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-A 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.