A molecular dynamics simulation study of peptides confined in aqueous nanodroplets

Huang, Yiming (2023) A molecular dynamics simulation study of peptides confined in aqueous nanodroplets. Memorial University of Newfoundland. (Unpublished)

[English] PDF (Undergraduate Honours Thesis) - Accepted Version Available under License - The author retains copyright ownership and moral rights in this thesis. Neither the thesis nor substantial extracts from it may be printed or otherwise reproduced without the author's permission. Download (23MB)

Abstract

We present a molecular simulation study of five peptides, CBS-5, CBS-9, KKKDDD, DKDKDK and GAD-1, in aqueous nanodroplets. The simulation is performed through the GROMACS/2021.4 package, employing the OPLS-AA force field. Hydrophobic and amphipathic peptides prefer to reside near the surface while the extremely hydrophilic DK peptides are kept deep inside the droplet at higher temperatures. At low temperature, the nanodroplet preserves a shell-like structure with higher density in the subsurface region as previously observed for pure water nanodroplets. Peptides con- fined in such heterogeneous nanodroplets show a temperature-dependent transition in conformation and spatial distribution. Together with the nanodroplet environment, a few counter ions (Na+ or Cl⁻) added to electrically neutralize the peptide significantly affect the unfolding process of GAD-1 at 300 K.

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