The pH dependence of matrix metalloproteinase (MMP) catalysis is described by a broad bell-shaped curve, indicating the involvement of two unspecified ionizable groups in proteolysis. Stromelysin-1 has a third pK a near 6, resulting in a uniquely sharp acidic catalytic optimum, which has recently been attributed to His 224 . This suggests the presence of a critical, but unidentified, S1 substructure. Integrating biochemical characterizations of inhibitor-enzyme interactions with active site topography from corresponding crystal structures, we isolated contributions to the pH dependence of catalysis and inhibition of active site residues

For an animal model to predict a compound's potential for treating human disease, inhibitor interactions with the cognate enzymes of separate species must be comparable. Rabbit and human isoforms of stromelysin-1 are highly homologous, yet there are clear and significant compound-specific differences in inhibitor potencies between these two enzymes. Using crystal structures of discordant inhibitors complexed with the human enzyme, we generated a rabbit enzyme homology model that was used to identify two unmatched residues near the active site that could explain the observed disparities. To test these observations, we designed and synthesized three chimeric mutants of the human enzyme containing the single (H224N and L226F) and double (H224N/L226F) mutations. A comparison of inhibitor potencies among the mutant and wild-type enzymes shows that the mutation of a single amino acid in the human enzyme, histidine 224 to asparagine, is sufficient to change the selectivity profile of the mutant to that of the rabbit isoform. These studies emphasize the importance of considering species differences, which can result from even minor protein sequence variations, for the critical enzymes in an animal disease model. Homology modeling provides a tool to identify key differences in isoforms that can significantly affect native enzyme activity.Cell-matrix interactions provide cells with an assessment of their immediate environment and afford signaling events that result in proliferation, differentiation, migration, or programmed cell death (1). These matrix interactions can be altered through the activities of a family of extracellular zincand calcium-dependent endopeptidases, the matrix metalloproteinases (MMPs).1 Collectively, these enzymes are responsible for the proteolytic degradation of extracellular matrix macromolecules with the subsequent release of stromal contacts (2).MMP activity is essential for tissue remodeling or cellular migration and is required for physiological processes such as fetal development, wound healing, angiogenesis, or inflammatory cell trafficking. However, it is critical to these processes that the matrix degradation be locally confined and temporally limited. Consequently, MMPs are highly regulated enzymes and, in general, are induced only in response to specific stimuli such as cytokines and growth factors. When induced, they are transiently expressed as latent enzymes that require complex interactions for activation (3). Once activated they are subject to rapid autodegradation. In addition, enzyme activity is modulated in situ by potent and specific natural inhibitors, the TIMPs that are expressed under many of the same conditions that induce MMP activity (4). If the balance between induction, activation, and inhibition processes becomes even slightly dysregulated, the result can be chronic and debilitating diseases such as cancer, arthritis, inappropriate angiogenesis, autoimmune disease, aneurysm, atherosclerosis, or heart failure (5).Because MMP expression in normal tissue is very low, enz...