De Novo Design of Heterotetrameric Coiled-Coils Christopher Ostaszewski

Format:

Book

Thesis/Dissertation

Author/Creator:

Ostaszewski, Christopher, author.

Contributor:

University of Pennsylvania. Chemistry., degree granting institution.

Language:

English

Subjects (All):

0219.

0307.

0487.

0494.

Local Subjects:

0219.

0307.

0487.

0494.

Physical Description:

1 electronic resource (50 pages)

Contained In:

Dissertations Abstracts International 87-07B

Place of Publication:

Ann Arbor : ProQuest Dissertations and Theses, 2025

Language Note:

English

Summary:

Beyond their myriad biological functions, proteins are a useful medium for creating new biomaterials. Known for their structural rigidity in nature, α-helices are form oligomeric coiled-coils. Previous research has identified a series of homotetramers that self-assemble into coiled-coils with a consistent hydrophobic core while allowing variations in the sequence and properties of the exterior. The assembled bundles (cylinders with a length of 4 nm) were polymerized to create micron-length rods. This construct allows variation in the base unit by changing the protein sequence, but the rod linkages on both ends are identical in a D2 symmetric bundle. Further control can be gained with by designing a new C2 symmetric bundle, a self-assembled heterotetrameric coiled-coil.In the first project, a probability-based sequence optimization was utilized to iterate upon the previous de novo designs and break the symmetry of the bundle. A pair of sequences were designed to self-assemble into the coiled-coil structure only when both proteins are present. The assemblage of homo-oligomers was mitigated through complementary charge interactions, energetically favoring only the mixed bundle. Artificial intelligence protein structure predictions and circular dichroism experiments have supported the formation of a single oligomer, the designed heterotetramer. The second project aimed to create heterotetramers by redesigning the hydrophobic residues. A multifaceted optimization combined a structural design of the coiled-coil with the sequence design of the residues interacting within the core. Several core designs were identified, each a potential oligomeric protein with exterior sequence variability. Representative sequences were generated and tested through protein oligomer structure predictors, corroborating the structural design of the heterotetrameric coiled-coil. The final project explored the rod formation from the heterotetramer designs. Asymmetry in a single bundle leads to two putative interfaces and orientations of a dimer of bundles, parallel and antiparallel. Protein structure predictions were utilized to create both dimer connections while each bundle is a recreation of the designed coiled-coil structure. The heterotetrameric bundles designed can be the base unit of rods, made more complex because the polymerization is asymmetric

Notes:

Advisors: Saven, Jeffery G. Committee members: Baumgart, Tobias; Dmochowski, Ivan J.; Lester, Marsha I.

Source: Dissertations Abstracts International, Volume: 87-07, Section: B.

Ph.D. University of Pennsylvania 2025

Vendor supplied data

Local Notes:

School code: 0175

ISBN:

9798276001258

Access Restriction:

Restricted for use by site license