Browsing by Author "Yu, Le Tracy"

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    Advancing Collagen Mimicry: Covalent Triple Helix Stabilization and Higher-order Nanostructure Design
    (2024-04-16) Yu, Le Tracy; Hartgerink, Jefferey
    Collagen plays critical roles in living systems, sparking interest in developing collagen mimics. This thesis advances collagen mimicry by enhancing collagen stability and developing higher-order nanostructures using collagen-like peptides. It addresses two main challenges: the low thermal stability and slow folding rate of collagen triple helices and the lack of understanding of sequence-structure relationships for collagen quaternary structure folding. Chapter 1 reviews collagen protein family, emphasizing their biological significance and structural characteristics, evaluating existing research on collagen triple helix stabilization, and designing artificial nanofibers assembled by collagen-like peptides. Chapter 2 introduces collagen stabilization employing electrostatic interactions between the amino acid side chains of glutamate and lysine for covalent bond formation post triple helix folding, a method termed "covalent capture." The formation of interstrand amide bonds significantly enhances the thermal stability and folding rate of triple helices. Chapter 3 expands this concept by introducing selectivity of covalent bond formation using chemically orthogonal protecting groups to prevent unwanted covalent bond formation. The approach allows for covalent capture of collagen triple helices with virtually any sequence. Chapter 4 describes the development of a hollow octadecameric assembly using collagen-like peptides derived from protein C1q. This bundle of six triple helices formation relies on an ABC heterotrimeric composition but not the disulfide bonds or C-terminal fragments that are present in nature. Chapter 5 describes efforts for atomic structure determination of the six triple helices bundle with cryo-EM. The structure unveiled a hollow hydrophobic channel and H-bonding networks between individual triple helices. Peptide mutant assemblies confirmed the structural importance of these components for oligomer formation. Chapter 6 explores the assembly space of higher-order structure formation using collagen-like peptides. It starts with sequence-structure relationship study of collagen oligomer formation through a library of peptide mutants of surfactant protein A. Findings suggest that sequences containing specific charged and hydrophobic residues contribute to quaternary structure formation. Leveraging this data, we designed collagen-like peptides to create structures including pH-responsive nanoribbons, layered oligomers, and 2D nanosheets, unprecedented in nature. This thesis advances our understanding of collagen folding and sets the stage for innovative collagen higher-order assembly designs.
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    Exploration of the hierarchical assembly space of collagen-like peptides beyond the triple helix
    (Springer Nature, 2024) Yu, Le Tracy; Kreutzberger, Mark A. B.; Bui, Thi H.; Hancu, Maria C.; Farsheed, Adam C.; Egelman, Edward H.; Hartgerink, Jeffrey D.; Bioengineering; Chemistry
    The de novo design of self-assembling peptides has garnered significant attention in scientific research. While alpha-helical assemblies have been extensively studied, exploration of polyproline type II helices, such as those found in collagen, remains relatively limited. In this study, we focus on understanding the sequence-structure relationship in hierarchical assemblies of collagen-like peptides, using defense collagen Surfactant Protein A as a model. By dissecting the sequence derived from Surfactant Protein A and synthesizing short collagen-like peptides, we successfully construct a discrete bundle of hollow triple helices. Amino acid substitution studies pinpoint hydrophobic and charged residues that are critical for oligomer formation. These insights guide the de novo design of collagen-like peptides, resulting in the formation of diverse quaternary structures, including discrete and heterogenous bundled oligomers, two-dimensional nanosheets, and pH-responsive nanoribbons. Our study represents a significant advancement in the understanding and harnessing of collagen higher-order assemblies beyond the triple helix.