapies may rely on disrupting pore functionality or oligomerization of these pathogenic determinants utilized by bacteria, and our study includes assessing the potential for dendrimers as pore blockers.
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Affiliation(s)
- Pradeep Sathyanarayana
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
| | - Sandhya S. Visweswariah
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India 560012
| | - K. Ganapathy Ayappa
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India 560012
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India 560012
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19
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Konshina AG, Dubovskii PV, Efremov RG. Stepwise Insertion of Cobra Cardiotoxin CT2 into a Lipid Bilayer Occurs as an Interplay of Protein and Membrane "Dynamic Molecular Portraits". J Chem Inf Model 2020; 61:385-399. [PMID: 33382618 DOI: 10.1021/acs.jcim.0c01137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For many peripheral membrane-binding polypeptides(MBPs), especially β-structural ones, the precise molecular mechanisms of membrane insertion remain unclear. In most cases, only the terminal water-soluble and membrane-bound states have been elucidated, whereas potential functionally important intermediate stages are still not understood in sufficient detail. In this study, we present one of the first successful attempts to describe step-by-step embedding of the MBP cardiotoxin 2 (CT2) from cobra Naja oxiana venom into a lipid bilayer at the atomistic level. CT2 possesses a highly conservative and rigid β-structured three-finger fold shared by many other exogenous and endogenous proteins performing a wide variety of functions. The incorporation of CT2 into the lipid bilayer was analyzed via a 2 μs all-atom molecular dynamics (MD) simulation without restraints. This process was shown to occur over a number of distinct steps, while the geometry of initial membrane attachment drastically differs from that of the final equilibrated state. In the latter one, the hydrophobic platform ("bottom") formed by the tips of the three loops is deeply buried into the lipid bilayer. This agrees well with the NMR data obtained earlier for CT2 in detergent micelles. However, the bottom is too bulky to insert itself into the membrane at once. Instead, the gradual immersion of CT2 initiated by the loop-1 was observed. This initial binding stage was also demonstrated in a series of MD runs with varying starting orientations of the toxin with respect to the bilayer surface. Apart from the nonspecific long-range electrostatic attraction and hydrophobic match/mismatch factor, several specific lipid-binding sites were identified in CT2. They were shown to promote membrane insertion by engaging in strong interactions with lipid head groups, fine-tuning the toxin-membrane accommodation. We therefore propose that the toxin insertion relies on the interplay of nonspecific and specific interactions, which are determined by the "dynamic molecular portraits" of the two players, the protein and the membrane. The proposed model does not require protein oligomerization for membrane insertion and can be further employed to design MBPs with predetermined properties with regard to particular membrane targets.
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Affiliation(s)
- Anastasia G Konshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Peter V Dubovskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia.,National Research University Higher School of Economics, 20 Myasnitskaya str., Moscow 101000, Russia.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141700, Russia
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20
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Pore-forming proteins: From defense factors to endogenous executors of cell death. Chem Phys Lipids 2020; 234:105026. [PMID: 33309552 DOI: 10.1016/j.chemphyslip.2020.105026] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
Pore-forming proteins (PFPs) and small antimicrobial peptides (AMPs) represent a large family of molecules with the common ability to punch holes in cell membranes to alter their permeability. They play a fundamental role as infectious bacteria's defensive tools against host's immune system and as executors of endogenous machineries of regulated cell death in eukaryotic cells. Despite being highly divergent in primary sequence and 3D structure, specific folds of pore-forming domains have been conserved. In fact, pore formation is considered an ancient mechanism that takes place through a general multistep process involving: membrane partitioning and insertion, oligomerization and pore formation. However, different PFPs and AMPs assemble and form pores following different mechanisms that could end up either in the formation of protein-lined or protein-lipid pores. In this review, we analyze the current findings in the mechanism of action of different PFPs and AMPs that support a wide role of membrane pore formation in nature. We also provide the newest insights into the development of state-of-art techniques that have facilitated the characterization of membrane pores. To understand the physiological role of these peptides/proteins or develop clinical applications, it is essential to uncover the molecular mechanism of how they perforate membranes.
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21
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Choi KM, Cho DH, Joo MS, Choi HS, Kim MS, Han HJ, Cho MY, Hwang SD, Kim DH, Park CI. Functional characterization and gene expression profile of perforin-2 in starry flounder (Platichthys stellatus). FISH & SHELLFISH IMMUNOLOGY 2020; 107:511-518. [PMID: 33217563 DOI: 10.1016/j.fsi.2020.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
The membrane attack complex/perforin (MACPF) superfamily consists of multifunctional proteins that form pores on the membrane surface of microorganisms to induce their death and have various immune-related functions. PFN2 is a perforin-like protein with an MACPF domain, and humans with deficient PFN2 levels have increased susceptibility to bacterial infection, which can lead to fatal consequences for some patients. Therefore, in this study, we confirmed the antimicrobial function of PFN2 in starry flounder (Platichthys stellatus). The molecular properties were confirmed based on the verified amino acid sequence of PsPFN2. In addition, the expression characteristics of tissue-specific and pathogen-specific PsPFN2 mRNA were also confirmed. The recombinant protein was produced using Escherichia coli, and the antimicrobial activity was then confirmed. The coding sequence of PFN2 (PsPFN2) in P. stellatus consists of 710 residues. The MACPF domain was conserved throughout evolution, as shown by multiple sequence alignment and phylogenetic analysis. PsPFN2 mRNA is abundantly distributed in immune-related organs such as the spleen and gills of healthy starry flounder, and significant expression changes were confirmed after artificial infection by bacteria or viruses. We cloned the MACPF domain region of PFN2 to produce a recombinant protein (rPFN2) and confirmed its antibacterial effect against a wide range of bacterial species and the parasite (Miamiensis avidus).
