Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders
Adenovirus-derived dodecamer (ADDomer) nanoparticles comprise 60 copies of Adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport and deployment of ADDomer-based therapeutics independent of a cold-chain. To expand the scope of ADDomer nanoparticles for new applications, we engineered ADDobodies. ADDobodies represent the crown domain of the PBP, genetically separated from its multimerization domain. We inserted heterologous sequences into hyper-variable loops in the crown domain. The resulting ADDobodies were expressed at high yields in Escherichia coli, are monomeric and maintain thermostability. We solved the X-ray structure of an ADDobody prototype validating our design. We demonstrated that ADDobodies can be used to select a specific binder against a target in in vitro selection experiments using ribosome display, with an enrichment factor of [~]104-fold in one selection round. We show that ADDobodies can be converted back into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 [A] structure determined by cryogenic electron microscopy (cryo-EM). Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.