Figure 2. Molecular modeling of the interactions between Abl kinase and MTAbl00, MTAbl01, MTAbl02 and MTAbl03 peptides, which contain grafts in loop 6.

Upper panel: Superimposition of the binding modes observed after 20 ns of molecular dynamics (MD) simulations for the four MTAbl peptides and after 50 ns MD simulations for abltide. The five MD frames were fitted onto the kinase backbone. The molecular surface of Abl kinase is shown in white. The grafted peptides and linear abltide are shown using ribbon representation and their side chains are shown using stick representations. The backbones of MTAbl peptides are shown as curvy lines. Lower panel: Evolution of the root mean square deviation of the grafted abltide (graft rmsd) over the MD simulations of the MTAbl peptides in complex with Abl kinase. The graft rmsd is computed as the backbone rmsd between the grafted abltides and the corresponding sequences in abltide after fitting the backbone of Abl kinase.