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Affiliation(s)
- Kwang-Min Choi
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, 455, Tongyeong, 650-160, Republic of Korea
| | - Dong-Hee Cho
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, 455, Tongyeong, 650-160, Republic of Korea
| | - Min-Soo Joo
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, 455, Tongyeong, 650-160, Republic of Korea
| | - Hye-Sung Choi
- Pathology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Myoung Sug Kim
- Pathology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Hyun-Ja Han
- Pathology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Mi Young Cho
- Pathology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Seong Don Hwang
- Pathology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, 45, Yongso-ro, Nam-Gu., Busan, Republic of Korea.
| | - Chan-Il Park
- Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University, 455, Tongyeong, 650-160, Republic of Korea.
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22
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Functional and Structural Variation among Sticholysins, Pore-Forming Proteins from the Sea Anemone Stichodactyla helianthus. Int J Mol Sci 2020; 21:ijms21238915. [PMID: 33255441 PMCID: PMC7727798 DOI: 10.3390/ijms21238915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022] Open
Abstract
Venoms constitute complex mixtures of many different molecules arising from evolution in processes driven by continuous prey-predator interactions. One of the most common compounds in these venomous cocktails are pore-forming proteins, a family of toxins whose activity relies on the disruption of the plasmatic membranes by forming pores. The venom of sea anemones, belonging to the oldest lineage of venomous animals, contains a large amount of a characteristic group of pore-forming proteins known as actinoporins. They bind specifically to sphingomyelin-containing membranes and suffer a conformational metamorphosis that drives them to make pores. This event usually leads cells to death by osmotic shock. Sticholysins are the actinoporins produced by Stichodactyla helianthus. Three different isotoxins are known: Sticholysins I, II, and III. They share very similar amino acid sequence and three-dimensional structure but display different behavior in terms of lytic activity and ability to interact with cholesterol, an important lipid component of vertebrate membranes. In addition, sticholysins can act in synergy when exerting their toxin action. The subtle, but important, molecular nuances that explain their different behavior are described and discussed throughout the text. Improving our knowledge about sticholysins behavior is important for eventually developing them into biotechnological tools.
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23
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Rivera-de-Torre E, Palacios-Ortega J, Garb JE, Slotte JP, Gavilanes JG, Martínez-Del-Pozo Á. Structural and functional characterization of sticholysin III: A newly discovered actinoporin within the venom of the sea anemone Stichodactyla helianthus. Arch Biochem Biophys 2020; 689:108435. [PMID: 32485153 DOI: 10.1016/j.abb.2020.108435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 01/19/2023]
Abstract
Actinoporins are a family of pore-forming toxins produced by sea anemones as part of their venomous cocktail. These proteins remain soluble and stably folded in aqueous solution, but when interacting with sphingomyelin-containing lipid membranes, they become integral oligomeric membrane structures that form a pore permeable to cations, which leads to cell death by osmotic shock. Actinoporins appear as multigenic families within the genome of sea anemones: several genes encoding very similar actinoporins are detected within the same species. The Caribbean Sea anemone Stichodactyla helianthus produces three actinoporins (sticholysins I, II and III; StnI, StnII and StnIII) that differ in their toxic potency. For example, StnII is about four-fold more effective than StnI against sheep erythrocytes in causing hemolysis, and both show synergy. However, StnIII, recently discovered in the S. helianthus transcriptome, has not been characterized so far. Here we describe StnIII's spectroscopic and functional properties and show its potential to interact with the other Stns. StnIII seems to maintain the well-preserved fold of all actinoporins, characterized by a high content of β-sheet, but it is significantly less thermostable. Its functional characterization shows that the critical concentration needed to form active pores is higher than for either StnI or StnII, suggesting differences in behavior when oligomerizing on membrane surfaces. Our results show that StnIII is an interesting and unexpected piece in the puzzle of how this Caribbean Sea anemone species modulates its venomous activity.
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Affiliation(s)
- Esperanza Rivera-de-Torre
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland; Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Juan Palacios-Ortega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain; Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - José G Gavilanes
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Álvaro Martínez-Del-Pozo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain.
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24
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Liposomal membrane permeability assessment by fluorescence techniques: Main permeabilizing agents, applications and challenges. Int J Pharm 2020; 580:119198. [PMID: 32169353 DOI: 10.1016/j.ijpharm.2020.119198] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/19/2020] [Accepted: 03/02/2020] [Indexed: 01/08/2023]
Abstract
Liposomes are lipid vesicles made of one or multiple lipid bilayers surrounding an internal aqueous core. They are broadly employed as models to study membrane structure and properties. Among these properties, liposome membrane permeability is crucial and widely assessed by fluorescence techniques. The first part of this review is devoted to describe the various techniques used for membrane permeability assessment. Attention is paid to fluorescence techniques based on vesicle leakage of self-quenching probes, dye/quencher pair or cation/ligand pair. Secondly, the membrane-active agents inducing membrane permeabilization is presented and details on their mechanisms of action are given. Emphasis is also laid on the intrinsic and extrinsic factors that can modulate the membrane permeability. Hence, a suitable liposomal membrane should be formulated according to the aim of the study and its application.
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25
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Omersa N, Aden S, Kisovec M, Podobnik M, Anderluh G. Design of Protein Logic Gate System Operating on Lipid Membranes. ACS Synth Biol 2020; 9:316-328. [PMID: 31995709 PMCID: PMC7308068 DOI: 10.1021/acssynbio.9b00340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Lipid membranes are becoming increasingly popular in synthetic biology due to their biophysical properties and crucial role in communication between different compartments. Several alluring protein-membrane sensors have already been developed, whereas protein logic gates designs on membrane-embedded proteins are very limited. Here we demonstrate the construction of a two-level protein-membrane logic gate with an OR-AND logic. The system consists of an engineered pH-dependent pore-forming protein listeriolysin O and its DARPin-based inhibitor, conjugated to a lipid vesicle membrane. The gate responds to low pH and removal of the inhibitor from the membrane either by switching to a reducing environment, protease cleavage, or any other signal depending on the conjugation chemistry used for inhibitor attachment to the membrane. This unique protein logic gate vesicle system advances generic sensing and actuator platforms used in synthetic biology and could be utilized in drug delivery.
