Browsing by Author "Sahin, Cagla"

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    Mass Spectrometry of RNA-Binding Proteins during Liquid–Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures
    (American Chemical Society, 2023) Sahin, Cagla; Motso, Aikaterini; Gu, Xinyu; Feyrer, Hannes; Lama, Dilraj; Arndt, Tina; Rising, Anna; Gese, Genis Valentin; Hällberg, B. Martin; Marklund, Erik. G.; Schafer, Nicholas P.; Petzold, Katja; Teilum, Kaare; Wolynes, Peter G.; Landreh, Michael; Center for Theoretical Biological Physics
    Liquid–liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid–liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.
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    Oleuropein derivatives from olive fruit extracts reduce α-synuclein fibrillation and oligomer toxicity
    (Elsevier, 2019) Mohammad-Beigi, Hossein; Aliakbari, Farhang; Sahin, Cagla; Lomax, Charlotte; Tawfike, Ahmed; Schafer, Nicholas P.; Amiri-Nowdijeh, Alireza; Eskandari, Hoda; Møller, Ian Max; Hosseini-Mazinani, Mehdi; Christiansen, Gunna; Ward, Jane L.; Morshedi, Dina; Otzen, Daniel E.; Center for Theoretical Biological Physics
    Aggregation of α-synuclein (αSN) is implicated in neuronal degeneration in Parkinson's disease and has prompted searches for natural compounds inhibiting αSN aggregation and reducing its tendency to form toxic oligomers. Oil from the olive tree (Olea europaea L.) represents the main source of fat in the Mediterranean diet and contains variable levels of phenolic compounds, many structurally related to the compound oleuropein. Here, using αSN aggregation, fibrillation, size-exclusion chromatography–multiangle light scattering (SEC-MALS)-based assays, and toxicity assays, we systematically screened the fruit extracts of 15 different olive varieties to identify compounds that can inhibit αSN aggregation and oligomer toxicity and also have antioxidant activity. Polyphenol composition differed markedly among varieties. The variety with the most effective antioxidant and aggregation activities, Koroneiki, combined strong inhibition of αSN fibril nucleation and elongation with strong disaggregation activity on preformed fibrils and prevented the formation of toxic αSN oligomers. Fractionation of the Koroneiki extract identified oleuropein aglycone, hydroxyl oleuropein aglycone, and oleuropein as key compounds responsible for the differences in inhibition across the extracts. These phenolic compounds inhibited αSN amyloidogenesis by directing αSN monomers into small αSN oligomers with lower toxicity, thereby suppressing the subsequent fibril growth phase. Our results highlight the molecular consequences of differences in the level of effective phenolic compounds in different olive varieties, insights that have implications for long-term human health.