It is believed that amyloid-beta (Aβ) aggregates play a role in the pathogenesis of Alzheimer’s disease. Aβ molecules form β-sheet structures with multiple interaction sites. This polymorphism gives rise to differences in morphology, physico-chemical property and level of cellular toxicity. We have investigated the conformational stability of various segmental polymorphisms using molecular dynamics simulations and find that the segmental polymorphic models of Aβ retain a U-shaped architecture. Our results demonstrate the importance of inter-sheet side chain-side chain contacts, hydrophobic contacts among the strands (β1 and β2) and of salt bridges in stabilizing the aggregates. Residues in β-sheet regions have smaller fluctuation while those at the edge and loop region are more mobile. The inter-peptide salt bridges between Asp23 and Lys28 are strong compared to intra-chain salt bridge and there is an exchange of the inter-chain salt-bridge with intra-chain salt bridge. As our results suggest that Aβ exists under physiological conditions as an ensemble of distinct segmental polymorphs, it may be necessary to account in the development of therapeutics for Alzheimer’s disease the differences in structural stability and aggregation behavior of the various Aβ polymorphic forms.

Recent epidemiological data have shown that patients suffering from Type 2 Diabetes Mellitus have an increased risk to develop Alzheimer's disease and vice versa. A possible explanation is the cross-sequence interaction between Aβ and amylin. Because the resulting amyloid oligomers are difficult to probe in experiments, we investigate stability and conformational changes of Aβ−amylin heteroassemblies through molecular dynamics simulations. We find that Aβ is a good template for the growth of amylin and vice versa. We see water molecules permeate the β-strand−turn−β-strand motif pore of the oligomers, supporting a commonly accepted mechanism for toxicity of β-rich amyloid oligomers. Aiming for a better understanding of the physical mechanisms of cross-seeding and cell toxicity of amylin and Aβ aggregates, our simulations also allow us to identify targets for the rational design of inhibitors against toxic fibril-like oligomers of Aβ and amylin oligomers.

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Recent mutagenesis studies using the hydrophobic segment of Ab suggest that aromatic p-stacking interactions may not be critical for fibril formation. We have tested this conjecture by probing the effect of Leu, Ile, and Ala mutation of the aromatic Phe residues at positions 19 and 20, on the double-layer hexametric chains of Ab fragment Ab 16-22 using explicit solvent all-atom molecular dynamics. As these simulations rely on the accuracy of the utilized force fields, we first evaluated the dynamic and stability dependence on various force fields of small amyloid aggregates. These initial investigations led us to choose AMBER99SB-ILDN as force field in multiple long molecular dynamics simulations of 100 ns that probe the stability of the wild-type and mutants oligomers. Single-point and double-point mutants confirm that size and hydrophobicity are key for the aggregation and stability of the hydrophobic core region (Ab [16][17][18][19][20][21][22] ). This suggests as a venue for designing Ab aggregation inhibitors the substitution of residues (especially, Phe 19 and 20) in the hydrophobic region (Ab [16][17][18][19][20][21][22] ) with natural and non-natural amino acids of similar size and hydrophobicity.

Diseases such as type 2 diabetes, Alzheimer’s and Parkinson’s share as common feature the accumulation of mis-folded disease-specific protein aggregates into fibrillar structures, or plaques. These fibrils may either be toxic by themselves, or act as reservoirs for smaller cytotoxic oligomers. This suggests to investigate molecules as potential therapeutics that either reduce fibril formation or increase fibril stability. One example is rat amylin, which can inhibit aggregation of human amylin, a hallmark of type 2 diabetes. In the present paper, we use molecular dynamics to compare the stability of various preformed aggregates, built out of either human amylin, rat amylin, or mixtures of both. We considered two types of fibril-like oligomers: a single-layer in-register conformation, and a double-layer conformation in which the first U-shaped layer consists of rat amylin and the second layer of human amylin. Our results explain the weak amyloid-inhibiting properties of rat amylin and suggest that membrane leakage due to pore formation is responsible for the toxicity of rat amylin observed in a recent experiment. Together, our results put in question the use of rat amylin or the similar FDA approved drug pramlintide as an inhibitor of human amylin aggregation. They also point to mixed human-rat amylin fibril-like oligomers as possible model-systems for studies of amyloid formation that involve cross-species transmission.

