Molecular dynamics simulations of matrix metalloproteinase 2: role of the structural metal ions

Herein we investigate the role played by the so-called "structural metal ions" in the catalytic domain of the matrix metalloproteinase 2 enzyme (MMP-2 or gelatinase A). We performed seven molecular dynamics simulations that differ in the number and position of the noncatalytic zinc and calcium ions bound to the MMP-2 catalytic domain. An additional simulation including the three fibronectin-type modules inserted into the catalytic domain was also carried out. The analysis of the trajectories confirms that the binding/removal of the structural ions does not perturb the secondary structure elements but influences the position of several solvent-exposed loop regions that are placed near the active site cleft. The position of these loops modulates the accessibility of important anchorage points for substrate binding that have been identified in the active site groove. On the basis of semiempirical quantum chemical calculations, we estimated the relative free energies of the MMP-2 models, obtaining thus that the binding of two zinc and two calcium ions to the MMP-2 catalytic domain is energetically favored. In this MMP-2 model, which shows the most compact structure, all of the substrate binding sites are readily accessible. Globally, our results help to rationalize at the atomic level the calcium and zinc dependence of the hydrolytic activity catalyzed by the MMPs.