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Biophys. J. BioFAST: First Published December 16, 2005. doi:10.1529/biophysj.105.071076
© 2005 by the Biophysical Society.

A more recent version of this article appeared on March 1, 2006.
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PROTEINS

Confinement Effects on the Thermodynamics of Protein Folding: Monte Carlo Simulations

Nitin Rathore 1*, Thomas A Knotts IV 2 and Juan J de Pablo 3

1 Novozymes North America Inc., Franklinton, NC
2 University of Wisconsin-Madison
3 University of Wisconsin - Madison

* To whom correspondence should be addressed. E-mail: rathore{at}cae.wisc.edu.

Submitted on July 20, 2005
Revised on September 21, 2005
Accepted on 21 November 2005


  Abstract
The effects of chaperonin-like cage induced confinement on protein stability have been studied for molecules of varying sizes and topologies. Minimalist models based on Go-like interactions are employed for the proteins, and density-of-states based Monte Carlo simulations are performed to accurately characterize the thermodynamic transitions. This method permits efficient sampling of conformational space and yields precise estimates of free energy and entropic changes associated with protein folding. We find that confinement driven stabilization is not only dependent on protein size and cage radius, but also on the specific topology. The choice of the confining potential is also shown to have an effect on the observed stabilization and the scaling behavior of the stabilization with respect to the cage size.

Key Words: density of states, entropy, free energy, stability




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T. A. Knotts IV, N. Rathore, and J. J. d. Pablo
An Entropic Perspective of Protein Stability on Surfaces
Biophys. J., June 1, 2008; 94(11): 4473 - 4483.
[Abstract] [Full Text] [PDF]


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Copyright © 2005 by the Biophysical Society.