Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

James A. Stapleton, Timothy A. Whitehead, Vikas Nanda

    Research output: Research - peer-reviewArticle

    • 7 Citations

    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.

    LanguageEnglish (US)
    Pages9632-9637
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume112
    Issue number31
    DOIs
    StatePublished - Aug 4 2015

    Profile

    Membrane Proteins
    Lipids
    Protein Engineering
    Cell Membrane
    Escherichia coli
    Amino Acids
    Mutation
    Membranes

    Keywords

    • Membrane proteins
    • OmpA
    • Protein design
    • Statistical potential
    • β-barrel

    ASJC Scopus subject areas

    • General

    Cite this

    Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. / Stapleton, James A.; Whitehead, Timothy A.; Nanda, Vikas.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, No. 31, 04.08.2015, p. 9632-9637.

    Research output: Research - peer-reviewArticle

    @article{aa1d10cce044471ea908c66fc8e849ac,
    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.",
    keywords = "Membrane proteins, OmpA, Protein design, Statistical potential, β-barrel",
    author = "Stapleton, {James A.} and Whitehead, {Timothy A.} and Vikas Nanda",
    year = "2015",
    month = "8",
    doi = "10.1073/pnas.1501836112",
    volume = "112",
    pages = "9632--9637",
    journal = "Proceedings of the National Academy of Sciences of the United States of America",
    issn = "0027-8424",
    number = "31",

    }

    TY - JOUR

    T1 - Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

    AU - Stapleton,James A.

    AU - Whitehead,Timothy A.

    AU - Nanda,Vikas

    PY - 2015/8/4

    Y1 - 2015/8/4

    N2 - 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.

    AB - 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.

    KW - Membrane proteins

    KW - OmpA

    KW - Protein design

    KW - Statistical potential

    KW - β-barrel

    UR - http://www.scopus.com/inward/record.url?scp=84938723751&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=84938723751&partnerID=8YFLogxK

    U2 - 10.1073/pnas.1501836112

    DO - 10.1073/pnas.1501836112

    M3 - Article

    VL - 112

    SP - 9632

    EP - 9637

    JO - Proceedings of the National Academy of Sciences of the United States of America

    T2 - Proceedings of the National Academy of Sciences of the United States of America

    JF - Proceedings of the National Academy of Sciences of the United States of America

    SN - 0027-8424

    IS - 31

    ER -