Nanoscale Interplay of Membrane Composition and Amyloid Self-Assembly

Modulation of Lipid Dynamics in the β-Amyloid Aggregates Induced Membrane Fragmentation

Nonspecific membrane disruption is considered a plausible mechanism for the cytotoxicity induced by β-amyloid (Aβ) aggregates. In scenarios of high local Aβ concentrations, a two-step membrane fragmentation model has been proposed. Initially, membrane-embedded Aβ oligomeric aggregates form, followed by membrane fragmentation. However, the key molecular-level interactions between Aβ oligomeric aggregates and lipids that drive the second-stage membrane fragmentation remain unclear. This study monitors the time-dependent changes in lipid dynamics and water accessibility of model liposomes during Aβ-induced membrane fragmentation. Our results indicate that lipid dynamics on the nanosecond to microsecond time scale undergo rapid acceleration upon initial incubation with membrane-incorporated Aβ oligomeric aggregates, followed by a slow deceleration process. Concurrently, lipid headgroups become less accessible to water. Both observations suggest a carpet-like mechanism of membrane disruption for the Aβ-induced membrane fragmentation process.

Aggregation and partitioning of amyloid peptide fragments in the presence of a lipid bilayer: A coarse grained molecular dynamics study

Amyloidogenicity and toxicity of amyloid peptides have been linked to the peptide aggregation and interactions with lipid bilayers. In this work we used the coarse grained MARTINI model to study the aggregation and partitioning of amyloid peptide fragments Aβ(1-28) and Aβ(25-35) in the presence of a dipalmitoylphosphatidylcholine bilayer. We explored the peptide aggregation starting from three initial spatial arrangements where free monomers were placed in solution outside the membrane, at the membrane-solution interface, or in the membrane. We found that Aβ(1-28) and Aβ(25-35) interact with the bilayer quite differently. The Aβ(1-28) fragments show strong peptide-peptide and peptide-lipid interactions leading to irreversible aggregation where the aggregates stay confined to their initial spatial location. The Aβ(25-35) fragments show weaker peptide-peptide and peptide-lipid interaction leading to reversible aggregation and accumulation at the membrane-solution interface irrespective of their initial spatial arrangement. Those findings can be explained in terms of the shape of the potential of mean force for the single-peptide translocation across the membrane.

In-cell 31P solid-state NMR measurements of the lipid dynamics and influence of exogeneous β-amyloid peptides on live neuroblastoma neuro-2a cells

Non-specific disruption of cellular membranes induced by aggregation of exogeneous β-amyloid (Aβ) peptides is considered a viable pathological mechanism in Alzheimer's disease (AD). The solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been widely applied in model liposomes to provide important insights on the molecular interactions between membranes and Aβ aggregates. Yet, the feasibility of in-cell ssNMR spectroscopy to probe Aβ-membrane interactions in native cellular environments has rarely been tested. Here we report the application of in-cell³¹P ssNMR spectroscopy on live mouse neuroblastoma Neuro-2a (N2a) cells under moderate magic angle spinning (MAS) conditions. Both cell viability and cytoplasmic membrane integrity are retained for up to six hours under 5 kHz MAS frequency at 277 K, which allow applications of direct-polarization ³¹P spectroscopy and ³¹P spin-spin (T₂) relaxation measurements. The ³¹P T₂ relaxation time constant of N2a cells is significantly increased compared with the model liposome prepared with comparable major phospholipid compositions. With the addition of 5 μM 40-residue Aβ (Aβ_1-40) peptides, the ³¹P T₂ relaxation is instantly accelerated. This work demonstrates the feasibility of using in-cell³¹P ssNMR to investigate the Aβ-membrane interactions in the biologically relevant cellular system.

Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism

The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.

Vascular smooth muscle cell senescence accelerates medin aggregation via small extracellular vesicle secretion and extracellular matrix reorganization

Vascular amyloidosis, caused when peptide monomers aggregate into insoluble amyloid, is a prevalent age-associated pathology. Aortic medial amyloid (AMA) is the most common human amyloid and is composed of medin, a 50-amino acid peptide. Emerging evidence has implicated extracellular vesicles (EVs) as mediators of pathological amyloid accumulation in the extracellular matrix (ECM). To determine the mechanisms of AMA formation with age, we explored the impact of vascular smooth muscle cell (VSMC) senescence, EV secretion, and ECM remodeling on medin accumulation. Medin was detected in EVs secreted from primary VSMCs. Small, round medin aggregates colocalized with EV markers in decellularized ECM in vitro and medin was shown on the surface of EVs deposited in the ECM. Decreasing EV secretion with an inhibitor attenuated aggregation and deposition of medin in the ECM. Medin accumulation in the aortic wall of human subjects was strongly correlated with age and VSMC senescence increased EV secretion, increased EV medin loading and triggered deposition of fibril-like medin. Proteomic analysis showed VSMC senescence induced changes in EV cargo and ECM composition, which led to enhanced EV-ECM binding and accelerated medin aggregation. Abundance of the proteoglycan, HSPG2, was increased in the senescent ECM and colocalized with EVs and medin. Isolated EVs selectively bound to HSPG2 in the ECM and its knock-down decreased formation of fibril-like medin structures. These data identify VSMC-derived EVs and HSPG2 in the ECM as key mediators of medin accumulation, contributing to age-associated AMA development.

Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations

One of the factors contributing to the toxicity of amyloid-β (Aβ) peptides is the destruction of membrane integrity through Aβ peptide-membrane interactions. The binding of Aβ peptides to membranes has been studied by experiments and theoretical simulations extensively. The exact binding mechanism, however, still remains elusive. In the present study, the molecular basis of the peptide-bilayer binding mechanism of the full-length Aβ42 monomer with POPC/POPS/CHOL bilayers is investigated by all-atom (AA) simulations. Three main binding models in coil, bend, and turn structures are obtained. Model 1 of the three models with the central hydrophobic core (CHC) buried inside the membrane is the dominant binding model. The structural features of the peptide, the peptide-bilayer interacting regions, the intrapeptide interactions, and peptide-water interactions are studied. The binding of the Aβ42 monomer to the POPC/POPS/CHOL bilayer is also explored by coarse-grained (CG) simulations as a complement. Both the AA and CG simulations show that residues in CHC prefer forming interactions with the bilayer, indicating the crucial role of CHC in peptide-bilayer binding. Our results can provide new insights for the investigation of the peptide-bilayer binding mechanism of the Aβ peptide.

How does excess phenylalanine affect the packing density and fluidity of a lipid membrane?

Phenylketonuria (PKU) is an autosomal recessive error of phenylalanine (Phe) metabolism, where untreated Phe becomes cytotoxic. Previous experiments found that excess Phe decreases the packing density and increases the fluidity and permeability of a lipid membrane. It was proposed that Phe forms cytotoxic nanoscopic amyloid-like fibrils. In another study, the Phe fibrils were not visible near the lipid membrane. So, what leads to the deleterious effect of Phe on the lipid membrane? We put forward a molecular mechanism for the observed effect of excess Phe on the lipid membrane using all-atom molecular dynamics simulation. This study suggests that Phe monomers spontaneously intercalate into the membrane and form small hydrogen-bonded clusters, some of which locally perturb the membrane. These local effects result in an overall reduction in the membrane packing density, enhancement of membrane fluidity, and an increase of water permeability, observed in experiments. The present study does not observe any effect of the nanoscopic fibrillar structure of Phe on the membrane. This study, therefore, provides alternative insights into the excess Phe cytotoxicity in PKU disease.

Synthesis and in vitro quantification of amyloid fibrils by barbituric and thiobarbituric acid-based chromene derivatives

Neurodegenerative disease is caused by the abnormal build-up of proteins in and around cells called amyloid. The amyloid fibril formation and its mechanism have been investigated with various techniques, including dye-binding assay. Thioflavin T (ThT) has been one of the most widely used dyes for quantifying amyloid deposits, but ThT has a weak fluorescence signal especially at low concentration of amyloid fibrils, low lipophilicity and positive charge that makes it unable to cross the blood-brain barrier (BBB) to detect amyloid fibrils in vivo. Hence, there is a strong motivation for designing and developing the new compounds for in vitro amyloid quantification and in vivo amyloid imaging. The need for new probes to detect amyloid fibrils, especially within the cell, is highlighted by the fact that an accurate understanding of the molecular details of amyloid fibril formation is required to design and develop strategies for controlling the amyloid formation, and this needs more reliable probes for amyloid identification. In this work, we synthesized and applied barbituric and thiobarbituric acid-based chromene derivatives, as new fluorescent dyes to quantitatively detect the amyloid fibrils of bovine serum albumin (BSA) and human insulin in comparison with native soluble proteins or amorphous aggregation. Our results showed that among the 14 synthesized compounds, five compounds 4a, 4h, 4j, 4k, and 4l could selectively and specifically bind to amyloid fibrils while other compounds demonstrated a low-affinity binding. Furthermore, according to the cell viability experiment, compounds 4a, 4j and 4l at low concentration of compounds are not toxic, especially compound 4j which could be used as a suitable candidate for in vivo study. Further studies are needed to determine all the properties of compounds, especially in vivo experiments.