title: Combining computational and experimental screening for rapid optimization of protein properties.
abstract: We present a combined computational and experimental method for the rapid optimization of proteins. Using beta-lactamase as a test case, we redesigned the active site region using our Protein Design Automation technology as a computational screen to search the entire sequence space. By eliminating sequences incompatible with the protein fold, Protein Design Automation rapidly reduced the number of sequences to a size amenable to experimental screening, resulting in a library of approximately equal 200,000 mutants. These were then constructed and experimentally screened to select for variants with improved resistance to the antibiotic cefotaxime. In a single round, we obtained variants exhibiting a 1,280-fold increase in resistance. To our knowledge, all of the mutations were novel, i.e., they have not been identified as beneficial by random mutagenesis or DNA shuffling or seen in any of the naturally occurring TEM beta-lactamases, the most prevalent type of Gram-negative beta-lactamases. This combined approach allows for the rapid improvement of any property that can be screened experimentally and provides a powerful broadly applicable tool for protein engineering.
authors.affiliation: Xencor, 111 West Lemon Avenue, Monrovia, CA 91016, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hayes
authors.forename: Jorg
authors.initials: J
authors.lastname: Bentzien
authors.forename: Marie L
authors.initials: ML
authors.lastname: Ary
authors.forename: Marian Y
authors.initials: MY
authors.lastname: Hwang
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Jacinto
authors.forename: Jöst
authors.initials: J
authors.lastname: Vielmetter
authors.forename: Anirban
authors.initials: A
authors.lastname: Kundu
authors.forename: Bassil I
authors.initials: BI
authors.lastname: Dahiyat
mesh_terms: D019943:Amino Acid Substitution; D001665:Binding Sites; D002439:Cefotaxime / Q000494:pharmacology; D019295:Computational Biology / Q000379:methods*; D004351:Drug Resistance; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D016297:Mutagenesis, Site-Directed; D019151:Peptide Library; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D019151:Peptide Library; D001618:beta-Lactamases; C034413:beta-lactamase TEM-1; D002439:Cefotaxime