title: Protein Engineering by Combined Computational and In Vitro Evolution Approaches.
abstract: Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.
authors.affiliation: Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
authors.forename: Lior
authors.initials: L
authors.lastname: Rosenfeld
authors.affiliation: Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Michael
authors.initials: M
authors.lastname: Heyne
authors.affiliation: Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. Electronic address: jshifman@mail.huji.ac.il.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Shifman
authors.affiliation: Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel. Electronic address: papo@bgu.ac.il.
authors.forename: Niv
authors.initials: N
authors.lastname: Papo
mesh_terms: D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D019020:Directed Molecular Evolution / Q000379:methods*; D006801:Humans; D009154:Mutation; D019151:Peptide Library; D010449:Peptide Mapping; D011485:Protein Binding; D015202:Protein Engineering / Q000379:methods*; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
chemical_list: D019151:Peptide Library; D011506:Proteins
keywords: binding affinity; combinatorial selection; computational protein design; novel binding domains; protein engineering; protein–protein interactions