San Francisco, CA
The Kortemme lab is interested in how biological molecules communicate with each other, and how this communication encodes the processing of information. How do biomolecules recognize one another, and how do their interactions transduce signals? How do molecules build up "modules" that act as "adaptors", "switches" and feedback-loops? How are modules wired together into the networks responsible for regulation and decision processes observed in biology? Computationally, we have developed a simple physical energy function for the prediction and design of protein-protein interactions, at the atomic level. Experimentally, we have applied this model to the computational redesign of a protein interface, created an artificial DNA binding protein with new specificity, and developed a computational strategy for the redesign of protein complexes to generate new pairs of interacting proteins. We are now applying and extending our computational model at different "resolution", ranging from details of atom-atom interactions to cellular communication networks. We are aiming to develop more accurate methods to model the structural details of molecular interactions. Can new interactions and modules with defined properties be engineered? Ultimately we would like to apply computational and experimental methods to better understand how cellular processes are regulated by molecular communication.