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1. Implications of the Actin Cytoskeleton on the Multi-Step Process of [PSI+] Prion Formation

   https://doi.org/10.3390/v14071581  

   Dorweiler, Jane E.; Lyke, Douglas R.; Lemoine, Nathan P.; Guereca, Samantha; Buchholz, Hannah E.; Legan, Emily R.; Radtke, Claire M.; Manogaran, Anita L. (July 2022, Viruses)

   Yeast prions are self-perpetuating misfolded proteins that are infectious. In yeast, [PSI+] is the prion form of the Sup35 protein. While the study of [PSI+] has revealed important cellular mechanisms that contribute to prion propagation, the underlying cellular factors that influence prion formation are not well understood. Prion formation has been described as a multi-step process involving both the initial nucleation and growth of aggregates, followed by the subsequent transmission of prion particles to daughter cells. Prior evidence suggests that actin plays a role in this multi-step process, but actin’s precise role is unclear. Here, we investigate how actin influences the cell’s ability to manage newly formed visible aggregates and how actin influences the transmission of newly formed aggregates to future generations. At early steps, using 3D time-lapse microscopy, several actin mutants, and Markov modeling, we find that the movement of newly formed aggregates is random and actin independent. At later steps, our prion induction studies provide evidence that the transmission of newly formed prion particles to daughter cells is limited by the actin cytoskeletal network. We suspect that this limitation is because actin is used to possibly retain prion particles in the mother cell. 

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2. Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches

   https://doi.org/10.3389/fbinf.2023.1321287  

   Soto, Patricia; Thalhuber, Davis T; Luceri, Frank; Janos, Jamie; Borgman, Mason R; Greenwood, Noah M; Acosta, Sofia; Stoffel, Hunter (January 2024, Frontiers in Bioinformatics)

   The Prion protein is the molecular hallmark of the incurable prion diseases affecting mammals, including humans. The protein-only hypothesis states that the misfolding, accumulation, and deposition of the Prion protein play a critical role in toxicity. The cellular Prion protein (PrP^C) anchors to the extracellular leaflet of the plasma membrane and prefers cholesterol- and sphingomyelin-rich membrane domains. Conformational Prion protein conversion into the pathological isoform happens on the cell surface.In vitroandin vivoexperiments indicate that Prion protein misfolding, aggregation, and toxicity are sensitive to the lipid composition of plasma membranes and vesicles. A picture of the underlying biophysical driving forces that explain the effect of Prion protein - lipid interactions in physiological conditions is needed to develop a structural model of Prion protein conformational conversion. To this end, we use molecular dynamics simulations that mimic the interactions between the globular domain of PrP^Canchored to model membrane patches. In addition, we also simulate the Doppel protein anchored to such membrane patches. The Doppel protein is the closest in the phylogenetic tree to PrP^C, localizes in an extracellular milieu similar to that of PrP^C, and exhibits a similar topology to PrP^Ceven if the amino acid sequence is only 25% identical. Our simulations show that specific protein-lipid interactions and conformational constraints imposed by GPI anchoring together favor specific binding sites in globular PrP^Cbut not in Doppel. Interestingly, the binding sites we found in PrP^Ccorrespond to prion protein loops, which are critical in aggregation and prion disease transmission barrier (β2-α2 loop) and in initial spontaneous misfolding (α2-α3 loop). We also found that the membrane re-arranges locally to accommodate protein residues inserted in the membrane surface as a response to protein binding. 

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3. From sequence to prion: comparison and evolutionary analysis of patterns controlling liquid-liquid phase separation and prion formation.

   Chernoff, Yury; Grizel, Anastasia; Stevenson, Jonathan; Anee, Ismat J; Paulius, Kristupas (November 2025, Proceedings of the Prion 2025 - Advancing the understanding and treatment of prion diseases. Anais eletrônicos..., Galoá)

   Introduction: Some proteins, including yeast prion protein Sup35 (eRF3) are capable of both stress-induced liquid-liquid phase separation (LLPS) and formation of prion state, propagated via solid fibrous aggregates (amyloids). Relationships between these processes are still poorly understood. Previous literature data suggested that prion formation by Sup35 is sporadically distributed in fungal evolution and depends on amino acid composition of its prion domain (PrD), rather than on a specific sequence which is highly variable. Objectives: Identify sequence patterns that control LLPS and amyloid formation by Sup35 PrD, and trace their conservation in fungal evolution. Methods: Fungal Sup35 PrDs of various evolutionary origins, as well as artificially synthesized “scrambled” variants of Saccharomyces cerevisiae Sup35 PrD, having identical amino acid composition but different sequences, were fused to fluorophores and expressed in S. cerevisiae cells. LLPS and amyloid/prion formation were assessed by fluorescence microscopy and biochemical approaches. Amino acid sequences were analyzed by various computational algorithms. Results/Discussion: While propagation of prion state depends on evolutionary distance from the host, both LLPS and ability to form an amyloid are associated with specific patterns of PrD amino acid distribution, that are broadly conserved among fungi. PrDs of different origins are capable of colocalizing within liquid condensates and influencing amyloid conversion by each other. Conclusion: LLPS and amyloid properties depend on specific evolutionarily conserved sequence patterns, indicating possible important biological roles for these processes. These patterns could potentially be used to predict LLPS and prion potential in other sequence contexts. Funding: NSF grant 2345660 

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4. Copper binding alters the core structure of amyloid fibrils formed by Y145Stop human prion protein

   https://doi.org/10.1039/D4CP03593C  

   Sridharan, Vidhyalakshmi; George, Tara; Conroy, Daniel; Shaffer, Zach; Surewicz, Witold; Jaroniec, Christopher (October 2024, Physical Chemistry Chemical Physics)

   Transmissible spongiform encephalopathies (or prion diseases) such as Creutzfeldt-Jacob disease, mad cow disease, and scrapie are characterized by accumulation in the brain of misfolded prion protein aggregates (PrPSc) that have... 

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5. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic

   https://doi.org/10.3390/ijms22168619  

   Bergasa-Caceres, Fernando; Rabitz, Herschel A. (August 2021, International Journal of Molecular Sciences)

   The initial steps of the folding pathway of the C-terminal domain of the murine prion protein mPrP(90–231) are predicted based on the sequential collapse model (SCM). A non-local dominant contact is found to form between the connecting region between helix 1 and β-sheet 1 and the C-terminal region of helix 3. This non-local contact nucleates the most populated molten globule-like intermediate along the folding pathway. A less stable early non-local contact between segments 120–124 and 179–183, located in the middle of helix 2, promotes the formation of a less populated molten globule-like intermediate. The formation of the dominant non-local contact constitutes an example of the postulated Nature’s Shortcut to the prion protein collapse into the native structure. The possible role of the less populated molten globule-like intermediate is explored as the potential initiation point for the folding for three pathogenic mutants (T182A, I214V, and Q211P in mouse prion numbering) of the prion protein. 

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