Basis for substrate recognition and distinction by matrix metalloproteinases

Boris I. Ratnikov, Piotr Cieplak, Kosi Gramatikoff, James Pierce, Alexey Eroshkin, Yoshinobu Igarashi, Marat Kazanov, Qing Sun, Adam Godzik, Andrei Osterman, Boguslaw Stec, Alex Strongin, Jeffrey W. Smith

Research output: Contribution to journalArticlepeer-review

52 Citations (Scopus)


Genomic sequencing and structural genomics produced a vast amount of sequence and structural data, creating an opportunity for structure-function analysis in silico [Radivojac P, et al. (2013) Nat Methods 10(3):221-227]. Unfortunately, only a few large experimental datasets exist to serve as benchmarks for functionrelated predictions. Furthermore, currently there are no reliable means to predict the extent of functional similarity among proteins. Here, we quantify structure-function relationships among three phylogenetic branches of the matrix metalloproteinase (MMP) family by comparing their cleavage efficiencies toward an extended set of phage peptide substrates that were selected from ∼64 million peptide sequences (i.e., a large unbiased representation of substrate space). The observed second-order rate constants [k(obs)] across the substrate space provide a distance measure of functional similarity among the MMPs. These functional distances directly correlate with MMP phylogenetic distance. There is also a remarkable and near-perfect correlation between the MMP substrate preference and sequence identity of 50-57 discontinuous residues surrounding the catalytic groove. We conclude that these residues represent the specificity-determining positions (SDPs) that allowed for the expansion of MMP proteolytic function during evolution. A transmutation of only a few selected SDPs proximal to the bound substrate peptide, and contributing the most to selectivity among the MMPs, is sufficient to enact a global change in the substrate preference of one MMP to that of another, indicating the potential for the rational and focused redesign of cleavage specificity in MMPs.

Original languageEnglish
Pages (from-to)E4148-E4155
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number40
Publication statusPublished - 7 Oct 2014
Externally publishedYes


  • MMPs
  • Protease |
  • Specificity-determining positions |


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