Basis for substrate recognition and distinction by matrix metalloproteinases

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4148-55. doi: 10.1073/pnas.1406134111. Epub 2014 Sep 22.


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 function-related 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.

Keywords: MMPs; protease; specificity-determining positions.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Binding Sites / genetics
  • Biocatalysis
  • Catalytic Domain*
  • Humans
  • Kinetics
  • Matrix Metalloproteinases / chemistry*
  • Matrix Metalloproteinases / genetics
  • Matrix Metalloproteinases / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Peptides / metabolism*
  • Phylogeny
  • Proteolysis
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Peptides
  • Matrix Metalloproteinases