Library analysis of SCHEMA‐guided protein recombination

Models, Molecular Protein Conformation Recombinant Fusion Proteins Molecular Sequence Data DNA, Recombinant Protein Engineering beta-Lactamases chimera 510 Recombination: Genetic lactamase Structure-Activity Relationship 03 medical and health sciences schema Peptide Library TEM-1 Amino Acid Sequence directed evolution Models: Molecular PSE-4 Recombination, Genetic 0303 health sciences 540 recombination DNA: Recombinant Algorithms
DOI: 10.1110/ps.0306603 Publication Date: 2004-02-24T22:18:09Z
ABSTRACT
AbstractThe computational algorithm SCHEMA was developed to estimate the disruption caused when amino acid residues that interact in the three‐dimensional structure of a protein are inherited from different parents upon recombination. To evaluate how well SCHEMA predicts disruption, we have shuffled the distantly‐related β‐lactamases PSE‐4 and TEM‐1 at 13 sites to create a library of 214 (16,384) chimeras and examined which ones retain lactamase function. Sequencing the genes from ampicillin‐selected clones revealed that the percentage of functional clones decreased exponentially with increasing calculated disruption (E = the number of residue–residue contacts that are broken upon recombination). We also found that chimeras with low E have a higher probability of maintaining lactamase function than chimeras with the same effective level of mutation but chosen at random from the library. Thus, the simple distance metric used by SCHEMA to identify interactions and compute E allows one to predict which chimera sequences are most likely to retain their function. This approach can be used to evaluate crossover sites for recombination and to create highly mosaic, folded chimeras.
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