Haydee Valdes, Natalia Diaz, Dimas Suarez, and Juan Fernandez-Recio (2010)
Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6(7):2204-2213.
Current understanding of the collagenolytic activity performed by the
matrix metalloproteinases (MMPs) assumes some degree of relative motion
between their catalytic and hemopexin-like domains, according to
evidence from low-resolution techniques for some of the MMP family
members. Herein, we employ protein protein docking calculations to
investigate the structure in aqueous solution of the full-length MMP-2
enzyme in its active form, for which there is not yet experimental
evidence of interdomain movement. After docking the domains as free
rigid-body subunits, the linker region connecting the catalytic and
hemopexin-like domains is taken into account a posteriori by merely
adding an empiric energy term computed from expected end-to-end
distance to the scoring function. Finally, full-length MMP-2 structures
are generated by model building the linker residues in the most stable
docking poses. The results add support to the hypothesis that the
interdomain dynamics of a single MMP-2 molecule in aqueous solution can
result in a manifold of conformations, with some preferred
orientations. Globally, this structural information could be helpful in
future experimental or computational studies aimed to elucidate the
dynamical behavior of the MMP-2 enzyme in solution.