Jeffrey B. Endelman

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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(More)
Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising 3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven(More)
Protein function can be tuned using laboratory evolution, in which one rapidly searches through a library of proteins for the properties of interest. In site-directed recombination, n crossovers are chosen in an alignment of p parents to define a set of p(n + 1) peptide fragments. These fragments are then assembled combinatorially to create a library of(More)
All Rights Reserved iii ABSTRACT For many protein design problems, limited understanding of the relationship between sequence and function necessitates searching through a library of proteins to find the properties of interest. To accelerate this process, molecular models and optimization algorithms can be combined to design diverse libraries enriched in(More)
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods developed for naturally occurring proteins, but this neglects the information contained in the unfolded sequences of(More)
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