Protein cages are unique building blocks in biological research due to their versatility and wide ranging potential applications in drug delivery and biological imaging and sensing. This dissertation addresses the use of two different protein cages, vaults and viral capsids, to package synthetic and biological materials, providing the groundwork for using these biocages in encapsulation and delivery applications.

The first part of this dissertation explores the use vaults with a goal of packaging materials in the particle interior. Three fundamental issues are addressed: 1) can a foreign material be packaged? 2) can release be controlled? 3) how do biological materials access the vault interior? For question 1, a fluorescent polyanionic semiconducting polymer [poly(2-methoxy-5-propyloxy sulfontate phenylene vinylene), MPS-PPV] was encapsulated inside vaults to form optically active protein cages. Polymer incorporation into vaults was confirmed by fluorescence spectroscopy and small-angle X-ray scattering. For question 2, a bifunctional amine-reactive reagent can be used for the reversible cross-linking of vaults to trap the polymer inside. For question 3, we examine vault fluctuations in solution. Three independent sets of experiments indicate that vaults can separate into open halves in solution and that these halves can sometimes exchange. Finally, we explored the possibility of engineering vaults with designed functions. Metal-binding proteins were fused to a vault binding domain. These vaults bind lead and copper ions and could be used for therapeutics and medical imaging reagents.

The second part of this dissertation discusses the use of a more rigid protein cage from Cowpea Chlorotic Mottle Virus to encapsulate luminescent species. The flexible polymer polystyrene-sulfonate conjugated with rhodamine-B (PSS-Rh), and the more rigid MPS-PPV are used to obtain optically active virus-like particles with different structures. The PSS-Rh polymer can be packaged into spherical structures and retain its fluorescent. However, its flexible conformation cannot control the shape of the biocage. MPS-PPV, however, whose conformation is sensitive to its local environment, can control the architecture of viral capsids. Results from fluorescence spectroscopy, TEM, and sucrose gradient separation indicate that MPS-PPV can be encapsulated into spherical particles or rod-like structures depending on the ionic strength and the MPS-PPV conformation during assembly.