Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water

Authors

  • Siegfried Höfinger,

    Corresponding author
    1. Department of Physics, Michigan Technological University, Houghton, Michigan, 49331-1295
    • Michigan Technological University, Department of Physics, 1400 Townsend Drive, Houghton, MI 49931-1295
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  • Benjamin Almeida,

    1. Novartis Institutes for BioMedical Research, Brunnerstraße 59, A-1235 Vienna, Austria
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  • Ulrich H. E. Hansmann

    1. Department of Physics, Michigan Technological University, Houghton, Michigan, 49331-1295
    2. John v. Neumann Institute for Computing, Forschungszentrum Jülich, 52425 Jülich, Germany
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Abstract

Parallel temperature molecular dynamics simulations are used to explore the folding of a signal peptide, a short but functionally independent domain at the N-terminus of proteins. The peptide has been analyzed previously by NMR, and thus a solid reference state is provided with the experimental structure. Particular attention is paid to the role of water considered in full atomic detail. Different partial aspects in the folding process are quantified. The major group of obtained structures matches the NMR structure very closely. An important biological consequence is that in vivo folding of signal peptides seems to be possible within aqueous environments. Proteins 2007. © 2007 Wiley-Liss, Inc.

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