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Molecular dynamics simulation of aluminum binding to amyloid-β and its effect on peptide structure

Permyakov, Eugene A., Turner, Matthew, Mutter, Shaun T., Kennedy-Britten, Oliver D. and Platts, James A. 2019. Molecular dynamics simulation of aluminum binding to amyloid-β and its effect on peptide structure. PLoS ONE 14 (6) , -. 10.1371/journal.pone.0217992

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Abstract

Multiple microsecond-length molecular dynamics simulations of complexes of Al(III) with amyloid-β (Aβ) peptides of varying length are reported, employing a non-bonded model of Al-coordination to the peptide, which is modelled using the AMBER ff14SB forcefield. Individual simulations reach equilibrium within 100 to 400 ns, as determined by root mean square deviations, leading to between 2.1 and 2.7 μs of equilibrated data. These reveal a compact set of configurations, with radius of gyration similar to that of the metal free peptide but larger than complexes with Cu, Fe and Zn. Strong coordination through acidic residues Glu3, Asp7 and Glu11 is maintained throughout all trajectories, leading to average coordination numbers of approximately 4 to 5. Helical conformations predominate, particularly in the longer Al-Aβ40 and Al-Aβ42 peptides, while β-strand forms are rare. Binding of the small, highly charged Al(III) ion to acidic residues in the N-terminus strongly disrupts their ability to engage in salt bridges, whereas residues outside the metal binding region engage in salt bridges to similar extent to the metal-free peptide, including the Asp23-Lys28 bridge known to be important for formation of fibrils. High helical content and disruption of salt bridges leads to characteristic tertiary structure, as shown by heat maps of contact between residues as well as representative clusters of trajectories.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Chemistry
Advanced Research Computing @ Cardiff (ARCCA)
Publisher: Public Library of Science
ISSN: 1932-6203
Funders: EPSRC
Date of First Compliant Deposit: 13 June 2019
Date of Acceptance: 23 May 2019
Last Modified: 17 Oct 2019 02:42
URI: http://orca.cf.ac.uk/id/eprint/123425

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