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

• DOI: 10.1073/pnas.1501836112
• Publication Date: 2015-07-22T02:10:15Z
• Authors: James A. Stapleton; Timothy A. Whitehead; Vikas Nanda
• Keywords: Models, Molecular; 0301 basic medicine; Protein Folding; 0303 health sciences; Proline; Molecular Sequence Data; Computational Biology; Flow Cytometry; Lipids; Fluorescence; Protein Structure, Secondary; Recombinant Proteins; 03 medical and health sciences; Escherichia coli; Electrophoresis, Polyacrylamide Gel; Mutant Proteins; Amino Acid Sequence; Sequence Alignment; Bacterial Outer Membrane Proteins

Significance The ability to construct novel proteins from basic principles of molecular structure is the fundamental goal of protein design. This is particularly challenging in the case of the β-barrel outer membrane proteins, where our understanding of the rules governing structure and function lags behind that of other classes of proteins. Here, we took a step toward understanding β-barrel membrane protein architecture by focusing on the outward-facing amino acid positions that contact the cell membrane. We replaced the membrane-facing surface of OmpA with new surfaces designed to resemble natural β-barrel surfaces. We were able to design versions of OmpA with mutations at about two-thirds of all surface positions, indicating that β-barrel membrane protein surface design is achievable.