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Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides

Mutter, Shaun, Deeth, Robert J., Turner, Matthew and Platts, James Alexis ORCID: 2017. Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides. Journal of Biomolecular Structure and Dynamics 36 (5) , pp. 1145-1153. 10.1080/07391102.2017.1313780

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Ligand field molecular mechanics (LFMM) parameters have been benchmarked for copper (II) bound to the amyloid-β1–16 peptide fragment. Several density functional theory (DFT) optimised small test models, representative of different possible copper coordination modes, have been used to test the accuracy of the LFMM copper bond lengths and angles, resulting in errors typically less than 0.1 Å and 5°. Ligand field molecular dynamics (LFMD) simulations have been carried out on the copper bound amyloid-β1–16 peptide and snapshots extracted from the subsequent trajectory. Snapshots have been optimised using DFT and the semi-empirical PM7 method resulting in good agreement against the LFMM calculated geometry. Analysis of substructures within snapshots shows that the larger contribution of geometrical difference, as measured by RMSD, lies within the peptide backbone, arising from differences in DFT and AMBER, and the copper coordination sphere is reproduced well by LFMM. PM7 performs excellently against LFMM with an average RMSD of 0.2 Å over 21 tested snapshots. Further analysis of the LFMD trajectory shows that copper bond lengths and angles have only small deviations from average values, with the exception of a carbonyl moiety from the N-terminus, which can act as a weakly bound fifth ligand.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Advanced Research Computing @ Cardiff (ARCCA)
Subjects: Q Science > QD Chemistry
Uncontrolled Keywords: ligand field molecular mechanics, molecular dynamics, amyloid-beta peptide, copper
Publisher: Taylor & Francis
ISSN: 0739-1102
Funders: EPSRC
Date of First Compliant Deposit: 8 May 2017
Date of Acceptance: 27 March 2017
Last Modified: 07 May 2023 15:25

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