title: Computational redesign of the lipid-facing surface of the outer membrane protein OmpA.
abstract: Advances in computational design methods have made possible extensive engineering of soluble proteins, but designed β-barrel membrane proteins await improvements in our understanding of the sequence determinants of folding and stability. A subset of the amino acid residues of membrane proteins interact with the cell membrane, and the design rules that govern this lipid-facing surface are poorly understood. We applied a residue-level depth potential for β-barrel membrane proteins to the complete redesign of the lipid-facing surface of Escherichia coli OmpA. Initial designs failed to fold correctly, but reversion of a small number of mutations indicated by backcross experiments yielded designs with substitutions to up to 60% of the surface that did support folding and membrane insertion.
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824; Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854;
authors.forename: James A
authors.initials: JA
authors.lastname: Stapleton
authors.affiliation: Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824; Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Whitehead
authors.affiliation: Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854; nanda@cabm.rutgers.edu.
authors.forename: Vikas
authors.initials: V
authors.lastname: Nanda
mesh_terms: D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000378:metabolism*; D005434:Flow Cytometry; D005453:Fluorescence; D008055:Lipids / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D011392:Proline / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001425:Bacterial Outer Membrane Proteins; D008055:Lipids; D050505:Mutant Proteins; D011994:Recombinant Proteins; C078167:OMPA outer membrane proteins; D011392:Proline
keywords: OmpA; membrane proteins; protein design; statistical potential; β-barrel