Research Interests

The overall research undertaken in our lab has two fundamental goals, both focused on the chemistry/biology interface. One goal is to develop new methods and technologies, while the second goal is to investigate fundamental questions. The philosophy of the lab is to mesh each of the goals so that they can feed into the other in a smooth and dynamic manner. The new technologies will be utilized to help answer fundamental questions and this basic research will necessitate the development of additional methods. The novel techniques will be developed with an eye on generality and additional applications. They will initially focus on combinatorial techniques that not merely employ vast collections of molecules, but unleash the power and intellectual satisfaction of focused design. The fundamental biological systems of interest will be focused on understanding the role protein-protein interactions play in the key cellular process of apoptosis (controlled cell death), how primary, secondary, and tertiary structure of proteins affect their quaternary structure and self assembly processes, and whether it is possible to convert overly reactive, non-specific compounds into specific ones that target key HIV and Alzheimer’s Disease proteins.

This project sets out to establish a general strategy for the development of modulators of protein-protein interactions by screening two phage display libraries of proteins against a library of small molecules to find mutant proteins that only dimerize in the presence of the small molecule. Protein library members will be selected that, together, generate an appropriately sized cavity (“hole”) that is filled by a specific small molecule (“bump”). The initial protein libraries will be based on four helix bundle dimers. The “hits” will be screened for activity, selectivity, and orthogonality, in the presence and absence of the small molecules, by forming a fusion to parts of the green fluorescent protein (GFP). The resulting four helix bundle/small molecule systems will be advanced both as rapidly generated small molecule sensors (as the GFP fusions) for chemical warfare agents and as tools to unraveling key cellular process through fusion to various other proteins of interest (i.e. "chemical inducers of dimerization"). Additionally, the hits will be analyzed to help understand the fundamentals of protein-small molecule recognition processes. In parallel, this screening strategy will be applied to understanding how Bcl-2 family members propagate apoptotic signals through protein-protein interactions with each other. The dimerization surface of each partner will be rationally diversified and mutants will be selected that dimerize only in the presence of small molecules. The resulting hits will be introduced into eukaryotic cell lines and probed with and without the small molecule dimerizing agents to determine the role the protein pair has on apoptotic signaling. This strategy should prove universal to other protein-protein systems and will allow their manipulation without the need to form potentially disrupting fusion proteins as commonly used in chemical inducers of dimerization applications.

Small Molecule Warhead/Peptide mRNA Display to Discover Anti-Retroviral and Anti-Amyloid Compounds

This project will develop a general method to modulate the reactivity or specificity of “warhead” functionality against key disease related proteins. These warheads will have known activity but may be not be viable for the development of drugs (due to a lack of binding specificity or the possession of broad-based reactivity). The technology will involve the development of mRNA libraries that not only present and tag a randomized peptide domain, but also a small molecule warhead. Specifically, this technique will be used to screen a small library of disulfide-containing molecules, with a wide range of redox properties, against the HIV nucleocapsid protein as a general strategy to discover molecules which can be developed into antiretroviral compounds. Additionally, the specificity of dye molecules known to non-specifically bind amyloid aggregates will be tuned through this technique to find labels and potential antagonists of specific amyloidogenic proteins such as beta-amyloid, which has been demonstrated to play a key role in Alzheimer’s Disease.

Semi-Rationally Designed Four Helix Bundle Proteins That Self-Assemble into Capsules With Novel
Sizes and Shapes

Many ferritin proteins self-assemble into protein capsules. This project will focus on formation of protein capsules with novel sizes and shapes by domain swapping of two four helix bundle ferritin proteins which naturally self-assemble into different size protein capsules. Whole helicies or parts of the helicies will be swapped to form a small library of proteins. These libraries will be screened for the formation of assemblies that differ in size and shape from those formed by the native proteins. Along with investigating the fundamental question of protein folding, this strategy will be applied to the templating of inorganic nano-particles of novel size, shape, and materials properties.