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Biophys. J. BioFAST: First Published November 8, 2004. doi:10.1529/biophysj.104.046375
© 2004 by the Biophysical Society.

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

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

Feng Ding 1, Sergey V Buldyrev 2 and Nikolay V Dokholyan 1*

1 The University of North Carolina at Chapel Hill
2 Center for Polymer Studies, Boston University, Boston, MA 02215

* To whom correspondence should be addressed. E-mail: dokh{at}med.unc.edu.

Submitted on May 24, 2004
Revised on August 4, 2004
Accepted on 20 October 2004


  Abstract
We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2Å backbone root-mean-square distance (RMSD) from the corresponding NMR structures. The minimum RMSD of Trp-cage conformations in the simulation can be smaller than 1.00Å. Our findings suggest that, at least for the case of Trp-cage, a detailed all-atom protein model with a physical molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success of folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulations studies may be mainly due to the special stabilizing features specific to this miniprotein.

Key Words: Trp-cage, discrete molecular dynamics, protein folding




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Copyright © 2004 by the Biophysical Society.