This report describes a 745-ps molecular dynamics simulation of the enzyme subtilisin Carlsbeg in a periodic box of dimethyl sulfoxide (DMSO). The starting coordinates for subtilisin and crystallographic waters were taken from the aqueous X-ray crystal structure. Although the overall structure of subtilisin is stable throughout the simulation, some structural perturbations are observed, The five N-terminal residues of the protein migrate away from the rest of the protein; whether this movement is the start of partial unfolding in DMSO is unclear. We compare these findings with recent simulations of this enzyme in CCL(4), acetonitrile, and water. The simulation results indicate that DMSO is capable of stripping waters and metal ions away from the protein surface. The total number of intraprotein hydrogen bonds is increased in DMSO compared to in water. Eighteen DMSO binding sites were identified based on root-mean-square fluctuations, most of which were hydrogen bonded to a protein amide hydrogen atom. Quantum mechanics calculations were used to investigate the hydrogen bonding strength between DMSO and protein amide hydrogen and between DMSO and water. These results are discussed in view of the known protein-dissolving property of DMSO.