Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN

Abstract

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.

Side‐chain hydrophobicity and the stability of Aβ16–22 aggregates

“…Hence, not aromatic interactions but rather the hydrophobicity and b-sheet propensity of these residues at position 19 and 20 might be the requirement for the aggregation of Ab. A similar result was also obtained by Senguen et al 11 on nine variant of Ab [16][17][18][19][20][21][22] . Increasingly, molecular dynamic simulations complement experiments as a tool to research the assembly of oligomer and protofibrils, effects of mutation, mechanism of toxicity and inhibition of amyloid aggregate.…”

“…3 In order to design such targeted inhibitors, it is important to understand which features of the primary sequence lead peptides to aggregate in amyloid disorders. A suitable test system to probe these questions is the segment Ab [16][17][18][19][20][21][22] , which is among the shortest sequences that form amyloid fibrils in aqueous solutions at neutral pH. 4 Proline scanning mutagenesis indicates that the aromatic residues at positions 19 and 20 in the central hydrophobic cluster (Leu17-Val18-Phe19-Phe20-Ala21) are particularly sensitive to replacement 5 making this region is a prime target in the design of inhibitors.…”

“…Increasingly, molecular dynamic simulations complement experiments as a tool to research the assembly of oligomer and protofibrils, effects of mutation, mechanism of toxicity and inhibition of amyloid aggregate. [12][13][14][15][16] In principle, amyloid aggregates and fibril structure can be studied by atomistic molecular dynamics simulations of the aggregation and fibril formation process, including conformational changes, seed formation, and protofilament packing. However, such simulations are often not practical due to the long-time scales involved in seed formation and in the fibrillation process.…”

“…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.…”

Hydration water mobility is enhanced around tau amyloid fibers

“…Because NS provides information on the average dynamics of all hydrogen atoms in the sample, we used MD simulations to assist the interpretation of our experimental results (see Discussion). We carried out all-atom MD simulations on the amyloid-prone hexapeptide 306 VQIVYK 311 , which belongs to the tau fiber core (8) and was therefore used as a model of the fiber core (32,33). The simulation was performed on the monomeric peptide in solution (Fig.…”