Software Algorithms for Design of Symmetric Protein Complexes Applied to Cryo-Electron Microscopy Scaffolds and Antibody Nanoparticles

Abstract

Innovation in the symmetric assembly and protein material design space has the potential to – eventually – reinvent medicine and nanotechnology. One leading strategy for design of symmetric assemblies uses genetic fusion of protein homo-oligomer subunits via α-helical linkers. For the nearly two decades since its inception in 2001, this method has been applied as it was originally formulated. In this dissertation, I present the development and application of a tripartite fusion method that builds on this work and addresses two of its principal limitations: linker flexibility and a dearth of geometric solutions. The method is applied to investigate two proof-of-principle design concepts: 1) target capture and structure determination on symmetric cryo-EM scaffolds 2) antibody display and integration into nanoparticles. Designs are characterized by native mass spectrometry, small angle X-ray scattering, and electron microscopy. The experimental results in both of these areas showcase the viability and promise of this design strategy for further use.