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Originally published as Biophys J. BioFAST on December 21, 2004.
doi:10.1529/biophysj.104.050427
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Biophysical Journal 88:1560-1569 (2005)
© 2005 The Biophysical Society

Folding Thermodynamics of Peptides

Anders Irbäck and Sandipan Mohanty

Complex Systems Division, Department of Theoretical Physics, Lund University, Lund, Sweden

Correspondence: Address reprint requests to A. Irbäck, Tel.: 46-46-222-3493; Fax: 46-46-222-9686; E-mail: anders{at}thep.lu.se.

A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with ~20 residues each. The test set contains both {alpha}-helical (Trp cage, Fs) and ß-sheet (GB1p, GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely sequence-based, is able to fold these different peptides for one and the same choice of model parameters. Furthermore, the melting behavior of the peptides is in good quantitative agreement with experimental data. Apparent folded populations obtained using different observables are compared, and are found to be very different for some of the peptides (e.g., Betanova). In other cases (in particular, GB1m2 and GB1m3), the different estimates agree reasonably well, indicating a more two-state-like melting behavior.




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