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Affiliation(s)
- Neža Omersa
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Saša Aden
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Matic Kisovec
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
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26
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Šakanović A, Kranjc N, Omersa N, Podobnik M, Anderluh G. More than one way to bind to cholesterol: atypical variants of membrane-binding domain of perfringolysin O selected by ribosome display. RSC Adv 2020; 10:38678-38682. [PMID: 35517550 PMCID: PMC9057304 DOI: 10.1039/d0ra06976k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 11/25/2022] Open
Abstract
Herein, we report a high-throughput approach for the selection of peripheral protein domains that bind specifically to cholesterol in lipid membranes. We discovered variants of perfringolysin O, with non-conserved amino acid substitutions at regions crucial for cholesterol recognition, demonstrating an unprecedented amino acid sequence variability with binding ability for cholesterol. The developed approach provides an effective platform for a comprehensive study of protein lipid interactions. By using developed ribosomal display, we discovered variants of perfringolysin O, a pore forming toxin from bacteria Clostridium perfringens, with non-conserved amino acid substitutions at regions crucial for cholesterol recognition.![]()
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Affiliation(s)
- Aleksandra Šakanović
- Department of Molecular Biology and Nanobiotechnology
- National Institute of Chemistry
- Ljubljana
- Slovenia
- Biosciences Doctoral Program
| | - Nace Kranjc
- Department of Molecular Biology and Nanobiotechnology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology
- National Institute of Chemistry
- Ljubljana
- Slovenia
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27
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Huang Y, Soliakov A, Le Brun AP, Macdonald C, Johnson CL, Solovyova AS, Waller H, Moore GR, Lakey JH. Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A. Biochemistry 2019; 58:4882-4892. [PMID: 31686499 PMCID: PMC6899464 DOI: 10.1021/acs.biochem.9b00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/31/2019] [Indexed: 11/28/2022]
Abstract
Numerous bacterial toxins and other virulence factors use low pH as a trigger to convert from water-soluble to membrane-inserted states. In the case of colicins, the pore-forming domain of colicin A (ColA-P) has been shown both to undergo a clear acidic unfolding transition and to require acidic lipids in the cytoplasmic membrane, whereas its close homologue colicin N shows neither behavior. Compared to that of ColN-P, the ColA-P primary structure reveals the replacement of several uncharged residues with aspartyl residues, which upon replacement with alanine induce an unfolded state at neutral pH. Here we investigate ColA-P's structural requirement for these critical aspartyl residues that are largely situated at the N-termini of α helices. As previously shown in model peptides, the charged carboxylate side chain can act as a stabilizing helix N-Cap group by interacting with free amide hydrogen bond donors. Because this could explain ColA-P destabilization when the aspartyl residues are protonated or replaced with alanyl residues, we test the hypothesis by inserting asparagine, glutamine, and glutamate residues at these sites. We combine urea (fluorescence and circular dichroism) and thermal (circular dichroism and differential scanning calorimetry) denaturation experiments with 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy of ColA-P at different pH values to provide a comprehensive description of the unfolding process and confirm the N-Cap hypothesis. Furthermore, we reveal that, in urea, the single domain ColA-P unfolds in two steps; low pH destabilizes the first step and stabilizes the second.
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Affiliation(s)
- Yan Huang
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, People’s Republic of China
| | - Andrei Soliakov
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Anton P. Le Brun
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- Australian
Centre for Neutron Scattering, Australian
Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia
| | - Colin Macdonald
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Christopher L. Johnson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Helen Waller
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Geoffrey R. Moore
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
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28
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Omersa N, Podobnik M, Anderluh G. Inhibition of Pore-Forming Proteins. Toxins (Basel) 2019; 11:E545. [PMID: 31546810 PMCID: PMC6784129 DOI: 10.3390/toxins11090545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022] Open
Abstract
Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.
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Affiliation(s)
- Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Marjetka Podobnik
- 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.
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29
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Pore-Forming Proteins from Cnidarians and Arachnids as Potential Biotechnological Tools. Toxins (Basel) 2019; 11:toxins11060370. [PMID: 31242582 PMCID: PMC6628452 DOI: 10.3390/toxins11060370] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022] Open
Abstract
Animal venoms are complex mixtures of highly specialized toxic molecules. Cnidarians and arachnids produce pore-forming proteins (PFPs) directed against the plasma membrane of their target cells. Among PFPs from cnidarians, actinoporins stand out for their small size and molecular simplicity. While native actinoporins require only sphingomyelin for membrane binding, engineered chimeras containing a recognition antibody-derived domain fused to an actinoporin isoform can nonetheless serve as highly specific immunotoxins. Examples of such constructs targeted against malignant cells have been already reported. However, PFPs from arachnid venoms are less well-studied from a structural and functional point of view. Spiders from the Latrodectus genus are professional insect hunters that, as part of their toxic arsenal, produce large PFPs known as latrotoxins. Interestingly, some latrotoxins have been identified as potent and highly-specific insecticides. Given the proteinaceous nature of these toxins, their promising future use as efficient bioinsecticides is discussed throughout this Perspective. Protein engineering and large-scale recombinant production are critical steps for the use of these PFPs as tools to control agriculturally important insect pests. In summary, both families of PFPs, from Cnidaria and Arachnida, appear to be molecules with promising biotechnological applications.
