Alzheimer’s disease (AD) is the most common cause of late-life dementia1
. The pathognomonic neuropathologic features of AD are extracellular amyloid deposits comprising primarily fibrils of the amyloid β-protein (Aβ) and intracellular neurofibrillary tangles formed by tau protein2
. Compelling evidence supports a seminal role of Aβ in AD. Fibrils originally were thought to be central to AD pathogenesis3
, but recent studies support the hypothesis that the proximate neurotoxic agents in AD are Aβ oligomers4–6
. In fact, recent experiments have shown that some pathways of Aβ oligomerization and fibril formation are independent7,8
and that fibrillization may be protective9
Aβ is produced naturally and ubiquitously in vivo
as an ~4 kDa peptide10
. It exists predominately in two forms, Aβ40 and Aβ42, that contain 40 or 42 amino acids, respectively (). Despite the small structural difference between Aβ40 and Aβ42 (the C-terminal Ile-Ala sequence), the peptides display significantly different behaviors in vitro
and in vivo
. Aβ42 is the principal component in parenchymal plaques11–13
. An increase in the Aβ42/Aβ40 concentration ratio is associated with familial forms of early onset AD14,15
. Treatments that reduce Aβ42 levels have been shown to correlate with decreased risk for AD16
. In addition, Aβ42 displays enhanced neurotoxicity relative to Aβ4017–19
. In vitro
studies have shown that Aβ42 displays fibril nucleation and elongation rates that are significantly higher than those of Aβ4020–22
and that Aβ42 forms larger oligomers than does Aβ4023,24
. These results support the conclusion that development of efficacious therapeutic agents for AD would be facilitated by knowledge in at least two areas: (1) the structural dynamics of Aβ monomer folding and oligomerization; and (2) differences in the dynamics between Aβ40 and Aβ42.
The primary structures of Aβ40 and Aβ42. The sequences are displayed in one-letter amino acid code beginning from the left with the N-terminal Asp1.
Experimental studies of Aβ monomer structure and dynamics are complicated by the lack of existence of a stable fold and the propensity of the peptide to aggregate into amorphous assemblies or multiple fibrillar forms 25,26
. NMR experiments on Aβ fragments or full-length Aβ40 and Aβ42 done in the absence of solvent additives consistently reveal little regular structure27–35
. A small increase in C-terminal rigidity has been observed in Aβ42 versus Aβ4034
. Consistent with these data, studies of region-specific endoprotease sensitivity showed increased resistance of the Aβ42 C-terminus29
. These studies have provided relatively coarse insights into local Aβ structure, but they were not capable of elucidating the Aβ conformational ensemble in atomic detail. Substantial helical structure was revealed in Aβ studied in mixtures of fluorinated alcohols36–40
with water. However, the relevance of these systems for understanding extra-membranous assembly is unclear.
Molecular dynamics (MD) simulations complement experimental studies through their ability to define the conformational space and dynamics of a macromolecule(s)43
. This approach is being applied actively in the Aβ field (for recent reviews, see Teplow et al.44
and Urbanc et al.45
). Recently, we studied Aβ42 dynamics computationally, integrating these data with experimental results obtained using ion mobility spectroscopy–mass spectrometry46
. We found that Aβ42 conformational space is dominated by loops and turns. Comparative studies with Aβ40 were not done. Sgourakis et al.
performed Aβ simulations using both Aβ40 and Aβ42 in an explicit water environment47
. Structured regions were observed, one of which was a β-hairpin within the C-terminal peptide segment Ile31–Ala42. The simulation employed a virtual cubic space that was designed to contain a collapsed peptide that then was solvated by explicit waters. This system size may not accommodate extended conformers and thus not completely sample conformational space, a result that would produce a biased view of Aβ structure and dynamics. Here, using replica-exchange MD (REMD) with an all-atom protein model, we sample and compare the conformational spaces and the corresponding free energy surfaces of Aβ40 and Aβ42. We assess the relevance of the data by comparison with experimental information extant. Through comparison of the structural dynamics of Aβ40 and Aβ42, we establish their shared and distinct features. Finally, we discuss the implications of these findings for understanding and potentially controlling neurotoxic Aβ assembly.