MD simulation of apoD and apoD-Met₉₃SO.

(A) B-factors calculated from the MD simulations of apoD, apoD-Met₉₃SO and crystallographic B-factors are shown. (B) Snapshots from the apoD-Met₉₃SO simulation. Initially the sulfoxide oxygen of Met₉₃SO remains in the initially modelled conformation, similar to Met93 in the ligand-free crystal structure. Simulation of apoD-Met₉₃SO suggested that the sulfoxide oxygen of Met₉₃SO could accept hydrogen bonds from the amide-nitrogen groups of Phe₈₉ and Ser₉₀. (upper structure). After 7 ns, the side-chain flips out of the pocket and is surrounded by water molecules. A representative snapshot of the populations of side-chain conformations is shown (lower structure).