Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
Fig 11
The opening of the N-terminal channel, involving loops D1 and P1.
A: the overall structure of PfM1-AAP with highlighted loops; B: the Arg product bound to the active site; C: The interaction of Arg with Arg325 and Glu572 during the release from the active site. The salt bridges and hydrogen bonds are shown in a black-dotted line. D: The distance between the centre of mass of P1 and D1 loops in the1μs cMD simulations of the PfM1-AAP the ligand-unbound (red) and ligand-bound forms (black).