Homology models of the LmbC and LmbC G308V amino acid binding pocket and an RMSD analysis of these models during MD simulations.

Structures of the substrate binding pockets from LmbC (A–C) and LmbC G308V (D–F) homology models with bound PPL during the course of a 20-ns-long, non-restrained MD simulation are shown at 0 ns (left column), 8.05 ns (middle column), and 19.09 ns (right column). The nonribosomal code of each model is displayed at left. The individual letters of the code are colored to correspond to those of the individual amino acids in the structures. A time-based RMSD analysis of the substrate during a 20-ns-long, non-restrained MD simulation of LmbC (blue line) and LmbC G308V (red line). The RMSD was calculated over all substrate C atoms. The positions of the frames 0, 805 and 1909 (corresponding to the time 0 ns, 8.05 ns, and 19.09 ns) are marked with vertical lines.