Crystal Structure of the Catalytic Domain of Matrix Metalloproteinase-1 in Complex with the Inhibitory Domain of Tissue Inhibitor of Metalloproteinase-1

Iyer, Shalini; Wei, Shuo; Brew, Keith; Acharya, K. Ravi

doi:10.1074/jbc.m607625200

Cited by 62 publications

(57 citation statements)

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“…Although the crystallographic structures of the corresponding complexes of N-TIMP-2 are not available, a NMR study of the effects of MMP-3cd binding on the conformational dynamics of N-TIMP-2 has been reported (14) and crystallographic structures are available for complexes of TIMP-2 with MMP-13 and MT1-MMP (6, 7). Analyses of the chemical nature of the contact surfaces and atoms in the interfaces of the N-TIMP-1⅐MMP-1cd and N-TIMP-1⅐MMP-3cd complexes have been previously reported (5,22). Analyses of the interaction sites indicate that the interface in the MMP-1 complex is significantly less hydrophobic than in the MMP-3 complex (60 versus 70% non-polar) ( Table 4).…”

Section: Sources Of Binding Energy For the Different N-timp/mmpcdmentioning

confidence: 82%

“…The thermodynamic profiles reported here show that the interactions of both N-TIMP-1 and N-TIMP-2 with MMP-3cd have nearly 4 -5-fold smaller (negative) heat capacity changes, greater (positive) entropy changes, and less favorable enthalpy changes than those for the corresponding interactions with MMP-1cd. These may reflect conformational changes in MMP-3cd in its complexes with both N-TIMPs but only minor changes in MMP-1cd in corresponding complexes (4,5); a redistribution of dynamics when N-TIMPs bind to MMP-3cd may also underlie the "anomalous" profiles. Disorder to order structural transitions in protein interactions have been linked to negative ⌬C p values of greater magnitude than predicted from the composition of buried surfaces (42); it appears that the converse might apply to the interactions of the two N-TIMPs with MMP-3cd where the interacting N-TIMPs may be more ordered than their complexes.…”

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confidence: 99%

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Entropy Increases from Different Sources Support the High-affinity Binding of the N-terminal Inhibitory Domains of Tissue Inhibitors of Metalloproteinases to the Catalytic Domains of Matrix Metalloproteinases-1 and -3

Wei

Doren

et al. 2011

Journal of Biological Chemistry

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The matrix metalloproteinases (MMPs) 3 catalyze the turnover of components of the extracellular matrix and have important roles in tissue remodeling, wound healing, embryo implantation, cell migration, and shedding of cell surface proteins (1, 2). MMP-1 is a well characterized collagenase that catalyzes the turnover of collagen fibrils in the matrix, whereas MMP-3 (stromelysin 1) cleaves multiple extracellular matrix components and functions in tissue remodeling and other processes (2). Collagenolysis is a key feature of biological processes including development, morphogenesis, and wound repair yet unregulated collagen breakdown contributes to important diseases including cancer, arthritis, emphysema, and fibrosis (1). An understanding of the molecular basis of the regulation of MMP activities is crucial for understanding MMP-associated diseases and developing therapies for them. The tissue inhibitors of metalloproteinases (TIMP-1 to Ϫ4) are a family of four endogenous MMP inhibitors that can form high affinity 1:1 complexes with most MMPs. TIMP-3 also inhibits some members of the distantly related disintegrin metalloproteinase (ADAM) and disintegrin metalloproteinase with thrombospondin type 1 motif (ADAMTS) families (2). A loss of balance between the TIMPs and their target proteases is linked to diseases such as cancer and arthritis (2, 3).TIMPs are slow, tight-binding inhibitors of the MMPs with K i values typically in the sub-to low nanomolar range (3). Mammalian TIMPs have two domains, a larger (ϳ125 residue) N-terminal domain that can be expressed separately and carries the MMP inhibitory activity (2, 3) and a smaller C-terminal domain that is absent from the TIMPs of some invertebrates (3). In the crystal structures of the MMP-3⅐TIMP-1, MMP-1⅐N-TIMP-1, MT1-MMP⅐TIMP-2, and MMP-13⅐TIMP-2 complexes (4 -7), most of the MMP interaction surface is located within the N-domains of the TIMPs; as shown in Fig. 1, the N-terminal region (residues 1-5) inserts into the active site of the MMP, whereas the ␣-amino group together with the carbonyl oxygen of Cys 1 coordinate the catalytic zinc (4 -7). Modification of the ␣-amino group by addition of an alanine (8, 9), carbamylation (10), or acetylation (11) radically reduces the inhibitory activities of TIMPs for MMPs. In the all inhibitory TIMP⅐MMP complexes, the side chain of residue 2 of the TIMP (Ser or Thr in vertebrate TIMPs) sits over the mouth of the key S 1 Ј subsite of the MMP active site (4 -7), and substitution by glycine results in large loss of affinity for most MMPs (9, 12). However, both the Ala extension and Thr 2 to Gly mutation in N-TIMP-3 have little effect on the inhibition of ADAM-17, 13). The inhibitory domain of TIMP has an OB-fold structure, a 5-stranded ␤-barrel structure with two small helices. Other regions in TIMPs that contact MMPs include the connector between the C and D ␤ strands and the loops connecting the A to B, and E to F strands (4 -7). In * This work was supported, in whole or in part, by National Institutes of Health Grants R01 AR...

