SCHEMA-Guided Protein Recombination

This chapter examines the different aspects of SCHEMA-guided protein recombination. SCHEMA is a scoring function that predicts which elements in homologous proteins can be swapped without disturbing the integrity of the structure. Using the structural coordinates of the parent proteins, SCHEMA identifies pairs of residues that are interacting, and determines the number of interactions that are broken when a chimeric protein inherits portions of its sequence from different parents. The SCHEMA disruption of a chimeric sequence made by recombining sequence elements from homologous proteins is presented. The best methods available for creating the libraries identified by SCHEMA as enriched in folded chimeras are sequence-independent site directed chimeragenesis and chemical synthesis. These techniques can recombine parents with any level of sequence identity at multiple sites and easily create libraries encoding thousands of chimeras. It is observed that when the parents do not exhibit sufficient identity at the desired crossover locations, synonymous mutations can often be introduced to allow recombination at that site. It is found that SCHEMA only calculates the disruption arising from recombination, not from mutation.