Molecular Dynamics Simulations of the Unfolding of Barnase in Water and 8 M Aqueous Urea

Molecular dynamics simulations of barnase have been conducted both in water and in 8 M urea solution for 500 ps at 25 °C and for 2000 ps at 85 °C. The final structure of the aqueous simulation at room temperature matches closely the structure obtained by NMR and the experimentally observed protections from isotopic exchange. The comparison of the structures generated by the aqueous simulation at 85 °C reveals a trajectory composed of groups of geometrically related structures separated by narrow regions of rapid change in structure. The first of these regions displays changes in backbone rmsd to the crystal structure and solvent-accessible area suggestive of a transition state, while the properties observed during the final 300 ps of the simulation are consistent with a stable intermediate. These assignments were confirmed by calculation of the “progress along the reaction coordinate” φ-values using an empirical equation based on a linear response method. The pathway of unfolding defined in this fashion agrees well with the experimental results of site-directed mutagenesis in terms of secondary structure content of the transition state and the intermediate and reproduces the relative stability of the different elements of secondary structure. The results of the simulations in urea suggest a mechanism at the molecular level for its well-known enhancement of the denaturation of proteins. The analysis of radial distribution functions shows that the first solvation shell of the protein is enriched in urea relative to the bulk solvent. The displacement of water molecules allows greater exposure of hydrophobic side chains, as witnessed particularly in the analysis of solvent-accessible surface areas at the higher temperature. Almost all urea molecules in the first shell form at least one hydrogen bond with the protein. They provide a more favorable environment for accommodation of the remaining water molecules, and they facilitate the separation of secondary structure elements by acting as a bridge between groups previously forming intraprotein hydrogen bonds.