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Engineering artificial protein assemblies based on natural protein oligomeric domains

  • Author(s): Lai, Yen-Ting
  • Advisor(s): Yeates, Todd O
  • Wong, Gerard Chee Lai
  • et al.
Abstract

Protein based nanotechnology is an emerging field, which could someday provide novel protein materials for biomedical, biotechnology and other industries. In Nature, many proteins occur as ordered homomeric assemblies, such as virus capsids and microtubules. These natural protein assemblies not only play crucial functions in their biological context, but also can be adopted for various applications. As an example, the capsids of adenoviruses can be used for gene delivery for potential gene therapy. However, there are only limited numbers of natural protein assemblies available for such applications. It will be of great advantage if protein assemblies with novel properties can be designed and engineered to fulfill the needs of specific applications.

Engineering ordered protein assemblies has been a challenging task for protein engineers. Compared to the more advanced field of DNA based nanotechnology, protein based nanotechnology is still in its infancy. Specific interactions can be easily engineered in DNA molecules through complementary hydrogen bonding between base pairs, which can facilitate the assemblies of DNA molecules into various shapes. On the other hand, protein interactions are much more difficult to engineer and hence protein engineers need to design artificial protein assemblies based on a limited number of distinct interactions. As can be learned from natural protein assemblies and crystallography, symmetric operations can expand a small number of distinct interactions into a network of interactions that can embody ordered protein assemblies.

Based on the concept of symmetry, principles for designing ordered protein assemblies can be derived. Two strategies are conceived to fulfill the design principles in my dissertation. The first is to fuse two natural oligomeric domains through the use of helix linkers. Carefully designed fusion proteins can lead to self-assembled protein architectures. A model system of the helix-fusion strategy is studied in great detail by x-ray crystallography and other biophysical methods, while several other helix-fusion systems are also characterized. The second strategy involves merging natural oligomeric domains into chimeric proteins that are capable of forming higher-order assemblies. Several design targets by this chimeric-protein based approach are characterized and presented. My study shows that large protein assemblies can be achieved through the two strategies. Together with other contemporary engineering strategies, the field of protein-based nanotechnology might one day rival the DNA-based counterpart.

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