The stability of proteins is marginal, and can be perturbed by changes in solvent environment. Addition of co-solvents are known to modulate the equilibrium between the folded and the unfolded states of the protein. Denaturants, such as urea and GdmCl, push the equilibrium towards the unfolded state and are commonly used indirectly measure the stability of proteins. Another class of compounds, known as 'protecting' osmolytes, stabilize the folded state of proteins and are used to maintain the intracellular stability of proteins in organisms that inhabit extreme environmental conditions. Prominent examples include trimethylamine N-oxide (TMAO), glycerol and sugars.
We are employing all-atom REMD simulations to elucidate the molecular mechanism of the effects of co-solvents on protein stability. The Trp-cage miniprotein is used as a model compound for investigation. We have studied the effect of varying concentration of urea on protein stability. The simulations are able to capture the experimentally observed linear dependence of unfolding free energy on urea concentration. We find that denaturation is driven by direct interaction of urea with the protein, through both electrostatic and van der Waals forces. Our simulations show that hydrogen bonding of urea to the peptide backbone is not a dominant effect. Increasing urea concentration led to sampling unfolded conformations with greater solvent exposure.
We are currently investigating the effect of TMAO on protein stability, and the mechanism through which TMAO counteracts the denaturing effect of urea.
Deepak R. Canchi and Angel E. Garcia Co-solvent effects on protein stability', Ann. Rev. Phys. Chem. 64: 273-293 (2013) link
Deepak R. Canchi, Jayasimha, P, Rau, DC, Makhatadze, GI, and García, AE Molecular mechanism for the preferential exclusion of TMAO from protein surfaces', " J. Phys. Chem B. 116: 12095-12104 (2012).link
Deepak R. Canchi and Angel E. Garcia,'"Backbone and Sidechain contributions in Protein Denaturation by Urea' link, Biophysical Journal 100: 1526-1533 (2011)
Deepak R Canchi, Dietmar Paschek and Angel E. Garcia,Equilibrium study of protein denaturation by urea link J. Am. Chem. Soc 132 (7), pp 2338–2344(2010)