Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Torkelson, Kaylyn; Pfaendtner, Jim

doi:10.1021/acs.biomac.4c00527

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Journal Article · Wed Sep 18 00:00:00 EDT 2024 · Biomacromolecules

DOI:https://doi.org/10.1021/acs.biomac.4c00527· OSTI ID:2512404

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University of Washington, Seattle, WA (United States)
North Carolina State University, Raleigh, NC (United States)

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

View Accepted Manuscript (DOE)

Research Organization:: University of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0019288

OSTI ID:: 2512404

Journal Information:: Biomacromolecules, Journal Name: Biomacromolecules Journal Issue: 10 Vol. 25; ISSN 1525-7797

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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