1. Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipidsGašper Šolinc, Marija Srnko, Franci Merzel, Ana Crnković, Mirijam Kozorog, Marjetka Podobnik, Gregor Anderluh, 2025, izvirni znanstveni članek Povzetek: The structure and function of membrane proteins depend on their interactions with lipids that constitute membranes. Actinoporins are α-pore-forming proteins that bind preferentially to sphingomyelin-containing membranes, where they oligomerize and form transmembrane pores. Through a comprehensive cryo-electron microscopic analysis of a pore formed by an actinoporin Fav from the coral Orbicella faveolata, we show that the octameric pore interacts with 112 lipids in the upper leaflet of the membrane, reveal the roles of lipids, and demonstrate that the actinoporin surface is suited for binding multiple receptor sphingomyelin molecules. When cholesterol is present in the membrane, it forms a cluster of four molecules associated with each protomer. Atomistic simulations support the structural data and reveal additional effects of the pore on the lipid membrane. These data reveal a complex network of protein-lipid and lipid-lipid interactions and an underrated role of lipids in the structure and function of transmembrane protein complexes.
Objavljeno v DiRROS: 12.05.2025; Ogledov: 66; Prenosov: 33
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2. In vitro evolution driven by epistasis reveals alternative cholesterol-specific binding motifs of perfringolysin OAleksandra Šakanović, Nace Kranjc, Neža Omersa, Saša Aden, Andreja Kežar, Matic Kisovec, Apolonija Bedina Zavec, Simon Caserman, Robert J. Gilbert, Marjetka Podobnik, Ana Crnković, Gregor Anderluh, 2024, izvirni znanstveni članek Objavljeno v DiRROS: 12.09.2024; Ogledov: 535; Prenosov: 701
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3. Sequestration of membrane cholesterol by cholesterol-binding proteins inhibits SARS-CoV-2 entry into Vero E6 cellsMagdalena Kulma, Aleksandra Šakanović, Apolonija Bedina Zavec, Simon Caserman, Neža Omersa, Gašper Šolinc, Sara Orehek, Iva Hafner Bratkovič, Urška Kuhar, Brigita Slavec, Uroš Krapež, Matjaž Ocepek, Toshihide Kobayashi, Katarzyna Kwiatkowska, Roman Jerala, Marjetka Podobnik, Gregor Anderluh, 2024, izvirni znanstveni članek Objavljeno v DiRROS: 05.08.2024; Ogledov: 563; Prenosov: 319
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4. Protein gas vesicles of bacillus megaterium as enhancers of ultrasound-induced transcriptional regulationVid Jazbec, Nina Varda, Ernest Šprager, Maja Meško, Sara Vidmar, Rok Romih, Marjetka Podobnik, Andreja Kežar, Roman Jerala, Mojca Benčina, 2024, izvirni znanstveni članek Objavljeno v DiRROS: 01.08.2024; Ogledov: 689; Prenosov: 450
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5. Structural basis for the multitasking nature of the potato virus Y coat proteinAndreja Kežar, Luka Kavčič, Martin Pólak, Jiři Nováček, Ion Gutiérrez-Aguirre, Magda Tušek-Žnidarič, Anna Coll Rius, Katja Stare, Kristina Gruden, Maja Ravnikar, David Pahovnik, Ema Žagar, Franci Merzel, Gregor Anderluh, Marjetka Podobnik, 2019, izvirni znanstveni članek Povzetek: Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY’s flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA–coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein’s amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
Ključne besede: plant pathogens, potato virus Y, viral RNA
Objavljeno v DiRROS: 23.07.2024; Ogledov: 570; Prenosov: 354
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6. Nanoscale transformations of amphiboles within human alveolar epithelial cellsRuggero Vigliaturo, Maja Jamnik, Goran Dražić, Marjetka Podobnik, Magda Tušek-Žnidarič, Giancarlo Della Ventura, Günther Redhammer, Nada Žnidaršič, Simon Caserman, Reto Gieré, 2022, izvirni znanstveni članek Povzetek: Amphibole asbestos is related to lung fibrosis and several types of lung tumors. The disease-triggering mechanisms still challenge our diagnostic capabilities and are still far from being fully understood. The literature focuses primarily on the role and formation of asbestos bodies in lung tissues, but there is a distinct lack of studies on amphibole particles that have been internalized by alveolar epithelial cells (AECs). These internalized particles may directly interact with the cell nucleus and the organelles, exerting a synergistic action with asbestos bodies (AB) from a different location. Here we document the near-atomic- to nano-scale transformations induced by, and taking place within, AECs of three distinct amphiboles (anthophyllite, grunerite, “amosite”) with different Fe-content and morphologic features. We show that: (i) an Fe-rich layer is formed on the internalized particles, (ii) particle grain boundaries are transformed abiotically by the internal chemical environment of AECs and/or by a biologically induced mineralization mechanism, (iii) the Fe-rich material produced on the particle surface does not contain large amounts of P, in stark contrast to extracellular ABs, and (iv) the iron in the Fe-rich layer is derived from the particle itself. Internalized particles and ABs follow two distinct formation mechanisms reaching different physicochemical end-states.
Ključne besede: amphiboles, human alveolar epithelial cells, asbestos, lung cancer, nanoscale investigation, acS/TEM-EDXS, dual-EELS, asbestos-related tumors
Objavljeno v DiRROS: 16.07.2024; Ogledov: 610; Prenosov: 353
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9. Pore-forming moss protein bryoporin is structurally and mechanistically related to actinoporins from evolutionarily distant cnidariansGašper Šolinc, Tomaž Švigelj, Neža Omersa, Tina Snoj, Katja Pirc, Nada Žnidaršič, Akiko Yamaji-Hasegawa, Toshihide Kobayashi, Gregor Anderluh, Marjetka Podobnik, 2022, izvirni znanstveni članek Objavljeno v DiRROS: 11.10.2022; Ogledov: 1171; Prenosov: 778
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10. Design of protein logic gate system operating on lipid membranesNeža Omersa, Saša Aden, Matic Kisovec, Marjetka Podobnik, Gregor Anderluh, 2020, izvirni znanstveni članek Ključne besede: pore-forming toxin, listeriolysin O, protein logic gates, lipid membrane, DARPin, pH
Objavljeno v DiRROS: 25.11.2020; Ogledov: 2725; Prenosov: 1227
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