Biology subjects

Ziaunys, M.

Publications and source records attributed to Ziaunys, M..

7 recordsLinked to original sources

bioRxiv2025

Formation of Condition-Dependent Alpha-Synuclein Fibril Strain in Artificial Cerebrospinal Fluid

-Synuclein (aSyn) is an intrinsically disordered protein involved in neurotransmission and synaptic plasticity. The pathological aggregation of this protein is a hallmark of synucleinopathies such as Parkinsons disease (PD) or Multiple System Atrophy (MSA). Misfolded aSyn, which primarily originates in cell cytosol, transmits between neurons, promoting a prion-like propagation. However, the extracellular environments such as interstitial and cerebrospinal fluids (ISF & CSF) play a major role in its clearance and pathological transformation. The molecular components of CSF, including proteins, glycosaminoglycans, and metal ions may influence the aggregate morphology, structure and cytotoxicity to cells. To better understand how extracellular composition affects aggregates and their formation, we employed artificial cerebrospinal fluid (aCSF) to mimic potential aggregation processes occurring in CSF. We observed distinct aCSF-specific aSyn fibrils that exhibited low stability outside aCSF, and the removal of key CSF components led to its structural alterations. Cryo-electron microscopy revealed that these fibrils possess an electron density pocket coordinated with polar basic AAs (K43, K45, H50) that is also observed in aggregates obtained from MSA patients. Our findings illustrate the importance of physiologically relevant conditions in studying aSyn aggregation and may explain why disease-related fibril structure replication in vitro has not yet been successful.

biochemistry↗

bioRxiv2024

Heterotypic droplet formation by pro-inflammatory S100A9 and neurodegenerative disease-related alpha-synuclein

Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a rapidly emerging field of study, aimed at understanding the process of biomolecular condensate formation and its role in cellular functions. LLPS has been shown to be responsible for the generation of promyelocytic leukemia protein bodies, stress granules, and intrinsically disordered protein condensates. Recently, it has been discovered that different neurodegenerative disease-related proteins, such as alpha-synuclein (related to Parkinsons disease) and amyloid-beta (Alzheimers disease) are capable of forming heterotypic droplets. Other reports have also shown non-LLPS cross-interactions between various amyloidogenic proteins and the resulting influence on their amyloid fibril formation. This includes the new discovery of pro-inflammatory S100A9 affecting the aggregation of both amyloid-beta, as well as alpha-synuclein. Combined, these observations suggest that protein interactions during LLPS and heterotypic droplet formation may be a critical step in the onset of neurodegenerative diseases. In this study, we explore the formation of heterotypic droplets by S100A9 and alpha-synuclein using a range of different spectroscopic and microscopic techniques. We show that the protein mixture is capable of assembling into both homotypic, as well as heterotypic condensates and that this cross-interaction alters the aggregation mechanism of alpha-synuclein. In addition, it also stabilizes a specific fibril conformation, which has a higher propensity for self-replication. These results provide insight into the influence of S100A9 on the process of neurodegenerative disease-related protein LLPS and aggregation, bringing us one step closer to developing a potential cure or treatment modality.

biochemistry↗

bioRxiv2024

Calcium-mediated amyloid co-aggregation of S100A1 and S100A8 proteins

The S100 family consists of calcium binding proteins that are largely known for their contribution to the neuroinflammatory processes. They are associated with various cardiac and neurological functions as well as related diseases. A few S100 proteins can form unspecific or amyloid aggregates in neuropathologies and thus play a part in dementia pathogenesis. Among all S100 proteins, S100B and S100A9 aggregation properties are the most investigated, however, there is a lack of studies regarding other S100 members. In particular, S100A1 and S100A8 are also associated with neuropathies, but their interactions or aggregation are poorly understood. Therefore, in this study, we explored whether S100A1 and S100A8 proteins can form heterodimers, interact or co-aggregate. Our results revealed that S100A1 and S100A8 interactions and amyloid aggregation are driven by calcium ions. We observed that while S100A1 remains mostly stable, S100A8 forms various types of spherical or unspecific aggregates. While they do not form stable heterodimers like calprotectin, their transient interactions facilitate the formation of worm-like amyloid fibrils and the process is regulated by different calcium ion concentrations. At calcium ions saturation, both proteins are stabilized leading to inhibition of aggregation. Overall, by employing a diverse range of techniques from amyloid and protein-specific fluorescence detection to electron-electron double resonance spectroscopy, we elucidated interactions between S100 proteins that might otherwise be overlooked, enhancing our understanding of their aggregation behaviour.

