Hybrid native partitioning of interactions among nonconserved residues in chimeric proteins

Given any operational criterion for pairwise interatomic interactions, for a pair of structurally homologous proteins there exists for both proteins a unique equivalent partitioning of the nonconserved residue positions into mutually noninteracting clusters. In the formation of a chimeric protein derived from these two parental sequences, if nonnative-like interactions are to be avoided in its tertiary structure, then all of the nonconserved residues of each cluster must necessarily be either maintained or interchanged simultaneously. This hybrid native partitioning criterion is applied to known gene shuffling results. When the degree of estimated disruption is modest, the HybNat algorithm provides an efficient predictor of structural integrity. This supports the expectation that a substantial fraction of sequences that conform to the hybrid native partitioning criterion will yield tertiary structures that largely preserve the native-like interactions of the parental proteins.