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• W1998091903 abstract "Macromolecular function arises from structure, and many diseases are associated with misfolding of proteins. Molecular simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution, but the reliability of these predictions is a function of the parameters used for the simulation. There are many biomolecular force fields available, but most are validated using stably folded structures. Here, we present the results of molecular dynamics simulations on the intrinsically disordered amyloid β-peptide (Aβ), whose misfolding and aggregation give rise to the symptoms of Alzheimer’s disease. Because of the link between secondary structure changes and pathology, being able to accurately model the structure of Aβ would greatly improve our understanding of this disease, and it may facilitate application of modeling approaches to other protein misfolding disorders. To this end, we compared five popular atomistic force fields (AMBER03, CHARMM22 + CMAP, GROMOS96 53A6, GROMOS96 54A7, and OPLS-AA) to determine which could best model the structure of Aβ. By comparing secondary structure content, NMR shifts, and radius of gyration to available experimental data, we conclude that AMBER03 and CHARMM22 + CMAP over-stabilize helical structure within Aβ, with CHARMM22 + CMAP also producing elongated Aβ structures, in conflict with experimental findings. OPLS-AA, GROMOS96 53A6, and GROMOS96 54A7 produce very similar results in terms of helical and β-strand content, calculated NMR shifts, and radii of gyration that agree well with experimental data." @default.
• W1998091903 created "2016-06-24" @default.
• W1998091903 creator A5011328557 @default.
• W1998091903 creator A5025714037 @default.
• W1998091903 creator A5049055647 @default.
• W1998091903 creator A5081565182 @default.
• W1998091903 date "2013-09-13" @default.
• W1998091903 modified "2023-10-14" @default.
• W1998091903 title "Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide" @default.
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• W1998091903 doi "https://doi.org/10.1080/07391102.2013.838518" @default.
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