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Originally published as Biophys J. BioFAST on December 16, 2005.
doi:10.1529/biophysj.105.071076
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Biophysical Journal 90:1767-1773 (2006)
© 2006 The Biophysical Society

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

Nitin Rathore *, Thomas A. Knotts, IV {dagger} and Juan J. de Pablo {dagger}

* Novozymes North America Inc., Franklinton, North Carolina; and {dagger} Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin

Correspondence: Address reprint requests to Juan J. de Pablo, 1415 Engineering Dr., Madison, WI 53706. Tel.: 608-262-7727; Fax: 608-262-5434, Email: depablo{at}engr.wisc.edu.

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.




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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.
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Copyright © 2006 by the Biophysical Society.