A unique protein engineering platform to co-evolve protein-protein pairs using combinatorial biology approaches

Engineering novel proteins through directed evolution have become a foundation of protein engineering in biotech. However, these techniques are incapable of simultaneous engineering of protein-protein pairs through library-on-library selections. An efficient synthetic system for bidirectional, simultaneous protein-protein coevolution could serve as a platform to simulate natural coevolution and for biotechnology applications

The Garcia Lab at Stanford has invented a unique protein engineering platform to co-evolve protein-protein pairs using combinatorial biology approaches. The method adopts Z domain-affibody pairs as a model system to generate co-evolved interfaces that were extensively characterized by 10 X-ray crystal structures, next-generation sequencing (NGS), isothermal titration calorimetry (ITC), and bioinformatics. The approach enabled efficient isolation of completely re-wired interfaces with a wide range of affinities and orthogonalities. Deep sequencing enabled the inventors to reconstruct evolutionary pathways of protein pairs and they have since sequenced thousands of protein-protein complexes with different degrees of specificity, cross-reactivity and orthogonality. These sequences could find applications in many types of synthetic biology methods. The integration of a synthetic coevolution platform with machine learning enables the interrogation of a protein-protein interaction with exceptional granularity.