The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity

Abstract

Tissue inhibitors of metalloproteinases (TIMPs) are widely distributed in the animal kingdom and the human genome contains four paralogous genes encoding TIMPs 1 to 4. TIMPs were originally characterized as inhibitors of matrix metalloproteinases (MMPs), but their range of activities has now been found to be broader as it includes the inhibition of several of the disintegrin-metalloproteinases, ADAMs and ADAMTSs. TIMPs are therefore key regulators of the metalloproteinases that degrade the extracellular matrix and shed cell surface molecules. Structural studies of TIMP-MMP complexes have elucidated the inhibition mechanism of TIMPs and the multiple sites through which they interact with target enzymes, allowing the generation of TIMP variants that selectively inhibit different groups of metalloproteinases. Engineering such variants is complicated by the fact that TIMPs can undergo changes in molecular dynamics induced by their interactions with proteases. TIMPs also have biological activities that are independent of metalloproteinases; these include effects on cell growth and differentiation, cell migration, anti-angiogenesis, anti- and pro-apoptosis, and synaptic plasticity. Receptors responsible for some of these activities have been identified and their signaling pathways have been investigated. A series of studies using mice with specific TIMP gene deletions has illuminated the importance of these molecules in biology and pathology.

Fig. 1

Structure of TIMP-1 and its metalloproteinase interaction regions. (A) A ribbon structure of the three-dimensional structure of TIMP-1 showing the locations of the disulfide bonds, the two domains, domain interface and regions (IR I to V) that interact with metzincins and their component residues. This image was generated using Chimera [177]. (B) The structure of the core of the TIMP interaction site indicating interactions with individual subsites in MMP active sites.

Fig. 2

A phylogenetic tree showing the inferred evolutionary relationships between vertebrate TIMPs-1, -2, -3, and -4, rooted by the single TIMP from Drosophila melanogaster. This was generated using Phylogeny.fr (www.phylogeny.fr) in “One Click” mode [178].

Fig. 3

An alignment of the complete amino acid sequences of TIMPs from invertebrates. The location of secondary structure elements projected from the known three-dimensional structures of mammalian TIMPs are marked underneath. “E” denotes residues in extended structures (β-strands) while bars identify α-helices. The species from which the TIMPs are derived are abbreviated as follows: Hydra, Hydra magnipapillata; Nematostella, Nematostella vectensis (sea anemone); Mytilus, Mytilus californianus (mussel); Strong, Strongylocentrus purpuratus (sea urchin); Crassostrea, Crassostrea gigas (oyster); HumanT3, human TIMP-3; Branchiostoma, Branchiostoma floridae (Florida lancelet); Drosophilam, Drosophila melanogaster; Tribolium, Tribolium castaneum (red flour beetle); Culex, Culex quinquefasciatus (Southern house mosquito); Aedes, Aedes aegypti (yellow fever mosquito); Clytia, Clytia hemisphaerica (jellyfish).

Fig. 4

A comparison of some bacterial homologues with the N-domains of human TIMP-2 and -3 and Drosophila melanogaster TIMP. The sequences are from the following sources: Acaryochloris, hypothetic protein AM1_44443 from Acaryochloris marina MBIC11017; Bacillus_cerQ1, cbiN-domain protein from Bacillus cereus Q1; Bacillus_cer, hypothetical protein from Bacillus cereus G9241; Bacillus_thur, hypothetical protein BT9727_1673 from Bacillus thuringiensis serovar konkukian str. 97-27; Bacillus_cereus9241, hypothetical protein from Bacillus cereus G9241; Geobacillus, hypothetical protein GYMC10DRAFT_3737 from Geobacillus sp. Y412MC10; Plesiocystis, hypothetical protein PPSIR1 _33491 from Plesiocystis pacifica SIR-1. Other abbreviations are HumanT2, human N-TIMP-2; HumanT3, human N-TIMP-3; DmT, N-terminal domain of D. melanogaster TIMP.