Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination

This paper presents a new approach to site-directed recombination, swapping combinations of selected discontiguous fragments from a source protein in place of corresponding fragments of a target protein. By being both asymmetric (differentiating source and target) and selective (swapping discontiguous fragments), our method focuses experimental effort on a more restricted portion of sequence space, constructing hybrids that are more likely to have the properties that are the objective of the experiment. Furthermore, since the source and target need to be structurally homologous only locally (rather than overall), our method supports swapping fragments from functionally important regions of a source into a target “scaffold”; e.g., to humanize an exogenous therapeutic protein. A protein fragment swapping plan is defined by the residue position boundaries of the fragments to be swapped; it is assessed by an average potential score over the resulting hybrid library, with singleton and...

• Type: Conference
• Year: 2009
• Where: RECOMB
• Authors: Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg
• Keywords: Computational Biology, Discontiguous Fragments, RECOMB 2009, Site-directed Recombination, Swapping Discontiguous Fragments