Simulations of the Folding/Unfolding of Proteins Under Different Solvent and Confinement Conditions

When: Thursday, October 24, 2013 at 4:00 pm
Where: DA 114
Speaker: Angel García
Organization: Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute
Sponsor: Physics Colloquium

Proteins exhibit marginal stability, determined by the balance of many competing effects. This stability can be perturbed by changes in temperature, pH, pressure, confinement 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. 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 contributions. 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.

We also study the equilibrium folding/unfolding thermodynamics of the Trp-cage that is confined to the interior of a 2 nm radius fullerene ball. The interactions of the fullerene surface are changed from non-polar to polar to mimic the interior of the GroEL/ES chaperonin that assists proteins to fold in vivo. We find that non-polar confinement stabilizes the folded state of the protein due to the effects of volume reduction that destabilize the unfolded state, and also due to interactions with the fullerene surface. For the Trp-cage, polar confinement has a net destabilizing effect that results from the stabilizing confinement and the competitive exclusion effect that keeps the protein away from the surface hydration shell, and stronger interactions between charged side chains in the protein with the polar surface that competes against the formation of an ion pair that stabilizes the protein folded state. We show that confinement effects due to volume reduction can be overcome by sequence specific interactions of the protein side chains with the encapsulating surface.

This work has been done in collaborations with graduate students D R Canchi, Camilo Jimenez, Charles English and Jianhui Tian. This research has been supported by grants from NSF MCB-0543769 and MCB-1050966.

Host: Assistant Professor Paul Whitford