Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock.

Abstract

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.