Structural differences of matrix metalloproteinases. Homology modeling andenergy minimization of enzyme-substrate complexes

Matrix metalloproteinases are extracellular enzymes taking part in the remo deling of extracellular matrix. The structures of the catalytic domain of M MPI, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach to the homolo gy modeling of matrix metalloproteinases, exemplified by the modeling of MM P2, MMP9, MMP12 and MMP14 is described. The models were refined using an en ergy minimization procedure developed for matrix metalloproteinases. This p rocedure includes incorporation of parameters for zinc and calcium ions in the AMBER 4.1 force field, applying a non-bonded approach and a full ion ch arge representation. Energy minimization of the apoenzymes yielded structur es with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The st ructural differences between the eight enzyme-substrate complexes were stud ied with particular emphasis on the active site, and possible sites for obt aining selectivity among the MMP's are discussed. Differences in the P1' po cket are well-documented and have been extensively exploited in inhibitor d esign. The present work indicates that selectivity could be further improve d by considering the P2 pocket as well.