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Published August 2003 | public
Journal Article

Library analysis of SCHEMA-guided protein recombination


The 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 beta-lactamases PSE-4 and TEM-1 at 13 sites to create a library of 2^(14) (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.

Additional Information

© 2003 The Protein Society. Published by Cold Spring Harbor Laboratory Press. Received February 17, 2003; Final revision May 1, 2003; Accepted May 1, 2003. This work was supported by the Army Research Office, NIH Fellowship F32 GM64949-01 (J.J.S.), Howard Hughes Medical Institute graduate research fellowship (M.M.M.), National Defense Science and Engineering Fellowship (J.B.E.), National Science Foundation (C.A.V.), and Burroughs-Welcome Fund (C.A.V.). Z.G.W. acknowledges support by the W.M. Keck Foundation. S.L.M. is supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, and an IBM Shared University Research Grant. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.

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