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30
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Pang Y, Gou M, Yang K, Lu J, Han Y, Teng H, Li C, Wang H, Liu C, Zhang K, Yang Y, Li Q. Crystal structure of a cytocidal protein from lamprey and its mechanism of action in the selective killing of cancer cells. Cell Commun Signal 2019; 17:54. [PMID: 31133022 PMCID: PMC6537362 DOI: 10.1186/s12964-019-0358-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background In previous research, we found that lamprey immune protein (LIP) possessed cytocidal activity against tumor cells, but the mechanism of the selective recognition and killing of tumor cells by LIP was not identified. Methods Superresolution microscopy, crystallographic structural analysis, glycan chip assay, SPR experiments, FACS assays, computational studies and mass spectrometric analysis firmly establish the mode of action of LIP, which involves dual selective recognition and efficient binding. Results We determined the overall crystallographic structure of LIP at a resolution of 2.25 Å. LIP exhibits an elongated structure with dimensions of 105 Å × 30 Å × 30 Å containing an N-terminal lectin module and a C-terminal aerolysin module. Moreover, the Phe209-Gly232 region is predicted to insert into the lipid bilayer to form a transmembrane β-barrel, in which the hydrophobic residues face the lipid bilayer, and the polar residues constitute the hydrophilic lumen of the pore. We found that LIP is able to kill various human cancer cells with minimal effects on normal cells. Notably, by coupling biochemical and computational studies, we propose a hypothetical mechanism that involves dual selective recognition and efficient binding dependent on both N-linked glycans on GPI-anchored proteins (GPI-APs) and sphingomyelin (SM) in lipid rafts. Furthermore, specific binding of the lectin module with biantennary bisialylated nonfucosylated N-glycan or sialyl Lewis X-containing glycan structures on GPI-APs triggers substantial conformational changes in the aerolysin module, which interacts with SM, ultimately resulting in the formation of a membrane-bound oligomer in lipid rafts. Conclusions LIP holds great potential for the application of a marine protein towards targeted cancer therapy and early diagnosis in humans. Electronic supplementary material The online version of this article (10.1186/s12964-019-0358-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Kai Yang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Jiali Lu
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Hongming Teng
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Changzhi Li
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Haina Wang
- Center for Molecular Medicine, School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116023, China
| | - Caigang Liu
- Department of Breast Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Kejia Zhang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China.,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China
| | - Yongliang Yang
- Center for Molecular Medicine, School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116023, China.
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, 116081, China. .,Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.
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31
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Yap WY, Hwang JS. Response of Cellular Innate Immunity to Cnidarian Pore-Forming Toxins. Molecules 2018; 23:E2537. [PMID: 30287801 PMCID: PMC6222686 DOI: 10.3390/molecules23102537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
A group of stable, water-soluble and membrane-bound proteins constitute the pore forming toxins (PFTs) in cnidarians. They interact with membranes to physically alter the membrane structure and permeability, resulting in the formation of pores. These lesions on the plasma membrane causes an imbalance of cellular ionic gradients, resulting in swelling of the cell and eventually its rupture. Of all cnidarian PFTs, actinoporins are by far the best studied subgroup with established knowledge of their molecular structure and their mode of pore-forming action. However, the current view of necrotic action by actinoporins may not be the only mechanism that induces cell death since there is increasing evidence showing that pore-forming toxins can induce either necrosis or apoptosis in a cell-type, receptor and dose-dependent manner. In this review, we focus on the response of the cellular immune system to the cnidarian pore-forming toxins and the signaling pathways that might be involved in these cellular responses. Since PFTs represent potential candidates for targeted toxin therapy for the treatment of numerous cancers, we also address the challenge to overcoming the immunogenicity of these toxins when used as therapeutics.
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Affiliation(s)
- Wei Yuen Yap
- Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Jung Shan Hwang
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
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32
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Boyd CM, Bubeck D. Advances in cryoEM and its impact on β-pore forming proteins. Curr Opin Struct Biol 2018; 52:41-49. [PMID: 30125772 PMCID: PMC6302071 DOI: 10.1016/j.sbi.2018.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 01/04/2023]
Abstract
Deployed by both hosts and pathogens, β-pore-forming proteins (β-PFPs) rupture membranes and lyse target cells. Soluble protein monomers oligomerize on the lipid bilayer where they undergo dramatic structural rearrangements, resulting in a transmembrane β-barrel pore. Advances in electron cryo-microscopy (cryoEM) sample preparation, image detection, and computational algorithms have led to a number of recent structures that reveal a molecular mechanism of pore formation in atomic detail.
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Affiliation(s)
- Courtney M Boyd
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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33
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Kozorog M, Sani M, Separovic F, Anderluh G. Listeriolysin O Binding Affects Cholesterol and Phospholipid Acyl Chain Dynamics in Fluid Cholesterol‐Rich Bilayers. Chemistry 2018; 24:14220-14225. [DOI: 10.1002/chem.201802575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Mirijam Kozorog
- Department of Molecular Biology and NanobiotechnologyNational Institute of Chemistry Hajdrihova 19 1000 Ljubljana Slovenia
| | - Marc‐Antoine Sani
- School of ChemistryBio21 InstituteThe University of Melbourne VIC 3010 Australia
| | - Frances Separovic
- School of ChemistryBio21 InstituteThe University of Melbourne VIC 3010 Australia
| | - Gregor Anderluh
- Department of Molecular Biology and NanobiotechnologyNational Institute of Chemistry Hajdrihova 19 1000 Ljubljana Slovenia
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34
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Leychenko E, Isaeva M, Tkacheva E, Zelepuga E, Kvetkina A, Guzev K, Monastyrnaya M, Kozlovskaya E. Multigene Family of Pore-Forming Toxins from Sea Anemone Heteractis crispa. Mar Drugs 2018; 16:E183. [PMID: 29794988 PMCID: PMC6025637 DOI: 10.3390/md16060183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/23/2022] Open
Abstract
Sea anemones produce pore-forming toxins, actinoporins, which are interesting as tools for cytoplasmic membranes study, as well as being potential therapeutic agents for cancer therapy. This investigation is devoted to structural and functional study of the Heteractis crispa actinoporins diversity. Here, we described a multigene family consisting of 47 representatives expressed in the sea anemone tentacles as prepropeptide-coding transcripts. The phylogenetic analysis revealed that actinoporin clustering is consistent with the division of sea anemones into superfamilies and families. The transcriptomes of both H. crispa and Heteractis magnifica appear to contain a large repertoire of similar genes representing a rapid expansion of the actinoporin family due to gene duplication and sequence divergence. The presence of the most abundant specific group of actinoporins in H. crispa is the major difference between these species. The functional analysis of six recombinant actinoporins revealed that H. crispa actinoporin grouping was consistent with the different hemolytic activity of their representatives. According to molecular modeling data, we assume that the direction of the N-terminal dipole moment tightly reflects the actinoporins' ability to possess hemolytic activity.
