Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane

Mounting evidence suggests that the neuronal cell membrane is the main site of oligomer-mediated neuronal toxicity of amyloid-β peptides in Alzheimer’s disease. To gain a detailed understanding of the mutual interference of amyloid-β oligomers and the neuronal membrane, we carried out microseconds of all-atom molecular dynamics (MD) simulations on the dimerization of amyloid-β (Aβ)42 in the aqueous phase and in the presence of a lipid bilayer mimicking the in vivo composition of neuronal membranes. The dimerization in solution is characterized by a random coil to β-sheet transition that seems on pathway to amyloid aggregation, while the interactions with the neuronal membrane decrease the order of the Aβ42 dimer by attenuating its propensity to form a β-sheet structure. The main lipid interaction partners of Aβ42 are the surface-exposed sugar groups of the gangliosides GM1. As the neurotoxic activity of amyloid oligomers increases with oligomer order, these results suggest that GM1 is neuroprotective against Aβ-mediated toxicity.

In Alzheimer’s disease (AD), amyloid-β peptide (Aβ) aggregates into fibrils and subsequently accumulates as plaques within the neural tissue (1). An increasing number of studies suggest that the smaller soluble oligomers formed in the earlier stages of the aggregation process are the main cytotoxic species affecting the severity and progression of AD (2–4). Aβ dimers have been reported to be the smallest toxic oligomer that affects synaptic plasticity and impairs memory (5, 6). Therefore, a detailed characterization of Aβ dimerization is an essential step toward developing a better understanding of the aggregation process. However, its transient nature (resulting from its high aggregation tendency), its plasticity, and its equilibrium with both the monomer and higher-order oligomers all make the Aβ dimer extremely challenging to study experimentally. In fact, a large amount of the experimental studies performed on Aβ dimers employ some kind of cross-linking to stabilize them (7–9). On the other hand, covalently cross-linked Aβ dimers are certainly of biological relevance, as such species have been retrieved from the brains of AD patients and their neurotoxicity has been demonstrated (6, 10). Apart from this, recent technological developments, such as advanced single-molecule fluorescence spectroscopy and imaging, opened the way to characterize amyloid oligomers without the need to stabilize them by cross-linking (11, 12). Molecular dynamics (MD) simulations are also able to provide atomic insight into the temporal evolution of the dimer structure without the need of cross-linking (13, 14). Previous simulations of Aβ dimers were modeled in the aqueous phase only, and thus they lacked essential details from the cellular context. Consideration of the latter is particularly important if one wishes to reveal the mechanism of toxicity that has been shown to rely on direct contact with the lipid membrane of neurons by Aβ oligomers (15, 16).Many studies have been done to understand the consequences of Aβ–membrane interactions; however, it is extremely difficult to capture these transient interactions with experimental methods. This becomes possible with MD simulations and this problem is addressed in the current work. We use an aggregate of 24 μs of MD simulations to investigate the dimerization of the full-length Aβ42 peptide both in solution and in the presence of a model lipid bilayer including six lipid types to mimic the composition of a neuronal cell membrane (17–19): 38% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 24% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), 5% 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS), 20% cholesterol (CHOL), 9% sphingomyelin (SM), and 4% monosialotetrahexosylganglioside (GM1) (Fig. 1A). For modeling Aβ we employ Charmm36m, a force field adjusted for intrinsically disordered proteins (IDPs), to model their preference to adopt extended structures. When applied to monomeric Aβ, Charmm36m yields more than 80% of the structures in a random coil and extended state, and the remaining ones feature transient β-hairpins, which is in acceptable agreement with experimental data (20). Moreover, Charmm36m outperforms other force fields when it comes to modeling peptide aggregation (21, 22). To the best of our knowledge, this simulation study breaks ground on two fronts: 1) It exceeds the simulation time of previous studies modeling Aβ–membrane interactions by an order of magnitude, and 2) it studies the aggregation of Aβ on a bilayer containing more than three different lipid types. Lipid bilayers of a complexity comparable to the one modeled here have been thus far studied only at the coarse-grained level (23, 24). We also analyze the aggregation pathways by transition networks (25–27), which elucidate the similarities and differences between Aβ dimerization steps both in solution and at the neuronal membrane. We find that the neuronal membrane reduces the dynamics of membrane-bound Aβ42 while it also inhibits β-sheet formation. Here, the sugar groups of GM1 form hydrogen bonds with the peptide, thereby reducing the possibilities for other hydrogen bonds to otherwise form. In contrast, the dimerization in the aqueous phase is characterized by a random coil to β-sheet transition, leading to β-sheet structures similar to the ones found in Aβ fibrils.Open in a separate windowFig. 1.(A) A snapshot of the neuronal membrane containing 38% POPC, 24% POPE, 5% POPS (collectively shown as gray surface with their phosphorous atoms indicated by gray spheres), 20% CHOL (red sticks), 9% SM (green spheres), and 4% GM1 (yellow spheres). In the following, PC, PE, and PS are synonymously used for POPC, POPE, and POPS, respectively. (B and C) Radial distribution functions for (B) lipid pairings of identical type and (C) lipid–CHOL pairings. The P atoms of PC, PE, PS, and SM and the O atoms of CHOL and GM1 were used as reference atoms for the RDF calculations. The RDFs are averaged over both membrane leaflets. The x axis shows the distances between the respective atom pairs. Since CHOL resides deeper inside the membrane, it is possible that the O atom of CHOL and the reference atoms of the other lipids are above each other, explaining why not all of the RDFs approach zero for x=0. The colors of the functions refer to the lipids as indicated in the color key in B. Pairs with RDF >1 are considered to form clusters.