Based on the general structure function principle in

Based on the general structure-function principle in biology [[19], [20], [21]], toxic oligomers are expected to have well-defined three-dimensional structures to carry out their pathological functions. A common amyloid toxicity mechanism also suggests that toxic oligomers of different amyloid proteins may have similar structures. For example, experimental studies using atomic force miscopy (AFM) showed that various amyloid peptides could form pore-like structures in the membrane, causing membrane leakage and disruption [[22], [23], [24]]. Using an 11-residue peptide fragment from a slow-aggregating αB crystalline (with the sequence of 90KVKVLGDVIEV100, named K11V), Laganowsky et al. discovered that the short peptides could form a stable toxic hexamer [12]. Using x-ray crystallography, the hexamer was found to feature a β-barrel or β-cylindrin structure. β-barrel is a common protein topology, which is adopted by both soluble and membrane proteins. In addition, Do et al. combined experimental characterizations with computational modeling to show that the C-terminal fragments of amyloid-β (Aβ) with a length of 11 residues might form similar β-barrel oligomers [20]. The potential formation of β-barrel oligomers during the aggregation of hIAPP8-20 has been supported by a recent mass spectra and ion mobility study [25]. Moreover, the β-barrel structure as a model for small Aβ40 oligomers was also supported by hydrogen exchange mass spectrometry experiments [20]. Other experimental studies of Aβ-membrane interactions suggested the insertion of Aβ into the membrane and formation of an ion channel like configuration, causing an abnormal flux of ions into the cell [[26], [27], [28]]. Hence, these β-barrel oligomers with the capability to be incorporated into the membrane and thus compatible to the “amyloid pore” hypothesis [[22], [23], [24]] have been postulated as the early aggregation intermediates exerting toxic effects on Ellagic acid [12]. The formation of β-barrel oligomers was also observed in previous computational studies of several short peptides [[29], [30], [31], [32]]. Using Monte Carlo [33] simulations, Irback & Mitternacht found that Aβ16-22 (i.e., the amyloid core of Amyloid-β with a sequence of 16KLVFFAE22) could form β-barrels. Via enhanced sampling with replica exchange molecular dynamics (REMD), β-barrel conformations have been observed in all-atom aqueous simulations of NHVTLSQ of the beta-2 microglobulin protein [30] and KLVFFAE of Aβ peptide [29]. However, the detailed structure and dynamics of β-barrel oligomers – including size dependence, structural characterization, and conversion to protofibrils or fibrils – remain unknown. Recently, Zhang et al. investigated the fibril-barrel transitions of K11 V using a structure-based constraint to model both barrels and fibrils [31], however the independent insights from unconstrained simulations remain to be seen. Molecular insights of the structures and dynamics of β-barrel oligomers as aggregation intermediates may help understand the origin of amyloid toxicity and design novel therapeutics targeting these toxic species. Recently, all-atom discrete molecular dynamics (DMD) simulations – a predictive and computationally efficient molecular dynamics approach [[34], [35], [36], [37]] – have been used to capture the assembly dynamics of Aβ16-22 from monomers to oligomers and to fibril-like cross-β structures [38], where the formation of β-barrel oligomers was not the focus. Motivated by recent experimental and computational studies, we used the same approach to evaluate whether Aβ16-22 could also form β-barrel oligomers and to investigate the detailed structures and dynamics of these well-structured oligomers. Indeed, the 7-residue peptide could form β-barrel oligomers as the aggregation intermediates. We proposed a network-based approach to identify β-barrels in simulations and characterized β-barrels with various sizes. The formation of β-barrels was driven by minimizing the exposure of hydrophobic residues to solvent along with maximizing the number of backbone hydrogen bonds, although the closure of a β-sheet into a β-barrel also resulted into conformational strains in the structure. We also observed the conformational inter-conversion between β-barrels and double-layer β-sheets, suggesting their co-existence with comparable free energies. The potential of mean force (PMF) analysis of DMD simulations further characterized the free energy barrier between these two states. With double-layer β-sheets resembling the cross-beta core of fibrils, our results suggested the β-barrel oligomers as “off-pathway” aggregates towards fibrillization in solution. Future aggregation simulations with full-length amyloid peptides and/or in the membrane environment are necessary to decipher the general roles of β-barrel oligomers in amyloid toxicity.