Substrate hydrolysis by matrix metalloproteinase-9

The catalytic clefts of all matrix metalloproteinases (MMPs) have a similar architecture, raising questions about the redundancy in substrate recognit ion across the protein family. In the present study, an unbiased phage disp lay strategy was applied to define the substrate recognition profile of MMP -9. Three groups of substrates were identified, each occupying a distinct s et of subsites within the catalytic pocket. The most prevalent motif contai ns the sequence Pro-X-X-Hy-(Ser/Thr) at P-3 through P-2'. This sequence is similar to the MMP cleavage sites within the collagens and is homologous to substrates the have been selected for other MMPs. Despite this similarity, most of the substrates identified here are selective for MMP-9 over MMP-7 and MMP-13. This observation indicates that substrate selectivity is confer red by key subsite interactions at positions other than P-3 and P-1'. This study shows that MMP-9 has a unique preference for Arg at both P-2 and P-1, and a preference for Ser/Thr at P-2'. Substrates containing the consensus MMP-9 recognition motif were used to query the protein data bases. A surpri singly limited List of putative physiologic substrates was identified. The functional implications of these proteins lead to testable hypotheses regar ding physiologic substrates for MMP-9.