Nature has evolved and designed proteins to perform an exquisite array of tasks, but in the pursuit of biotechnological interests, these proteins must often be improved, altered, or even completely redesigned. In the post-genomic era, protein sequence information is abundant and readily available, and structural biology efforts are rapidly increasing the amount of protein structure information. However, the level of intricacy and complexity of most proteins is still such that rational design efforts are often unsuccessful in imparting an improved or new function to a protein. Fortunately, protein engineers can utilize an experimental algorithm that mimics Darwinian evolution to introduce new functions into proteins. In this algorithm, termed directed evolution, thousands or even millions of protein variants are generated by the introduction of mutations to the gene encoding the protein of interest. The library of protein variants is then screened to identify those members of the population with the highest levels of function or activity: a molecular survival of the fittest. One of the major focuses of the Link group is to apply directed evolution to medically relevant proteins.
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.