De Novo Design of Protein Nanoparticles with Programmable and Tunable Function

Abstract

Assembly of designed symmetric protein nanoparticles from multiple copies of one or more distinct protein subunits warrants unique shapes, size diversity, structural regularity, and polyvalency. Current efforts of protein nanoparticles are aimed toward engineering natural and de novo nanoparticles for a myriad of applications including multivalent display of target proteins, packaging of macromolecular materials, and scaffolding for molecular imaging techniques (Divine et al. 2020; Bale et al. 2016; Butterfield et al. 2017; McConnell et al. 2020; Liu et al. 2018; Liu, Huynh, and Yeates 2019; Vulovic et al. 2020; Boyoglu-Barnum et al. 2020; Ueda et al. 2020; Marcandalli et al. 2019; Walls et al. 2020). In this thesis, I present the development of an accessible and versatile software application for the arrangement of protein scaffolds into asymmetric and symmetric nanomaterials–including nanoparticles, using this application to design the first three component, non-porous, pH-responsive antibody nanoparticles (O432) as a platform for targeted delivery, and extension of all one- and two-component nanoparticles docked and designed with this application toward developing an undergraduate research curriculum. Additional stories are presented, which describe assays used to explore the O432 nanoparticles as tools for targeted delivery and general design rules that govern interfaces of designed protein nanoparticles.