Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein

Savva, Loizos and Platts, James A. ORCID: https://orcid.org/0000-0002-1008-6595 2023. Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein. Journal of Biomolecular Structure and Dynamics 41 (11) , pp. 5230-5245. 10.1080/07391102.2022.2082534

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Abstract

We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Advanced Research Computing @ Cardiff (ARCCA) Chemistry
Publisher:	Taylor and Francis Group
ISSN:	0739-1102
Date of First Compliant Deposit:	27 July 2022
Date of Acceptance:	22 May 2022
Last Modified:	08 Nov 2024 22:45
URI:	https://orca.cardiff.ac.uk/id/eprint/151513

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