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Biophys. J. BioFAST: First Published September 1, 2006. doi:10.1529/biophysj.106.087668
© 2006 by the Biophysical Society.

A more recent version of this article appeared on November 15, 2006.
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Sandipan Mohanty
Ulrich H.E. Hansmann
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BIOPHYSICAL THEORY AND MODELING

Folding of Proteins with diverse Folds

Sandipan Mohanty 1 and Ulrich H.E. Hansmann 2*

1 Forschungszentrum Jülich
2 Michigan Technological University

* To whom correspondence should be addressed. E-mail: hansmann{at}mtu.edu.

Submitted on April 21, 2006
Revised on June 29, 2006
Accepted on 28 July 2006


  Abstract
Using parallel tempering simulations with high statistics, we investigate the folding and thermodynamic properties of three small proteins with distinct native folds: the all-helical 1RIJ, the all-sheet beta3s, and BBA5 which has a mixed helix-sheet fold. In all three cases simulations with our energy function find the native structures as global minima in free energy at experimentally relevant temperatures. However, the folding process strongly differs for the three molecules indicating that the folding mechanism is correlated with the form of the native structure.

Key Words: Monte Carlo simulation, Protein folding, all-atom model, effective potential, parallel tempering




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Copyright © 2006 by the Biophysical Society.