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Affiliation(s)
- Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
- School of Natural Sciences, Far Eastern Federal University, Sukhanova Street 8, Vladivostok 690091, Russia.
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
- School of Natural Sciences, Far Eastern Federal University, Sukhanova Street 8, Vladivostok 690091, Russia.
| | - Ekaterina Tkacheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Elena Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Aleksandra Kvetkina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Konstantin Guzev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Margarita Monastyrnaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
| | - Emma Kozlovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia.
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35
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Podobnik M, Kisovec M, Anderluh G. Molecular mechanism of pore formation by aerolysin-like proteins. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630149 DOI: 10.1098/rstb.2016.0209] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aerolysin-like pore-forming proteins are an important family of proteins able to efficiently damage membranes of target cells by forming transmembrane pores. They are characterized by a unique domain organization and mechanism of action that involves extensive conformational rearrangements. Although structures of soluble forms of many different members of this family are well understood, the structures of pores and their mechanism of assembly have been described only recently. The pores are characterized by well-defined β-barrels, which are devoid of any vestibular regions commonly found in other protein pores. Many members of this family are bacterial toxins; therefore, structural details of their transmembrane pores, as well as the mechanism of pore formation, are an important base for future drug design. Stability of pores and other properties, such as specificity for some cell surface molecules, make this family of proteins a useful set of molecular tools for molecular recognition and sensing in cell biology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Matic Kisovec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
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36
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Tanaka K, Caaveiro JMM, Morante K, Tsumoto K. Haemolytic actinoporins interact with carbohydrates using their lipid-binding module. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630155 DOI: 10.1098/rstb.2016.0216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pore-forming toxins (PFTs) are proteins endowed with metamorphic properties that enable them to stably fold in water solutions as well as in cellular membranes. PFTs produce lytic pores on the plasma membranes of target cells conducive to lesions, playing key roles in the defensive and offensive molecular systems of living organisms. Actinoporins are a family of potent haemolytic toxins produced by sea anemones vigorously studied as a paradigm of α-helical PFTs, in the context of lipid-protein interactions, and in connection with nanopore technologies. We have recently reported that fragaceatoxin C (FraC), an actinoporin, engages biological membranes with a large adhesive motif allowing the simultaneous attachment of up to four lipid molecules prior to pore formation. Since actinoporins also interact with carbohydrates, we sought to understand the molecular and energetic basis of glycan recognition by FraC. By employing structural and biophysical methodologies, we show that FraC engages glycans with low affinity using its lipid-binding module. Contrary to other PFTs requiring separate domains for glycan and lipid recognition, the small single-domain actinoporins economize resources by achieving dual recognition with a single binding module. This mechanism could enhance the recruitment of actinoporins to the surface of target tissues in their marine environment.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Koji Tanaka
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Koldo Morante
- Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan .,Department of Bioengineering, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
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Rezelj S, Kozorog M, Švigelj T, Ulrih NP, Žnidaršič N, Podobnik M, Anderluh G. Cholesterol Enriched Archaeosomes as a Molecular System for Studying Interactions of Cholesterol-Dependent Cytolysins with Membranes. J Membr Biol 2018; 251:491-505. [DOI: 10.1007/s00232-018-0018-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/05/2018] [Indexed: 12/31/2022]
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38
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Lenarčič T, Albert I, Böhm H, Hodnik V, Pirc K, Zavec AB, Podobnik M, Pahovnik D, Žagar E, Pruitt R, Greimel P, Yamaji-Hasegawa A, Kobayashi T, Zienkiewicz A, Gömann J, Mortimer JC, Fang L, Mamode-Cassim A, Deleu M, Lins L, Oecking C, Feussner I, Mongrand S, Anderluh G, Nürnberger T. Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins. Science 2018; 358:1431-1434. [PMID: 29242345 DOI: 10.1126/science.aan6874] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/31/2017] [Indexed: 01/05/2023]
Abstract
Necrosis and ethylene-inducing peptide 1-like (NLP) proteins constitute a superfamily of proteins produced by plant pathogenic bacteria, fungi, and oomycetes. Many NLPs are cytotoxins that facilitate microbial infection of eudicot, but not of monocot plants. Here, we report glycosylinositol phosphorylceramide (GIPC) sphingolipids as NLP toxin receptors. Plant mutants with altered GIPC composition were more resistant to NLP toxins. Binding studies and x-ray crystallography showed that NLPs form complexes with terminal monomeric hexose moieties of GIPCs that result in conformational changes within the toxin. Insensitivity to NLP cytolysins of monocot plants may be explained by the length of the GIPC head group and the architecture of the NLP sugar-binding site. We unveil early steps in NLP cytolysin action that determine plant clade-specific toxin selectivity.
