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| Home > Publications database > Effects of ion type and concentration on the structure and aggregation of the amyloid peptide A β16−22$$ {\boldsymbol{\beta}}_{16-22} $$ |
| Home > Publications database > Effects of ion type and concentration on the structure and aggregation of the amyloid peptide A β16−22$$ {\boldsymbol{\beta}}_{16-22} $$ |
| Journal Article | FZJ-2023-05505 |
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2025
Wiley-Liss
New York, NY
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Please use a persistent id in citations: doi:10.1002/prot.26635 doi:10.34734/FZJ-2023-05505
Abstract: Among the various factors controlling the amyloid aggregation process, the influences ofions on the aggregation rate and the resultingstructures are important aspects to con-sider, which can be studied by molecular simulations. There is a wide variety of proteinforce fields and ion models, raising the question of which model to use in such studies. Toaddress this question, we perform molecular dynamics simulations of Aβ16–22, a fragmentof the Alzheimer's amyloidβpeptide, using different protein force fields, AMBER99SB-disp (A99-d) and CHARMM36m (C36m), and different ion parameters. The influences ofNaCl and CaCl2at various concentrations are studied and compared with the systemswithout the addition of ions. Our results indicate a sensitivity of the peptide-ion interac-tions to the different ion models. In particular, we observe a strong binding of Ca2+to res-idue E22 with C36m and also with the Åqvist ion model used together with A99-d, whichslightly affects the monomeric Aβ16–22structures and the aggregation rate, but signifi-cantly affects the oligomer structures formedin the aggregation simulations. For example,at high Ca2+concentrations, there was a switch from an antiparallel to a parallelβ-sheet.Such ionic influences are of biological relevance because local ion concentrations canchange in vivo and could help explain thepolymorphism of amyloid fibrils.
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