Urea’s Action on Hydrophobic Interactions

Abstract

For more than a century, urea has been commonly used as an agent for denaturing proteins. However, the mechanism behind its denaturing power is still not well understood. Here we show by molecular dynamics simulations that a 7 M aqueous urea solution unfolds a chain of purely hydrophobic groups which otherwise adopts a compact structure in pure water. The unfolding process arises due to a weakening of hydrophobic interactions between the polymer groups. We also show that the attraction between two model hydrophobic plates, and graphene sheets, is reduced when urea is added to the solution. The action of urea is found to be direct, through its preferential binding to the polymer or plates. It is, therefore, acting like a surfactant capable of forming hydrogen bonds with the solvent. The preferential binding and the consequent weakened hydrophobic interactions are driven by enthalpy and are related to the difference in the strength of the attractive dispersion interactions of urea and water with the polymer chain or plate. This relation scales with square root(epsilon(b)), where epsilon(b) is the Lennard Jones (LJ) energy parameter for each group on the chain. Larger values of epsilon(b) increase the preferential binding and result in a larger decrease of the hydrophobic interactions, with a crossover at very weak dispersions. We also show that the indirect mechanism, in which urea acts as a chaotrope, is not a likely cause of urea's action as a denaturant. These findings suggest that, in denaturing proteins, urea (and perhaps other denaturants) forms stronger attractive dispersion interactions with the protein side chains and backbone than does water and, therefore, is able to dissolve the core hydrophobic region.

Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO)

“…The enthalpic factor results from a decreased H-bonding ability of water, whereas the entropic factor stems from the crowding effect of TMAO; both act to destabilize the unfolded state ensemble. Because the tripeptide used in the current study is relatively small, it is possible to use molecular dynamics simulations (68,74,75), in conjunction with vibrational frequency calculations (76), to directly calculate the FFCFs of the nitrile probe under different cosolvent conditions and to provide further molecular insights. We hope that the current study will inspire new computational efforts in this regard.…”

A hypothesis to reconcile the physical and chemical unfolding of proteins

“…The second view is based on the direct interaction of urea with the protein. Most studies are based on model compounds and theoretical and modeling approaches, such as molecular dynamics (29)(30)(31)(32)(33)(34)(35).…”

Probing cellulose amphiphilicity

“…In fact, we have added up to 20 wt% of urea and not only was no phase separation observed but also the cellulose dissolution and rheology properties were improved. As mentioned above, we believe that urea is weakening the hydrophobic interactions (in a similar way as it does during protein unfolding) increasing cellulose solubility and preventing the hydrophobic regions of cellulose to come together to form a gelled network (Zangi et al 2009). …”