Development of Protein- and Virus-Based Materials for Environmental and Agricultural Applications

Proteins are biopolymers of defined sequence whose amino acid side chains define their structure and function. There is an almost infinite number of sequences for naturally occurring proteins, suggesting there is a trove of undiscovered functional proteins waiting to be identified. Newer tools such as metagenomic screens and bioinformatics allow us to rapidly screen and identify putative functions for new proteins, and the development of in silico structure simulators such as AlphaFold can give us information about these new proteins without having to express, purify, and crystallize them. Further, the decades of technology advancements for molecular cloning and protein expression systems can facilitate the optimization and evolution of proteins with specific or novel functions designed from existing backbones or combined from two separate functional sequences for a bifunctional fusion protein. With all these tools in hand, protein-based biotechnology could be a wellspring of new technologies for some of the most difficult challenges ahead, such as food security, environmental sustainability, and waste management. My current and prior training have equipped me to identify and develop new protein- and virus-based nanomaterials for applications in agriculture and biocatalysis.

My doctoral training was primarily based on enzyme immobilization established through the sequestration of a reactive protein to a solid phase material, such as a nanoparticle. To immobilize the enzyme on a nanomaterial, one can adsorb the enzyme directly through non-covalent interactions, link the enzyme to the material through a covalent interaction, or use protein affinity interactions to drive site-specific interactions. One distinctive yet flexible strategy to achieve this enzyme immobilization is by fusing the enzyme to a binding protein for which the complementary sequence is attached to the material. This creates a more generalized plug-and-play immobilization system, as the binding domain could be attached to any number of enzymes. My background in creating an enzyme immobilization system and developing the process for its application, as well as verifying several candidate enzymes via metagenomic screen, gives me a unique perspective on the path of development to application of enzyme-based technologies.

Building on this experience, I am now developing bionanotechnology platforms using plant virus nanoparticles. Viruses are proteins which repeat several hundred to thousand times in the same nanoparticle, displaying the same chemical surface over and over for each capsid protein. This can be exploited for residue-specific chemical reactions to covalently load hundreds of active ingredient molecules onto the virus. Viral nanoparticles find application in a variety of areas, including nanodelivery systems, drug delivery, agricultural delivery, and gene delivery. Depending on the application, a covalent or non-covalent approach for loading of functional molecules can be considered. My current project involve the optimization of Tobacco mild green mosaic virus (TMGMV) for agrochemical delivery and nucleic acid delivery in plants. To achieve this, my current research has focused on covalent modification of the surface exposed residues of TMGMV and transforming TMGMV into spherical nanoparticles for small molecule and nucleic acid encapsulation. The applications have spanned pest management, development of immune responsive material for plants, and developing new strategies for cargo loading in rod-shaped viral nanoparticles.

Looking forward, these experiences give me the background required to develop biotechnology for environmental applications. The challenges I hope to take on include waste management, resource recovery from agricultural and municipal runoff, and in situ bioremediation using gene delivery in plants. A combination of fusion protein design, enzyme immobilization, and viral nanoparticle development can be used in tandem to assess and address these applications.