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Affiliation(s)
- Tea Lenarčič
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Isabell Albert
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Hannah Böhm
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vesna Hodnik
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Katja Pirc
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Apolonija B Zavec
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Rory Pruitt
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Peter Greimel
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Akiko Yamaji-Hasegawa
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,Molecular Membrane Neuroscience, Brain Science Institute, RIKEN Institute, Wako, Saitama 351-0198, Japan
| | - Toshihide Kobayashi
- Lipid Biology Laboratory, RIKEN, Wako Saitama 351-0198, Japan.,UMR 7213 CNRS, University of Strasbourg, 67401 Illkirch, France
| | - Agnieszka Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Jasmin Gömann
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Jenny C Mortimer
- Joint Bioenergy Institute, Emeryville, CA 94608, USA.,Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lin Fang
- Joint Bioenergy Institute, Emeryville, CA 94608, USA.,Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adiilah Mamode-Cassim
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS-Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave-d'Ornon Cedex, France
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, University of Liège, Gembloux, Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, University of Liège, Gembloux, Belgium
| | - Claudia Oecking
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Germany.,Göttingen Center for Molecular Biosciences, University of Göttingen, Germany
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire, UMR 5200 CNRS-Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave-d'Ornon Cedex, France
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Thorsten Nürnberger
- Centre of Plant Molecular Biology, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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Largo E, Gladue DP, Torralba J, Aguilella VM, Alcaraz A, Borca MV, Nieva JL. Mutation-induced changes of transmembrane pore size revealed by combined ion-channel conductance and single vesicle permeabilization analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1015-1021. [PMID: 29317201 DOI: 10.1016/j.bbamem.2018.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Permeabilization of the Endoplasmic Reticulum (ER) is instrumental in the progression of host-cell infection by many viral pathogens. We have described that permeabilization of ER model membranes by the pore-forming domain of the Classical Swine Fever Virus (CSFV) p7 protein depends on two sequence determinants: the C-terminal transmembrane helix, and the preceding polar loop that regulates its activity. Here, by combining ion-channel activity measurements in planar lipid bilayers with imaging of single Giant Unilamellar Vesicles (GUVs), we demonstrate that point substitutions directed to conserved residues within these regions affect ER-like membrane permeabilization following distinct mechanisms. Whereas the polar loop appeared to be involved in protein insertion and oligomerization, substitution of residues predicted to face the lumen of the pore inhibited large conducting channels (>1 nS) over smaller ones (120 pS). Quantitative analyses of the ER-GUV distribution as a function of the solute size revealed a selective inhibition for the permeation of solutes with sizes larger than 4 kDa, further demonstrating that the mutation targeting the transmembrane helix prevented formation of the large pores. Collectively, our data support the idea that the pore-forming domain of p7 may assemble into finite pores with approximate diameters of 1 and 5 nm. Moreover, the observation that the mutation interfering with formation of the larger pores can hamper virus production without affecting ER localization or homo-oligomerization, suggests prospective strategies to block/attenuate pestiviruses.
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Affiliation(s)
- Eneko Largo
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Douglas P Gladue
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - Johana Torralba
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Vicente M Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Manuel V Borca
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain.
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40
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Pore-forming toxins in Cnidaria. Semin Cell Dev Biol 2017; 72:133-141. [DOI: 10.1016/j.semcdb.2017.07.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023]
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41
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Moreno-Hagelsieb G, Vitug B, Medrano-Soto A, Saier MH. The Membrane Attack Complex/Perforin Superfamily. J Mol Microbiol Biotechnol 2017; 27:252-267. [PMID: 29145176 DOI: 10.1159/000481286] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022] Open
Abstract
The membrane attack complex/perforin (MACPF) superfamily consists of a diverse group of proteins involved in bacterial pathogenesis and sporulation as well as eukaryotic immunity, embryonic development, neural migration and fruiting body formation. The present work shows that the evolutionary relationships between the members of the superfamily, previously suggested by comparison of their tertiary structures, can also be supported by analyses of their primary structures. The superfamily includes the MACPF family (TC 1.C.39), the cholesterol-dependent cytolysin (CDC) family (TC 1.C.12.1 and 1.C.12.2) and the pleurotolysin pore-forming (pleurotolysin B) family (TC 1.C.97.1), as revealed by expansion of each family by comparison against a large protein database, and by the comparisons of their hidden Markov models. Clustering analyses demonstrated grouping of the CDC homologues separately from the 12 MACPF subfamilies, which also grouped separately from the pleurotolysin B family. Members of the MACPF superfamily revealed a remarkably diverse range of proteins spanning eukaryotic, bacterial, and archaeal taxonomic domains, with notable variations in protein domain architectures. Our strategy should also be helpful in putting together other highly divergent protein families.
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Abstract
Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor. Molecular dynamics simulation further suggested which other amino acid residues may also allosterically influence the pH-sensor. LLO was engineered to the point where it can, in a pH-regulated manner, perforate artificial and cellular membranes. The single mutant Tyr406Ala bound to membranes and oligomerized similarly to the wild-type LLO, however, the final membrane insertion step was pH-affected by the introduced mutation. We show that the mutant toxin can be activated at the surface of artificial membranes or living cells by a single wash with slightly acidic pH buffer. Y406A mutant has a high potential in development of novel nanobiotechnological applications such as controlled release of substances or as a sensor of environmental pH.
