Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

Abstract

Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer’s disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the μs/replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of ns/replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models, that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.

Exploring the aggregation free energy landscape of the amyloid-β protein (1–40)

“…The β-hairpin structures sampled in the monomer simulations are essentially the same as the β-hairpin structure that has been found in the complex of Aβ40 with an affibody protein Z Aβ3 , which stabilizes the hairpin structure through intermolecular contacts (16). The hairpin structure has also previously been observed in all-atom simulations of Aβ40 (17) and Aβ42 (17,18). In vitro, these two structural classes are of similar stability as witnessed by there being a reversible α to β conformational transition in monomeric Aβ42, which occurs on changing the polarity of the solvent (19).…”

Alzheimer’s Protective A2T Mutation Changes the Conformational Landscape of the Aβ1–42 Monomer Differently Than Does the A2V Mutation

“…Based on the protease-resistant nature of residues A21-A30, this region was proposed as the nucleus site for Ab monomer misfolding (activation) (12). A link between monomer misfolding and aggregation propensity and toxicity has been proposed based on experiments (13)(14)(15)(16) and simulations (17)(18)(19)(20)(21)(22)(23)(24)(25)(26) of the naturally occurring alloforms. Those alloforms contain substitutions that occur mainly within the turn region (residues [22][23][24][25][26][27][28][29][30].…”

A routine method for cloning, expressing and purifying Aβ(1–42) for structural NMR studies

“…NMR-based structural models include helical structures in membrane-mimetic solvents or micelles (Sticht et al 1995;Coles et al 1998;Watson et al 1998;Crescenzi et al 2002;Tomaselli et al 2006), predominately unstructured monomers under aqueous conditions at low temperatures (Vivekanandan et al 2011;Hou et al 2004), and insoluble fibrillar structures rich in beta sheet (Lührs et al 2005;Petkova et al 2002Petkova et al , 2006Paravastu et al 2008;Lu et al 2013). In addition to overcoming the limitations of X-ray diffraction imposed by the non-crystalline and highly polymorphic nature of Aβ peptides, NMR also provides additional information on dynamics, which could be used in conjunction with computational methods to better appreciate the conformational space populated by the peptide in its native, intrinsically disordered state (Sgourakis et al 2011;Rosenman et al 2013;Ball et al 2013). Such studies are, however, limited to the availability of an inexpensive source of milligram quantities of peptide, uniformly or selectively labeled with NMR-useful isotopes (i.e., 13 C, 15 N, 2 H, 19 F, etc.…”