Protein recombination

Protein engineering by site-directed recombination generates libraries of hybrid proteins (or "chimeras") by mimicking the mixing and inheritance that occur in natural reproduction. As shown in the left-hand figure, a set of homologous parent genes are recombined at defined breakpoint locations, yielding a combinatorial set of hybrids. Subsequent screening/selection then identifies hybrids with desirable functional characteristics.

We are developing techniques to optimize the planning of recombination experiments. For example, when selecting breakpoints, one must consider the trade-off between the stability and the diversity of the resulting hybrids. Given a family of homologous proteins, we select a small number of parents to be recombined at specific locations, generating a library of hybrids. Recombination may perturb the previously observed correlations between amino acid types for interacting residues, thereby possibly affecting stability. Furthermore, the resulting library may have more or less diversity; the choice of breakpoint location on the top yields hybrids that are identical to the parents, while that on the bottom results in sequence space being sampled relatively uniformly, with an equal number of mutations between each hybrid and each parent. Our methods simultaneously optimize both these criteria.

We are also developing techniques to optimize the robotic assembly of the planned library.