A minimalistic all-atom approach to protein folding

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Abstract

Using simple sequence-based potentials, the folding properties of a designed three-helix-bundle protein, an alpha-helix and a beta-hairpin are studied. The three-helix-bundle protein is modelled using 5-6 atoms per amino acid and is found to undergo a first-order-like folding transition in which chain collapse and helix formation cannot be separated, which is in-accord with experimental data. The other two sequences are studied using a model that contains all atoms and are indeed found to make an alpha-helix and a beta-hairpin, respectively, for exactly the same choice of parameters. The calculated melting curves are, moreover, in reasonable quantitative agreement with experimental data, for both peptides. The melting curves are found to be quite well described by a simple two-state model, although the energy distributions lack a clear bimodal shape.
Original languageEnglish
Pages (from-to)S1797-S1807
JournalJournal of Physics: Condensed Matter
Volume15
Issue number18
DOIs
Publication statusPublished - 2003

Subject classification (UKÄ)

  • Biophysics

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