Molecular dynamics simulations on the mycotoxin fumonisin B1

The solution conformational properties of the mycotoxin fumonisin B-1 have been studied using molecular dynamics methodology Fumonisins have been shown to inhibit sphinganine (sphingosine) N-acyltransferase (ceramide synthase) and show a wide range of toxic effects in many animals. This study of the solution properties of fumonisin B-1 attempts to add to the structural models necessary for the understanding of the binding and activity properties. The computational method uses a box with periodic boundaries, filled with explicit TIP3P water molecules, the substrate fumonisin B-1, and selected counterions for charge neutrality. The starting structure of fumonisin B-1 is added to the box by excluding water molecules. The explicit image method using 12-Angstrom cutoffs is applied to the system and molecular dynamics are carried out on different starting conformations at 300 K in 100-picosecond (ps) steps. Examination of the resulting equilibrated conformations suggests that the structure is relatively extended and that previous computational studies in vacuo, showing a compact folded structure, may not be consistent with the solution structure.