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43
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García-Linares S, Rivera-de-Torre E, Palacios-Ortega J, Gavilanes JG, Martínez-del-Pozo Á. The Metamorphic Transformation of a Water-Soluble Monomeric Protein Into an Oligomeric Transmembrane Pore. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2017. [DOI: 10.1016/bs.abl.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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44
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Baumann A, Jorge-Finnigan A, Jung-Kc K, Sauter A, Horvath I, Morozova-Roche LA, Martinez A. Tyrosine Hydroxylase Binding to Phospholipid Membranes Prompts Its Amyloid Aggregation and Compromises Bilayer Integrity. Sci Rep 2016; 6:39488. [PMID: 28004763 PMCID: PMC5177901 DOI: 10.1038/srep39488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/21/2016] [Indexed: 12/14/2022] Open
Abstract
Tyrosine hydroxylase (TH), a rate-limiting enzyme in the synthesis of catecholamine neurotransmitters and hormones, binds to negatively charged phospholipid membranes. Binding to both large and giant unilamellar vesicles causes membrane permeabilization, as observed by efflux and influx of fluorescence dyes. Whereas the initial protein-membrane interaction involves the N-terminal tail that constitutes an extension of the regulatory ACT-domain, prolonged membrane binding induces misfolding and self-oligomerization of TH over time as shown by circular dichroism and Thioflavin T fluorescence. The gradual amyloid-like aggregation likely occurs through cross-β interactions involving aggregation-prone motives in the catalytic domains, consistent with the formation of chain and ring-like protofilaments observed by atomic force microscopy in monolayer-bound TH. PC12 cells treated with the neurotoxin 6-hydroxydopamine displayed increased TH levels in the mitochondrial fraction, while incubation of isolated mitochondria with TH led to a decrease in the mitochondrial membrane potential. Furthermore, cell-substrate impedance and viability assays showed that supplementing the culture media with TH compromises cell viability over time. Our results revealed that the disruptive effect of TH on cell membranes may be a cytotoxic and pathogenic factor if the regulation and intracellular stability of TH is compromised.
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Affiliation(s)
- Anne Baumann
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,Division of Psychiatry, Haukeland University Hospital, 5021 Bergen, Norway
| | - Ana Jorge-Finnigan
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5009 Bergen, Norway
| | - Kunwar Jung-Kc
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Alexander Sauter
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,Department of Clinical Dentistry, University of Bergen, 5009 Bergen, Norway
| | - Istvan Horvath
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | - Aurora Martinez
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,K.G. Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5009 Bergen, Norway
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Boyd CM, Parsons ES, Smith RAG, Seddon JM, Ces O, Bubeck D. Disentangling the roles of cholesterol and CD59 in intermedilysin pore formation. Sci Rep 2016; 6:38446. [PMID: 27910935 PMCID: PMC5133593 DOI: 10.1038/srep38446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/08/2016] [Indexed: 01/08/2023] Open
Abstract
The plasma membrane provides an essential barrier, shielding a cell from the pressures of its external environment. Pore-forming proteins, deployed by both hosts and pathogens alike, breach this barrier to lyse target cells. Intermedilysin is a cholesterol-dependent cytolysin that requires the human immune receptor CD59, in addition to cholesterol, to form giant β-barrel pores in host membranes. Here we integrate biochemical assays with electron microscopy and atomic force microscopy to distinguish the roles of these two receptors in mediating structural transitions of pore formation. CD59 is required for the specific coordination of intermedilysin (ILY) monomers and for triggering collapse of an oligomeric prepore. Movement of Domain 2 with respect to Domain 3 of ILY is essential for forming a late prepore intermediate that releases CD59, while the role of cholesterol may be limited to insertion of the transmembrane segments. Together these data define a structural timeline for ILY pore formation and suggest a mechanism that is relevant to understanding other pore-forming toxins that also require CD59.
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Affiliation(s)
- Courtney M. Boyd
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London SW7 2AZ, UK
| | - Edward S. Parsons
- Department of Chemistry and Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | - Richard A. G. Smith
- MRC Centre for Transplantation, King’s College London, 5th Floor Tower Wing, Guys’ Hospital, London SE1 9RT, UK
| | - John M. Seddon
- Department of Chemistry and Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
| | - Oscar Ces
- Department of Chemistry and Institute of Chemical Biology, 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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Morante K, Bellomio A, Gil-Cartón D, Redondo-Morata L, Sot J, Scheuring S, Valle M, González-Mañas JM, Tsumoto K, Caaveiro JMM. Identification of a Membrane-bound Prepore Species Clarifies the Lytic Mechanism of Actinoporins. J Biol Chem 2016; 291:19210-19219. [PMID: 27445331 PMCID: PMC5016661 DOI: 10.1074/jbc.m116.734053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 11/06/2022] Open
Abstract
Pore-forming toxins (PFTs) are cytolytic proteins belonging to the molecular warfare apparatus of living organisms. The assembly of the functional transmembrane pore requires several intermediate steps ranging from a water-soluble monomeric species to the multimeric ensemble inserted in the cell membrane. The non-lytic oligomeric intermediate known as prepore plays an essential role in the mechanism of insertion of the class of β-PFTs. However, in the class of α-PFTs, like the actinoporins produced by sea anemones, evidence of membrane-bound prepores is still lacking. We have employed single-particle cryo-electron microscopy (cryo-EM) and atomic force microscopy to identify, for the first time, a prepore species of the actinoporin fragaceatoxin C bound to lipid vesicles. The size of the prepore coincides with that of the functional pore, except for the transmembrane region, which is absent in the prepore. Biochemical assays indicated that, in the prepore species, the N terminus is not inserted in the bilayer but is exposed to the aqueous solution. Our study reveals the structure of the prepore in actinoporins and highlights the role of structural intermediates for the formation of cytolytic pores by an α-PFT.
