br Results and discussion In order to investigate

Results and discussion In order to investigate the assembly dynamics and aggregate structures of Aβ16-22, twelve molecular systems with the number of peptides varying from 1 to 12 were studied. In all simulations, the same peptide concentration (~15 mM) was maintained by adjusting the dimensions of simulation boxes. To obtain sufficient sampling and avoid potential biases from the starting configurations, we performed fifty independent simulations for all molecular systems, each of which started with different initial configurations and lasted 200 ns (details of simulations see Methods).
Conclusions In summary, we performed all-atom DMD simulations of Aβ16-22 aggregation with different number of peptides. Consistent with previous studies [60], Aβ16-22 shows a high propensity to form β-sheet aggregates. While monomers were mostly coils, even two peptides could form dimers with extensive β-sheet content. With the system size smaller than six, the peptides mainly formed single-layer β-sheets. Only when the number of peptides reached six and larger, the β-barrel oligomers could be observed. The observation of β-barrel oligomers was consistent with previous all-atom aqueous REMD and Monte Carlo studies [29,33]. Using the proposed β-barrel detection algorithm, our systematic analysis of β-barrels indicated they were mostly formed by six to nine peptides. High-order β-barrels of larger sizes could be observed but with significantly smaller probabilities (Fig. 7B). The β-barrels of six to eight peptides were mostly cylindrical (Fig. 9), and become more cylindroid with increasing sizes. These barrels were stabilized by maximizing the number of backbone hydrogen bonds and burying the NVP-ADW742 receptor residues, but the closing of a single β-sheet also imposed structural strains. As the result, we observed the dynamic inter-conversion from β-barrels to double-layer β-sheets via an intermediate state of highly-curved single-layer sheets, where the breaking of hydrogen bonds likely happened at β-strands with high strains (or large curvature). Calculation of the contact frequency maps of various β-barrels indicated that adjacent β-strands tent to be in anti-parallel alignment, similar to the experimentally solved K11 V β-barrel hexamer [12]. We also performed PMF analysis of the aggregation of eight peptides, where both single- and double-layers β-sheets were populated with similar probability (Fig. 2). Our computational analysis suggested that β-barrels were “off-pathway” intermediates towards fibrillization. Taken together, our unconstrained all-atom DMD simulations offered detailed structural and dynamic insights to the formation of β-barrel intermediates. Although our simulations were performed in a membrane free environment, the spontaneous formation of β-barrels in our simulations may indicate an intrinsic propensity of the amyloid-core fragment of Aβ to form the pore-like structures. How the amyloid peptides form oligomers after their insertion into membrane or whether pre-formed β-barrels could be incorporated into the membrane still need to be established. In addition, our observed β-barrels are formed by the Aβ16-22 fragment, questions like whether and how full length amyloid peptides form the β-barrel structures remain to be answered. Further studies such as the formation of these β-barrels in membrane environments and experimental validation and characterization of these toxic species are necessary to better understand the mechanism of amyloid toxicity and design therapeutic strategies targeting these novel toxic species.
Material and methods
Conflict of interest
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Acknowledgement The work is supported in part by NSF CAREER CBET-1553945 (Ding) and NIH MIRA R35GM119691 (Ding). The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH and NSF.
Introduction Protein misfolding and abnormal aggregation form fibrillar amyloid that is closely related to a number of devastating diseases, such as Alzheimer's, Parkinson's, and type 2 diabetes [1]. Alzheimer's disease (AD), the main type of dementia, is characterized by a progressive loss of memory, cognitive abilities impair, and extracellular amyloid plaques [2]. The extracellular amyloid plaques are composed of amyloid β-proteins (Aβ) ranging in length from 39 to 43 amino acid residues out of which the most abundant forms are 40 and 42, derived by proteolytic cleavage of amyloid precursor protein [3]. It has been recognized that Aβ plaques are the key etiological hallmark of AD [4], and the mechanistic details of Aβ aggregation have been extensively studied over the past decades [5]. It has revealed that protein fibrillogenesis is generally a multistep nucleation and elongation event that proceeds through several metastable intermediate species including oligomers, protofibrils, and finally fibrils [6]. Each of these aggregates has characteristic molecular conformations and different degrees of toxicity to the neuronal cells [7]. Thus, a reliable strategy to ameliorate the neurotoxicity of Aβ is to inhibit the amyloidogenesis of Aβ, preventing the formation of toxic aggregated species.