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Biophys. J. BioFAST: First Published December 21, 2004. doi:10.1529/biophysj.104.050427
© 2004 by the Biophysical Society.

A more recent version of this article appeared on March 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

Folding thermodynamics of peptides

Anders Irbäck 1* and Sandipan Mohanty 1

1 Lund University

* To whom correspondence should be addressed. E-mail: anders{at}thep.lu.se.

Submitted on July 25, 2004
Revised on October 5, 2004
Accepted on 1 December 2004


  Abstract
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both {alpha}-helical (Trp cage, Fs) and {beta}-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.

Key Words: Monte Carlo simulation, all-atom model, effective potential, peptide folding, two-state analysis




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Copyright © 2004 by the Biophysical Society.