Structure movements during molecular dynamic simulation process.

<p>Overlaid snapshots of the ribbon diagrams of NDM-1 Cα atoms and VNI-41 compound around the active site before (A) (snapshots interval 10 ps, N = 10) and after (B) (snapshots interval 150 ps, N = 10) the system reached equilibrium. Surface analyse of the active site cavity was performed on apo NDM-1(C), NDM-1/hydrolyzed ampicillin (D) and NDM-1/NVI-41(E). Atoms in the active site active site cavity are highlighted in colored balls. (F) The ribbon diagrams showing the active site associated loops (L3, L6, L10) moving toward the ligand and contraction of the active site. The structure of apo NDM-1, NDM-1/hydrolyzed ampicillin and NDM-1/NVI-41 is colored in blue, green and black respectively.