The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
Fig 4
Overview of the entrance path identified with COP (A) as well as RMSF and atom contacts (B, for COP) and binding energy data (C, for COP and COD). A: The VAO dimer is shown as cartoon in grey and its FAD cofactor is shown as sticks in yellow. The entrance path is shown through sphere representation of ligand positions in the trajectories and coloured in magenta. For clarity, we only show data for an entrance simulation where COP migrates to the left-hand subunit. B: Highest RMSF values (black boxplot boxes) and atom contact counts with the ligand (grey boxplot boxes) of residues in VAO. Magenta filling of the boxplots indicates that the residue belongs to the entrance path. Residues that do not have atom contacts with the ligand but are highly flexible only have a black boxplot (for RMSF). Because data was obtained from only one simulation, the atom contacts do not have any variation. C: Scatterplot of binding energies as a function of the distance between the ligand and FAD. Negative x-values indicate the distance to the FAD in the other subunit. This graph shows that the path is symmetrical for COP (in magenta).