Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide

We used computer simulations to compare the reversible folding of a 20-residue peptide, as described by sequence-based and structure-based energy functions. Sequence-based energy functions are transferable and can be used to describe the behavior of different proteins, since interactions are defined between atomic species. Conversely, structure-based energy functions are not transferable, since the interactions are defined relative to the native conformation, which is assumed to correspond to the global minimum of the energy. Our results indicate that the sequence-based and the structure-based descriptions are in qualitative agreement in characterizing the two-state behavior of the peptide that we studied. We also found, however, that several equilibrium properties, including the free-energy landscape, can be significantly different in the various models. These results suggest that the fact that a model describes the native state of a polypeptide chain does not necessarily imply that the thermodynamic and kinetic properties will also be reproduced correctly. © 2005 by the Biophysical Society.