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Coiled-coil peptide assemblies directed via hydrophobic patterning and programmable charge patchiness
Date
2025
Authors
Journal Title
Journal ISSN
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Publisher
University of Delaware
Abstract
Precise synthetic control of colloids whose surfaces are chemically or physically patterned with distinct interactive regions, typically referred to as ‘patchy’ particles, remains a fundamental challenge. While globular proteins naturally exhibit charge patchiness, their systematic modification is difficult to achieve. Conversely, synthetic peptides offer a powerful, sequence-defined platform for probing colloidal interactions and providing molecular insight into the solution behavior of more complex proteinaceous materials. Through targeted amino acid substitutions, both short- and long-range interactions can be precisely engineered. This dissertation bridges the conceptual and structural gap between proteins and colloids using a model peptide nanoparticle: the coiled-coil 'bundlemer'. By combining the bundlemer’s sequence-defined synthesis, stability to modification, and bottom-up self-assembly strategies, I have produced bundlemer nanoparticles with programmed hydrophobic and electrostatic surface patterning that direct bundlemer assembly. Using principles of colloidal science, I elucidated how these specific surface modifications influenced interparticle interactions and hierarchical assemblies. ☐ In the first part of my dissertation, I present a new library of coiled-coil bundlemers containing natural and non-natural amino acid modifications is presented. Incorporation of hydrophobic non-natural (furan and alkyne) and natural (phenylalanine, tyrosine, and tryptophan) amino acids revealed new lattice-forming sequences. The hydrophobic patterning on the bundlemer surface which induced lamellar lattice formation was characterized by transmission electron microscopy (TEM), cryogenic TEM, and small-angle X-ray scattering (SAXS). Through collaborative efforts, our colleague employed all-atom simulations which revealed preferential interactions between neighboring alkynes as the driving force leading to altered lattice packing and smaller intermolecular spacing. Additional sequence designs containing [2+2] photocycloaddition-capable residues are also discussed as a potential route to photochemically stabilize bundlemer lattices in situ. ☐ Next, I developed a series of bundlemer sequences that introduce charge patchiness through glutamic acid–lysine (EK) pairs. Building from single-charge (SC) bundlemers that form liquid-crystalline (LC) phases, I systematically positioned EK pairs along the bundlemer periphery to determine how charge patch location modulates assembly. A single EK pair at the bundlemer termini suppressed LC ordering, as determined by SAXS and polarized optical microscopy (POM). In contrast, substitutions at other positions preserved LC ordering, highlighting the critical role of charge patch location. Thermodynamic and hydrodynamic effects of patchiness were quantified under dilute conditions using dynamic and static light scattering (DLS/SLS). Furthermore, specific patterning of EK charge patches generated a pH responsive sequence that transitioned from an LC phase at low pH to a square lattice structure at neutral pH, as determined by TEM and SAXS. These results establish bundlemers as model nanoparticles for studying how charge patch density and spatial localization regulate interactions and hierarchical assembly in both proteinaceous materials and synthetic colloids. ☐ Finally, I exploited single-amino-acid level design to decouple the effects of EK charge patches on interparticle interactions and assembly. SC variants containing exclusively glutamic acid (E-only) or lysine (K-only) substitutions were synthesized and evaluated for LC formation. Charge inversion at the termini, specifically K-only substitutions, disrupted long-range order when compared to E-only analogs, independent of residue position. When E-only substitutions were made within the center of the bundlemer particle, a transition from a nematic LC phase to a square lattice was confirmed using SAXS. K-only substitutions within the center of the bundlemer enabled long-range ordering to persist, further emphasizing the critical role of amino acid identity and positioning within the first heptad of LC-forming bundlemer sequences. Guided by these results, I designed and synthesized a bundlemer sequence containing all E-only modifications on the particle periphery as a means to generate self-assembled lattice structures, providing a promising avenue for the design of sequence-encoded nanoparticle assembly. This work reinforces the utility of the bundlemer as a model material platform for understanding sequence–assembly–function relationships in peptides and proteins, while assisting in defining key molecular design rules which govern long-range LC ordering and lattice formation in the bundlemers. ☐ Overall, this dissertation establishes bundlemers as a tunable, sequence-defined platform for addressing long-standing challenges in patchy colloid design. By achieving precise control over patch anisotropy without compromising particle uniformity, this work unites principles of biomolecular self-assembly and colloidal physics, advancing the design of programmable, biologically inspired materials.
Description
"At the request of the author or degree granting institution, this graduate work is not available to view or purchase until January 05 2027."--ProQuest abstract/details page.
Keywords
Coiled-coil, Hydrophobic patterning, Patchy particles, Peptide assemblies, Peptide characterization