A minimalistic all-atom approach to protein folding

Summary, in English

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.

• Author: Anders Irbäck
• Department/s: Computational Biology and Biological Physics - Has been reorganised
• Publishing year: 2003
• Language: English
• Pages: 1797-1807
• Publication/Series: Journal of Physics: Condensed Matter
• Volume: 15
• Issue: 18
• Links: http://dx.doi.org/10.1088/0953-8984/15/18/313
• Document type: Journal article
• Publisher: IOP Publishing
• Topic: Biophysics
• Status: Published
• ISBN/ISSN/Other: ISSN: 1361-648X