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
AUTHORS (7)
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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