A. James Link

Engineering high-affinity inhibitors of anti-apoptotic proteins

The molecular cause of several cancers is an imbalance between pro-apoptotic and anti-apoptotic proteins. It is postulated that the excess anti-apoptotic protein sequesters all of the pro-apoptotic protein thus preventing execution of apoptosis (programmed cell death). One potential treatment for cancers of this type is a high-affinity competitive inhibitor to the anti-apoptotic protein. We are pursuing several different natural proteins as scaffolds for such an inhibitor as well as completely de novo library designs.

Evolving higher efficacy antimicrobial peptides

Some classes of antimicrobial peptides are used by microbes as a defense mechanism against other species. These peptides represent an avenue of treatment for multidrug resistant (MDR) bacterial infections that has not been thoroughly explored yet. We will utilize naturally occurring antimicrobial peptides and apply directed evolution in order to engineer molecules with higher efficacies and broader spectra of activity. Synthetic biology principles are also being investigated in order to generate novel methods of delivering antimicrobial peptides to infection sites.

Biotechnological uses of E. coli: understanding the cellular response

Protein engineers often use host organisms such as E. coli simply as factories with little regard for the physiological state of the cell. We plan to use transcriptional reporters along with genomic and proteomic approaches (including BONCAT) to catalog the response of the cell to biotechnological uses of E. coli such as heterologous protein expression and unnatural amino acid incorporation. The knowledge and insights gained from these large-scale studies will subsequently be used to inform strain engineering experiments to develop host strains of E. coli that are more useful in biotech contexts.

Analyzing differential proteomes with BONCAT (Bio-Orthogonal Non-Canonical Amino Acid Tagging)