Abstract:

Extensive molecular dynamics simulations were performed to study the distribution and dynamics of water and urea in the hydration shell of ribonuclease Sa(RNase Sa) under different urea concentrations. It is found that urea molecules have stronger interactions with protein than water molecules and are enriched on the surface of RNase Sa by displacing water molecules. Urea molecules prefer to interact with hydrophobic residues and form hydrogen bonds with the backbone of RNase Sa. The transitional and rotational dynamics of urea molecules are much slower than those of water molecules. Besides, the increased urea concentrations can slow down the transitional and rotational dynamics of water molecules, but have no regular influences on the dynamics of urea molecules. Our results can help understanding the different influences of urea and water molecules on the stability of proteins.

Key words: ribonuclease Sa, survival time correlation function, rotational time correlation function, molecular dynamics simulations