Folding thermodynamics of peptides

Details Folding thermodynamics of peptides Folding thermodynamics of peptides

2004-12-03

arxiv.org/abs/q-bio/0412007v1

Biophys. J. 88 (2005) 1560-1569

Biology

Quantitative Biology

Biomolecules

26 pages, 10 figures

Scientific paper

10.1529/biophysj.104.050427

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.

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