biochemistry↗

bioRxiv2024

Diverse effects of fluorescent labels on alpha-synuclein condensate formation during liquid-liquid phase separation

Liquid-liquid phase separation is an emerging field of study, dedicated to understanding the mechanism and role of biomolecule assembly into membraneless organelles. One of the main methods employed in studying protein and nucleic acid droplet formation is fluorescence microscopy. Despite functioning as an excellent tool for monitoring biomolecule condensation, a few recent reports have presented possible drawbacks of using fluorescently labeled particles. It was observed that fluorescent tags could alter the process of protein liquid-liquid phase separation and even promote their aggregation. In this study, we examined the influence of three different protein labels on alpha-synuclein phase separation in vitro and determined that the changes in droplet formation were related to both the type, as well as concentration of the fluorescently tagged alpha-synuclein. Both protein-based labels (mCherry and eGFP) induced the formation of significantly larger droplets, while fluorescein-tagged alpha-synuclein generated an abundance of small condensates. The study also revealed that alpha-synuclein with protein-based labels could self-associate at much lower concentrations than its untagged counterpart, forming either large droplets or protein aggregates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/602219v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@bf034aorg.highwire.dtl.DTLVardef@70fe04org.highwire.dtl.DTLVardef@34d9a9org.highwire.dtl.DTLVardef@1be0419_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Influence of S100A9 on Prion Protein Amyloid Aggregation

Protein aggregation in the form of amyloid fibrils has long been associated with the onset and development of various amyloidoses, including Alzheimers, Parkinsons or prion diseases. Recent studies of their fibril formation process have revealed that amyloidogenic protein cross-interactions may impact aggregation pathways and kinetic parameters, as well as the structure of the resulting aggregates. Despite a growing number of reports exploring this type of interaction, they only cover just a small number of possible amyloidogenic protein pairings. One such pair is between two neurodegeneration-associated proteins: the pro-inflammatory S100A9 and prion protein, which are known to co-localize in vivo. In this study, we examined their cross-interaction in vitro and discovered that the fibrillar form of S100A9 modulated the aggregation pathway of mouse prion protein 89-230 fragment, while non-aggregated S100A9 also significantly inhibited its primary nucleation process. These results complement previous observations of the pro-inflammatory proteins role in amyloid aggregation and highlight its potential role against neurodegenerative disorders.

biochemistry↗

bioRxiv2023

Liquid-liquid Phase Separation of Alpha-synuclein Increases the Structural Variability of Fibrils Formed during Amyloid Aggregation

Protein liquid-liquid phase separation (LLPS) is a rapidly emerging field of study on biomolecular condensate formation. In recent years, this phenomenon has been implicated in the process of amyloid fibril formation, serving as an intermediate step between the native protein transition into their aggregated state. The formation of fibrils via LLPS has been demonstrated for a number of proteins related to neurodegenerative disorders, as well as other amyloidoses. Despite the surge in amyloid-related LLPS studies, the influence of protein condensate formation on the end-point fibril characteristics is still far from fully understood. In this work, we compare alpha-synuclein aggregation under conditions, which promote or negate its LLPS and examine the differences between the formed aggregates. We show that alpha-synuclein phase separation generates a wide variety of assemblies with distinct secondary structures and morphologies. The LLPS-induced structures also possess higher levels of toxicity to cells, indicating that biomolecular condensate formation may be a critical step in the appearance of disease-related fibril variants.

biophysics↗

bioRxiv2023

Formation of amyloid fibrils by the regulatory 14-3-3ζ protein

The 14-3-3 is a highly conserved adaptor protein family with multi-layer functions, abundantly expressed in the brain. The 14-3-3 proteins modulate phosphorylation, regulate enzymatic activity and can act as chaperones. Most importantly, they play an important role in various neurodegenerative disorders due to their vast interaction partners. Particularly, the 14-3-3{xi} isoform is known to co-localize in aggregation tangles in both Alzheimers and Parkinsons diseases as a result of protein-protein interactions. These abnormal clumps consist of amyloid fibrils - insoluble aggregates, mainly formed by amyloid-{beta}, tau and -synuclein proteins. However, the molecular basis of if and how 14-3-3{xi} can aggregate into amyloid fibrils is unknown. In this study, we describe the formation of amyloid fibrils by 14-3-3{xi} utilizing a comprehensive approach that combines bioinformatic tools, amyloid-specific dye binding, secondary structure analysis and atomic force microscopy. The results presented herein characterize the amyloidogenic properties of 14-3-3{xi} and imply that the well-folded protein undergoes aggregation to {beta}-sheet-rich amyloid fibrils.

biochemistry↗