A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding

Authors

  • Daniel Hsieh,

    1. BioMaPS Institute and the Graduate Program in Computational Biology and Molecular Biophysics, Rutgers University, Piscataway, New Jersey 08854
    2. Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854
    3. Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
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  • Alexander Davis,

    1. Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
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  • Vikas Nanda

    Corresponding author
    1. Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854
    2. Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854
    • Department of Biochemistry, Robert Wood Johnson Medical School—UMDNJ, Piscataway, NJ 08854

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Abstract

Outer membrane β-barrel proteins differ from α-helical inner membrane proteins in lipid environment, secondary structure, and the proposed processes of folding and insertion. It is reasonable to expect that outer membrane proteins may contain primary sequence information specific for their folding and insertion behavior. In previous work, a depth-dependent insertion potential, Ez, was derived for α-helical inner membrane proteins. We have generated an equivalent potential for TM β-barrel proteins. The similarities and differences between these two potentials provide insight into unique aspects of the folding and insertion of β-barrel membrane proteins. This potential can predict orientation within the membrane and identify functional residues involved in intermolecular interactions.

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