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 (Unpublished)

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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.

Item Type: Other
URI: http://research.library.mun.ca/id/eprint/16027
Item ID: 16027
Additional Information: Includes bibliographical references (pages 40-42)
Department(s): Science, Faculty of > Physics and Physical Oceanography
Date: May 2023
Date Type: Submission
Library of Congress Subject Heading: Peptides; Molecular dynamics--Simulation methods; Nanofluids; Drops

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