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

Mutter, Shaun T., Deeth, Robert J., Turner, Matthew and Platts, James A. (2018) Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides. Journal of Biomolecular Structure and Dynamics, 36 (5). pp. 1145-1153. ISSN 0739-1102

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Abstract

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
Research Areas: A. > School of Science and Technology > Natural Sciences
Item ID: 26147
Notes on copyright: © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Depositing User: Shaun Mutter
Date Deposited: 07 Feb 2019 18:18
Last Modified: 03 May 2019 12:31
URI: https://eprints.mdx.ac.uk/id/eprint/26147

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