title: Consensus protein design without phylogenetic bias.
abstract: Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here, we show that randomization of a single protein represents a reliable alternative source of sequence diversity that is essentially free of phylogenetic bias. A small number of functional protein sequences selected from binary-patterned libraries suffice as input for the consensus design of active enzymes that are easier to produce and substantially more stable than individual members of the starting data set. Although catalytic activity correlates less consistently with sequence conservation in these extensively randomized proteins, less extreme mutagenesis strategies might be adopted in practice to augment stability while maintaining function.
authors.affiliation: Laboratory of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Jäckel
authors.forename: Jesse D
authors.initials: JD
authors.lastname: Bloom
authors.forename: Peter
authors.initials: P
authors.lastname: Kast
authors.forename: Frances H
authors.initials: FH
authors.lastname: Arnold
authors.forename: Donald
authors.initials: D
authors.lastname: Hilvert
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002826:Chorismate Mutase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000235:genetics; D004795:Enzyme Stability; D004798:Enzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D010802:Phylogeny; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: D004269:DNA, Bacterial; D004798:Enzymes; D019151:Peptide Library; D011506:Proteins; D002826:Chorismate Mutase