An Entropic Perspective of Protein Stability on Surfaces
Thomas A. Knotts IV 1, Nitin Rathore 2 and Juan De Pablo 3*
1 Brigham Young University
2 Amgen Inc.
3 University of Wisconsin - Madison
* To whom correspondence should be addressed. E-mail: depablo{at}engr.wisc.edu.
Submitted on October 2, 2007
Revised on December 19, 2007
Accepted on 22 January 2008
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Abstract |
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The interaction of proteins with surfaces regulates numerous processes in nature, science, and technology. In many applications, it is desirable to place proteins on surfaces in an active state, and tethering represents one manner to accomplish this. However, a clear understanding of how tether placement and design affects protein activity is lacking. Available theoretical models predict that proteins will be stabilized when tethered to substrates. Such models suggest that the surface reduces the number of states accessible to the unfolded state of the protein, thereby reducing the entropic cost of folding on the surface compared to the bulk case. Recent studies, however, have shown that this stabilization is not always seen. The purpose of this paper is to determine the validity of the theory with a thorough thermodynamic analysis of the folding of peptides attached to surfaces. Configuration Temperature Density of States Monte Carlo simulations are used to examine the behavior of four different peptides of different secondary and tertiary structure. It is found that the surface does reduce the entropic cost of folding for tethered peptides, as the theory suggests. This effect, however, does not always
translate into improved stability because the surface may also have a destabilizing enthalpic effect. The theory neglects this effect and assumes that the enthalpy of folding is the same on and off the surface. Both the enthalpic and entropic contributions to the stability are found to be topology and tether-placement specific; we show that stability cannot be predicted a priori. A detailed analysis of the folding of protein A shows how the same protein can be both stabilized and destabilized on a surface depending upon how the tethering enhances or hinders the ability of the peptide to form correct tertiary structures.
Key Words:
Monte Carlo, density of states, free energy, simulation, thermodynamics
