UCSF

This dissertation presents methods developed for two biological systems. In the first chapter, we describe computational methods for designing a de novo kinase reporter. Our reporter operates as a switch, undergoing a change in oligomeric state in response to kinase activation. We designed the reporter to induce liquid-liquid phase separation upon substrate phosphorylation, making it the first example of a de novo designed protein switch capable of forming biomolecular condensates. In the second chapter, we introduce a simple knowledge-based metric to assess the strengths of residue-residue interactions in a protein complex interface. This structural bioinformatics-based method precludes the need for modeling mutation-induced structural and energetic effects. We tested this method on an integrin interface for which current computational alanine scanning methods were not able to accurately rank hot spot residues according to the degree they destabilize the integrin complex. Encouragingly, we found that our metric could more accurately differentiate the subtle energetics of hot spot residues that regulate integrin interfacial stability. Together, these projects were developed to test the limits of current design methods and discover new design rules for protein binding.