Structural details of urea binding to barnase: a molecular dynamics analysis

Background: The molecular mechanism of urea-induced protein unfolding has n ot been established. It is generally thought that denaturation results from the stabilizing interactions of urea with portions of the protein that are buried in the native state and become exposed upon unfolding of the protei n. Results: We have performed molecular dynamics simulations of barnase (a 110 amino acid RNase from Bacillus amyloliquefaciens) with explicit water and urea molecules at 300K and 360K. The native conformation was unaffected in the 300K simulations at neutral and low pH, Two of the three runs at 360K a nd low pH showed some denaturation, with partial unfolding of the hydrophob ic core 2, The first solvation shell has a much higher density of urea mole cules (water/urea ratio ranging from 2.07 to 2.73) than the bulk (water/ure a ratio of 4.56). About one half of the first-shell urea molecules are invo lved in hydrogen bonds with polar or charged groups on the barnase surface, and between 15% and 18% of the first-shell urea molecules participate in m ultiple hydrogen bonds with barnase. The more stably bound urea molecules t end to be in crevices or pockets on the barnase surface. Conclusions: The simulation results indicate that an aqueous urea solution solvates the surface of a polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the protein than water does, and the presence of urea improves the interactions of wat er molecules with the hydrophilic groups of the protein. The results sugges t that urea denaturation involves effects on both nonpolar and polar groups of proteins.