Biology subjects

Ivanova, M. I.

Publications and source records attributed to Ivanova, M. I..

8 recordsLinked to original sources

bioRxiv2026

Backbone Thioamide Substitution Enhances the Activity of Short Peptides in Modulating the Aggregation of α-Synuclein

The non-amyloid-{beta} component (NAC) region of the Parkinson's-associated protein -synuclein plays a key role in its pathogenic aggregation, motivating the development of molecules that target this critical region. Here, we show that a minimal NAC-derived motif, 66VGGAVVT72, can be reprogrammed through backbone engineering to modulate -synuclein aggregation. Backbone thioamide substitution of this peptide enhances its interactions with -synuclein fibrils and accelerates aggregation, whereas N-methylation disrupts {beta}-sheet hydrogen bonding and inhibits fibrillization. Strikingly, combining these modifications yields hybrid peptides that inhibit the fibrillization of full-length -synuclein at sub-stoichiometric concentrations. Consistent with in vitro results, these backbone-modified peptides can also reduce seeded -synuclein aggregation in cells. These results establish that minimal amyloidogenic sequences can be systematically tuned from aggregation promoters to inhibitors through backbone-level perturbations, particularly thioamide incorporation.

biochemistry↗

bioRxiv2024

Differential Effects of Ganglioside Lipids on the Conformation and Aggregation of Islet Amyloid Polypeptide

Despite causing over 1 million deaths annually, Type 2 Diabetes (T2D) currently has no curative treatments. Aggregation of the islet amyloid polypeptide (hIAPP) into amyloid plaques plays an important role in the pathophysiology of T2D and thus presents a target for therapeutic intervention. The mechanism by which hIAPP aggregates contributes to the development of T2D is unclear but are proposed to involve disruption of cellular membranes. However, nearly all research on hIAPP-lipid interactions has focused on anionic phospholipids, which are primarily present in the cytosolic face of plasma membranes. We seek here to characterize the effects of three gangliosides, the dominant anionic lipids in the outer leaflet of the plasma membrane, on the aggregation, structure, and toxicity of hIAPP. Our results show a dual behavior that depends on the molar ratio between the gangliosides and hIAPP. For each ganglioside, a low lipid:peptide ratio enhances hIAPP aggregation and alters the morphology of hIAPP fibrils, while a high ratio eliminates aggregation and stabilizes an -helix-rich hIAPP conformation. A more negative lipid charge more efficiently promotes aggregation, and a larger lipid headgroup improves inhibition of aggregation. hIAPP also alters the phase transitions of the lipids, favoring spherical micelles over larger tubular micelles. We discuss our results in the context of available lipid surface area for hIAPP binding and speculate on a role for gangliosides in facilitating toxic hIAPP aggregation.

biophysics↗

bioRxiv2024

Nanodisc reconstitution and characterization of amyloid-β precursor protein C99

Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimers disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.

biochemistry↗

bioRxiv2023

Non-micellar ganglioside GM1 induces an instantaneous conformational change in Aβ42 leading to the modulation of the peptide amyloid-fibril pathway

Alzheimers disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies revealed that structural variation in A{beta} fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate A{beta} aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote A{beta} fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on A{beta}42amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a spontaneous change in the peptide secondary structure from random-coil to {beta}-turn with subsequent generation of predominantly {beta}-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 interacts with the amyloidogenic A{beta}42 primary nucleus leading to a possible formation of GM1-modified A{beta}42 fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between A{beta}42 fibrils and GM1-tweaked A{beta}42 aggregates. Moreover, GM1-modified A{beta}42 aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of A{beta}, A{beta}40, and A{beta}42.

biophysics↗

bioRxiv2022

Ganglioside GM1 produces Aβ40 cytotoxic protofibril structure

Monosialoganglioside GM1-bound amyloid {beta}-peptides have been found in patients brains exhibiting early pathological changes of Alzheimer s disease. Herein, we report the ability of non-micellar GM1 to modulate A{beta}40 aggregation resulting in the formation of stable, short, rod-like, and cytotoxic A{beta}40 protofibrils with the ability to potentiate both A{beta}40 and A{beta}42 aggregation.

biophysics↗

bioRxiv2020

Shared and divergent phase separation and aggregation properties of brain-expressed ubiquilins

The brain-expressed ubiquilins, UBQLNs 1, 2 and 4, are highly homologous proteins that participate in multiple aspects of protein homeostasis and are implicated in neurodegenerative diseases. Studies have established that UBQLN2 forms liquid-like condensates and accumulates in pathogenic aggregates, much like other proteins linked to neurodegenerative diseases. However, the relative condensate and aggregate formation of the three brain-expressed ubiquilins is unknown. We report that the three ubiquilins differ in aggregation propensity, revealed by in-vitro experiments, cellular models, and analysis of human brain tissue. UBQLN4 displays heightened aggregation propensity over the other ubiquilins and, like amyloids, UBQLN4 forms ThioflavinT-positive fibrils in vitro. Measuring fluorescence recovery after photobleaching (FRAP) of puncta in cells, we report that all three ubiquilins undergo liquid-liquid phase transition. UBQLN2 and 4 exhibit slower recovery than UBQLN1, suggesting the condensates formed by the brain-expressed ubiquilins have different compositions and undergo distinct internal rearrangements. We conclude that while all brain-expressed ubiquilins exhibit self-association behavior manifesting as condensates, they follow distinct courses of phase-separation and levels of aggregation. This variability among ubiquilins along the continuum from liquid-like to solid likely informs both the normal ubiquitin-linked functions of ubiquilins and their accumulation and potential contribution to toxicity in various neurodegenerative diseases.

neuroscience↗

bioRxiv2019

Small Molecule Induced Toxic Human-IAPP Species Characterized by NMR

In this study, the effect of CurDAc, a water-soluble curcumin derivative, on the formation and stability of amyloid fibers is revealed. CurDAc interaction with amyloid is structurally selective which is reflected in a strong interference with hIAPP aggregation, while showing weaker interactions with human-calcitonin and Amyloid-{beta}1-40 in comparison. Remarkably, CurDAc also exhibited potent fiber disaggregation for hIAPP generating a toxic oligomeric species.

biophysics↗

bioRxiv2019

Mechanistic Insights into the Protective Roles of Polyphosphate Against Amyloid Cytotoxicity

The universally abundant polyphosphate (polyP) accelerates fibril formation of disease-related amyloids and protects against amyloid cytotoxicity. To gain insights into the mechanism(s) by which polyP exerts these effects, we focused on -synuclein, a well-studied amyloid protein, which constitutes the major component of Lewy bodies found in Parkinsons Disease. Here we demonstrate that polyP is unable to accelerate the rate-limiting step of -synuclein fibril formation but effectively nucleates fibril assembly once -synuclein oligomers are formed. Binding of polyP to -synuclein either during fibril formation or upon fibril maturation substantially alters fibril morphology, and effectively reduces the ability of -synuclein fibrils to interact with cell membranes. The effect of polyP appears to be -synuclein fibril specific, and successfully prevents the uptake of fibrils into neuronal cells. These results suggest that altering the polyP levels in the extracellular space might be a potential therapeutic strategy to prevent the spreading of the disease.

cell biology↗