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Affiliation(s)
- Koldo Morante
- From the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,the Department of Biochemistry and Molecular Biology and.,Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, P. O. Box 644, 48080 Bilbao, Spain
| | - Augusto Bellomio
- the Department of Biochemistry and Molecular Biology and.,Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, P. O. Box 644, 48080 Bilbao, Spain
| | - David Gil-Cartón
- the Structural Biology Unit, Center for Cooperative Research in Biosciences, CICbiogune, 48160 Derio, Spain
| | - Lorena Redondo-Morata
- the U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France, and
| | - Jesús Sot
- the Department of Biochemistry and Molecular Biology and.,Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country, P. O. Box 644, 48080 Bilbao, Spain
| | - Simon Scheuring
- the U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France, and
| | - Mikel Valle
- the Structural Biology Unit, Center for Cooperative Research in Biosciences, CICbiogune, 48160 Derio, Spain
| | | | - Kouhei Tsumoto
- From the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan, .,the Institute of Medical Science, University of Tokyo, Minato-ku, 108-8639 Tokyo, Japan
| | - Jose M M Caaveiro
- From the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan,
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47
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Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly. Nat Commun 2016; 7:11598. [PMID: 27176125 PMCID: PMC4865846 DOI: 10.1038/ncomms11598] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/11/2016] [Indexed: 01/01/2023] Open
Abstract
The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly mechanism. The lysenin pore is assembled from nine monomers via dramatic reorganization of almost half of the monomeric subunit structure leading to a β-barrel pore ∼10 nm long and 1.6–2.5 nm wide. The lysenin pore is devoid of additional luminal compartments as commonly found in other toxin pores. Mutagenic analysis and atomic force microscopy imaging, together with these structural insights, suggest a mechanism for pore assembly for lysenin. These insights are relevant to the understanding of pore formation by other aerolysin-like pore-forming toxins, which often represent crucial virulence factors in bacteria. Pore-forming toxins act by forming oligomeric pores in lipid membranes. Here the authors report the crystal structure of the lysenin pore, providing insights into the assembly and function of the pore in addition to suggesting that its properties make lysenin potentially well-suited for nanopore sensing applications.
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48
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Ruan Y, Rezelj S, Bedina Zavec A, Anderluh G, Scheuring S. Listeriolysin O Membrane Damaging Activity Involves Arc Formation and Lineaction -- Implication for Listeria monocytogenes Escape from Phagocytic Vacuole. PLoS Pathog 2016; 12:e1005597. [PMID: 27104344 PMCID: PMC4841516 DOI: 10.1371/journal.ppat.1005597] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/04/2016] [Indexed: 12/15/2022] Open
Abstract
Listeriolysin-O (LLO) plays a crucial role during infection by Listeria monocytogenes. It enables escape of bacteria from phagocytic vacuole, which is the basis for its spread to other cells and tissues. It is not clear how LLO acts at phagosomal membranes to allow bacterial escape. The mechanism of action of LLO remains poorly understood, probably due to unavailability of suitable experimental tools that could monitor LLO membrane disruptive activity in real time. Here, we used high-speed atomic force microscopy (HS-AFM) featuring high spatio-temporal resolution on model membranes and optical microscopy on giant unilamellar vesicles (GUVs) to investigate LLO activity. We analyze the assembly kinetics of toxin oligomers, the prepore-to-pore transition dynamics and the membrane disruption in real time. We reveal that LLO toxin efficiency and mode of action as a membrane-disrupting agent varies strongly depending on the membrane cholesterol concentration and the environmental pH. We discovered that LLO is able to form arc pores as well as damage lipid membranes as a lineactant, and this leads to large-scale membrane defects. These results altogether provide a mechanistic basis of how large-scale membrane disruption leads to release of Listeria from the phagocytic vacuole in the cellular context.
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Affiliation(s)
- Yi Ruan
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Saša Rezelj
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Apolonija Bedina Zavec
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail: (SS); (GA)
| | - Simon Scheuring
- U1006 INSERM, Université Aix-Marseille, Parc Scientifique et Technologique de Luminy, Marseille, France
- * E-mail: (SS); (GA)
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49
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Wacklin HP, Bremec BB, Moulin M, Rojko N, Haertlein M, Forsyth T, Anderluh G, Norton RS. Neutron reflection study of the interaction of the eukaryotic pore-forming actinoporin equinatoxin II with lipid membranes reveals intermediate states in pore formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:640-52. [DOI: 10.1016/j.bbamem.2015.12.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 11/02/2015] [Accepted: 12/15/2015] [Indexed: 01/07/2023]
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50
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Weber DK, Yao S, Rojko N, Anderluh G, Lybrand TP, Downton MT, Wagner J, Separovic F. Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation. Biophys J 2016; 108:1987-96. [PMID: 25902438 DOI: 10.1016/j.bpj.2015.03.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 12/26/2022] Open
Abstract
Equinatoxin II (EqtII) is a soluble, 20 kDa pore-forming protein toxin isolated from the sea anemone Actinia equina. Although pore formation has long been known to occur in distinct stages, including monomeric attachment to phospholipid membranes followed by detachment of the N-terminal helical domain and oligomerization into the final pore assembly, atomistic-level detail of the protein-lipid interactions underlying these events remains elusive. Using high-resolution solution state NMR of uniformly-(15)N-labeled EqtII at the critical micelle concentration of dodecylphosphocholine, we have mapped the lipid-binding site through chemical shift perturbations. Subsequent docking of an EqtII monomer onto a dodecylphosphocholine micelle, followed by 400 ns of all-atom molecular dynamics simulation, saw several high-occupancy lipid-binding pockets stabilized by cation-π, hydrogen bonding, and hydrophobic interactions; and stabilization of the loop housing the conserved arginine-glycine-aspartate motif. Additional simulation of EqtII with an N-acetyl sphingomyelin micelle, for which high-resolution NMR data cannot be obtained due to aggregate formation, revealed that sphingomyelin specificity might occur via hydrogen bonding to the 3-OH and 2-NH groups unique to the ceramide backbone by side chains of D109 and Y113; and main chains of P81 and W112. Furthermore, a binding pocket formed by K30, K77, and P81, proximate to the hinge region of the N-terminal helix, was identified and may be implicated in triggering pore formation.
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Affiliation(s)
- Daniel K Weber
- School of Chemistry, University of Melbourne, Victoria, Australia; Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Shenggen Yao
- Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Nejc Rojko
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Terry P Lybrand
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Matthew T Downton
- IBM Research Collaboratory for Life Sciences, Victorian Life Sciences Computation Initiative, University of Melbourne, Victoria, Australia
| | - John Wagner
- IBM Research Collaboratory for Life Sciences, Victorian Life Sciences Computation Initiative, University of Melbourne, Victoria, Australia
| | - Frances Separovic
- School of Chemistry, University of Melbourne, Victoria, Australia; Bio21 Institute, University of Melbourne, Victoria, Australia.
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