This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.104.055335v1 88/5/3158    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Cavalli, A. Articles by Paci, E. Search for Related Content PubMed PubMed Citation Articles by Cavalli, A. Articles by Paci, E.

Comparison of Sequence-Based and Structure-Based Energy Functions for the Reversible Folding of a Peptide

Andrea Cavalli ^*, Michele Vendruscolo  and Emanuele Paci ^*

^* Biochemisches Institut der Universität Zürich, Zürich, Switzerland; and Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Correspondence: Address reprint requests to Dr. Emanuele Paci, University of Zurich, Dept. of Biochemistry, Winterthurestrasse 190, Zurich, 8057, Switzerland. Tel.: 41-1-635-5559; E-mail: paci{at}bioc.unizh.ch.

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.

This article has been cited by other articles:

				F. Cecconi, C. Guardiani, and R. Livi Testing Simplified Proteins Models of the hPin1 WW Domain Biophys. J., July 15, 2006; 91(2): 694 - 704. [Abstract] [Full Text] [PDF]

				D. K. West, D. J. Brockwell, P. D. Olmsted, S. E. Radford, and E. Paci Mechanical Resistance of Proteins Explained Using Simple Molecular Models Biophys. J., January 1, 2006; 90(1): 287 - 297. [Abstract] [Full Text] [PDF]