Seeding a protein solution with pre-formed fibrils can enhance dramatically the growth rate of amyloids. As the seeds do not need to be of the same protein, seeding may account for the observed correlations between amyloid diseases. In an effort to understand better the molecular mechanisms behind cross seeding we have studied in silico the effect of mutations on the seeding of amylin fibrils. Our investigations of the structural stability of decamers of wild type amylin peptides, of Y37L mutants, and of hetero-assemblies of wild-type and mutant amylin molecules, show that the experimental observed efficient cross seeding can be explained based on similarity in fibril structure of components. We find that amyloids with similar side chains packing at the β-sheet interface are structurally compatible, acting as a good template for the congruent incorporation of homologues peptides. In the Y37L mutants, lack of tyrosine-specific interactions causes significant higher flexibility of the C terminal than observed in the wild-type fibril. This effects elongation of the mutant fibril leading to the longer lag times during aggregation that are observed in experiments. Our study gives guidelines for the design of ligands that could stabilize amylin fibrils.

Small soluble amyloid oligomers are believed to play a significant role in the pathology of amyloid diseases. Recently, the atomic structure of a toxic oligomer formed by an 11 residue and its tandem repeat was found to have an out-off register antiparallel β-strands in the shape of a β-barrel. In the present article we investigate the effect of mutations in the hydrophobic cores on the structure and dynamic of the β-barrels using all atom multiple molecular dynamics simulations with an explicit solvent. Extending previous experiments with molecular dynamics simulations we systematically test how stability and formation of cylindrin depends on the interplay between hydrophobicity and steric effects of the core residues. We find that strong hydrophobic interactions between geometrically fitting residues keep the strands (both in register and out-off-register interface) in close proximity, which in turn stabilizes the side-chain and main-chain hydrogen bonds, and the salt bridges on the outer surface along the weak out-of-register interface. Our simulations also indicate presence of water molecules in the hydrophobic interior of the cylindrin β-barrel.

The aggregation modes of hexapeptide fragments of Tau, Insulin and Aβ peptide (VQIVYK, MVGGVV and LYQLEN) were found from their microcrystalline structures that had been recently resolved by X-ray analysis. The atomic structures reveal a dry self-complementary interface between the neighboring β-sheet layers, termed "steric zipper". In this study we perform several all-atom molecular dynamics simulations with explicit water to analyze stability of the crystalline fragments of 2-10 hexapeptides each and their analogs with single glycine replacement mutations to investigate the structural stability, aggregation behavior and thermodynamic of the amyloid oligomers. Upon comparing single and double layer models, our results reveal that additional strands contribute significantly to the structural stability of the peptide oligomers for double layer model, while in the case of single layer model the stability decreases (or remains the same in the case of LYQLEN). This is in agreement with the previous studies performed on different types of amyloid models. We also replaced the side-chains participating in the steric zipper interfaces with glycine. None of the mutants were structurally stable compared to the respective wild type model, except for mutants V2G and V6G in MVGGVV2 case. The exception can be explained by structural features of this particular polymorph. The double layer decamer and dodecamer aggregates of the wild type hexapeptides appear to be stable at 300K, which is confirmed by the conservation of high anti-parallel β-sheet content throughout the whole simulation time. Deletions of the side chains resulted in decline of secondary structure content compared to corresponding wild type indicating that the role of the replaced amino acid in stabilizing the structure. Detailed analysis of the binding energy reveals that stability of these peptide aggregates is determined mainly by the van der Waals and hydrophobic forces that can serve as quantitative measure of shape complementarities between the side chains. This observation implies that interactions among side chains forming the dehydrated steric zipper, rather than among those exposed to water, are the major structural determinant. The electrostatic repulsion destabilizes the studied double layer aggregates in two cases, while stabilizes the other two. Negative total binding free energy indicates that both wild type and mutants complex formation is favorable. However, the mutants complexation is less favorable than the wild type's. The present study provides the atomic level understanding of the aggregation behavior and the driving force for the amyloid aggregates, and could be useful for rational design of amyloid inhibitors and amyloid-specific biomarkers for diagnostic purposes.