Abstract
This chapter explores the use of large exchanges of structure (subdomains, domains, and whole proteins) to evolve new function in proteins. These include the formation of multifunctional proteins, tandem duplication, domain recruitment, and circular permutation. The chapter describes the examples of domain swapping performed to engineer proteins with desired function and properties. Studies are categorized under the intended goals of the protein engineering: engineering of allosteric regulation, creation of activators and inhibitors, improvement in stability or expression, modification of substrate specificity, improvement of catalytic efficiency, alteration of multimodular synthetases, improvement of therapeutic properties, creation of molecular biosensors, and creation of novel enzymes. The chapter discusses two methodologies for the evolution of protein function by domain swapping includes non-combinatorial and combinatorial. Non-combinatorial methods for the engineering of domain-swapped enzymes have primarily been employed in the rational design of proteins. Progress in utilizing domain swapping for protein engineering has been partially hindered by the lack of combinatorial methods for performing domain swapping on any two proteins independent of DNA homology.
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