Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Simulations of the Folding Unfolding of Proteins Under Different Solvent Condition

Proteins exhibit marginal stability, determined by the balance of many competing effects. This stability can be perturbed by changes in temperature, pH, pressure, and other solvent conditions. Osmolytes are small organic compounds that modulate the conformational equilibrium, folded (F) and unfolded (U), of proteins as cosolvents. Protecting osmolytes such as trimethylamine N-oxide (TMAO), glycerol, and sugars that push the equilibrium toward F play a crucial role in maintaining the function of intracellular proteins in extreme environmental conditions. Urea is a denaturing osmolyte that shifts the equilibrium toward U. Here we report the reversible folding/unfolding equilibrium, under various solution conditions that include urea, high pressure, and different charge states of the Trp-cage miniprotein (1-4).The folding/unfolding equilibrium is studied using all-atom Replica exchange MD simulations. For urea, the simulations capture the experimentally observed linear dependence of unfolding free energy on urea concentration. We find that the denaturation is driven by favorable direct interaction of urea with the protein through both electrostatic and van der Waals forces and quantify their contribution. Though the magnitude of direct electrostatic interaction of urea is larger than van der Waals, the difference between unfolded and folded ensembles is dominated by the van der Waals interaction. We also find that hydrogen bonding of urea to the peptide backbone does not play a dominant role in denaturation. The unfolded ensemble sampled depends on urea concentration, with greater urea concentration favoring conformations with greater solvent exposure. The m-value is predicted to increase with temperature and more strongly so with pressure (3, 4).

Figure 1: Preferential binding of urea to the protein side chains over the backbone. The left figure shows the binding of urea around the Trp-cage protein. Red spheres represent urea molecules closer to the backbone atoms, while blue spheres represent molecules closer to the sidechains. The figure on the left shows the preferential interaction of urea to the side chains and backbone.

We also explored the effect of protonation of charged groups in protein and found that the unfolded state ensemble changes little as a function of protonation. However, charge-charge interactions in the folded state ensemble are responsible for the change in stability of the protein. Our results show how atomic level simulations with explicit solvent models can be used to characterize the stability of proteins.

This research has been supported by grants from NSF MCB-0543769 and MCB-1050966.


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  3. D. Canchi, D. Paschek and A.E. Garcia, J. Amer. Chem. Soc. 132, 2238-2244 (2010).
  4. D. Canchi and A.E. Garcia, Biophys. J., 100, (2011) doi:10.1016/j.bpj.2011.01.028.

Deepak R. Canchi1, 2
Camilo Jimenez-Cruz1, 3
Angel E. Garcia1, 2, 3

1Center for Biotechnology and Interdisciplinary Studies
2Department of Chemical and Biological Engineering
3Department of Physics, Applied Physics and Astronomy
Rensselaer Polytechnic Institute
Troy, NY 12180 USA