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Section: Sources Of Binding Energy For the Different N-timp/mmpcdmentioning

confidence: 82%

mentioning

confidence: 99%

Entropy Increases from Different Sources Support the High-affinity Binding of the N-terminal Inhibitory Domains of Tissue Inhibitors of Metalloproteinases to the Catalytic Domains of Matrix Metalloproteinases-1 and -3

Wei

Doren

et al. 2011

Journal of Biological Chemistry

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“…The larger N-terminal domain (NTIMP) carries the MMP inhibitory activity, and the C-terminal domain mediates interactions with other proteins, including some pro-MMPs (7). Recombinant forms of NTIMPs are fully active as MMP inhibitors (10) and have been extensively used in crystallographic (11)(12), mutational (13)(14)(15)(16)(17)(18), and NMR studies (10, 19 -22) of TIMP⅐MMP interactions. The known structures of complexes between full-length TIMPs and MMP catalytic domains show that the main interaction interface of the TIMP is provided by the N-domain with a few * This work was supported by National Institutes of Health Grant RO1 AR40994.…”

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confidence: 99%

“…The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. 1 peripheral contacts from the C-domain (11,12,(23)(24)(25)(26)(27). NTIMPs have an oligonucleotide/oligosaccharide-binding fold, a 5-stranded ␤-barrel structure with two small helices.…”

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Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14

Zou

Brew

2016

Journal of Biological Chemistry

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The four tissue inhibitors of metalloproteinases (TIMPs) are potent inhibitors of the many matrixins (MMPs), except that TIMP1 weakly inhibits some MMPs, including MMP14. The broad-spectrum inhibition of MMPs by TIMPs and their N-domains (NTIMPs) is consistent with the previous isothermal titration calorimetric finding that their interactions are entropy-driven but differ in contributions from solvent and conformational entropy (⌬S solv , ⌬S conf ), estimated using heat capacity changes (⌬C p ). Selective engineered NTIMPs have potential applications for treating MMP-related diseases, including cancer and cardiomyopathy. Here we report isothermal titration calorimetric studies of the effects of selectivitymodifying mutations in NTIMP1 and NTIMP2 on the thermodynamics of their interactions with MMP1, MMP3, and MMP14. The weak inhibition of MMP14 by NTIMP1 reflects a large conformational entropy penalty for binding. The T98L mutation, peripheral to the NTIMP1 reactive site, enhances binding by increasing ⌬S solv but also reduces ⌬S conf . However, the same mutation increases NTIMP1 binding to MMP3 in an interaction that has an unusual positive ⌬C p . This indicates a decrease in solvent entropy compensated by increased conformational entropy, possibly reflecting interactions involving alternative conformers. The NTIMP2 mutant, S2D/S4A is a selective MMP1 inhibitor through electrostatic effects of a unique MMP-1 arginine. Asp-2 increases reactive site polarity, reducing ⌬C p , but increases conformational entropy to maintain strong binding to MMP1. There is a strong negative correlation between ⌬S solv and ⌬S conf for all characterized interactions, but the data for each MMP have characteristic ranges, reflecting intrinsic differences in the structures and dynamics of their free and inhibitor-bound forms.Isothermal titration calorimetry can dissect the sources of the free energy changes for protein interactions with other macromolecules and ligands (1). Measurements of the heat released or absorbed during the titration of a protein with a binding partner can quantify the enthalpy of binding (⌬H), association constant K a , and stoichiometry (N) (1), allowing the calculation of the changes in free energy (⌬G) and entropy (⌬S) of binding. Titrations in buffers with different enthalpies of ionization quantify ionization changes linked to binding, whereas the heat capacity change for binding, ⌬C p , measured as the temperature dependence of ⌬H, can be used to estimate the change in solvation entropy on binding (⌬S solv ). These parameters can be correlated with the character of the interaction interface and differences in dynamics and solvation between the free and bound conformer populations (2-4).Previously, we used isothermal titration calorimetry to elucidate the thermodynamic profiles of interactions between the N-terminal inhibitory domains of tissue inhibitors of metalloproteinases-1 and -2 (NT1 and NT2) 3 and the catalytic domains of matrix metalloproteinases -1 and -3 (MMP1c and MMP3c) (5, 6). TIMP1 and TIMP2 ...

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Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP‐9 and MMP‐14

et al. 2018

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MMP-14 and MMP-9 are two well-established cancer targets for which no specific clinically relevant inhibitor is available. Using a powerful combination of computational design and yeast surface display technology, we engineered such an inhibitor starting from a nonspecific MMP inhibitor, N-TIMP2. The engineered purified N-TIMP2 variants showed enhanced specificity toward MMP-14 and MMP-9 relative to a panel of off-target MMPs. MMP-specific N-TIMP2 sequence signatures were obtained that could be understood from the structural perspective of MMP/N-TIMP2 interactions. Our MMP-9 inhibitor exhibited 1000-fold preference for MMP-9 vs. MMP-14, which is likely to translate into significant differences under physiological conditions. Our results provide new insights regarding evolution of promiscuous proteins and optimization strategies for design of inhibitors with single-target specificities.

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Crystal Structure of the Catalytic Domain of Matrix Metalloproteinase-1 in Complex with the Inhibitory Domain of Tissue Inhibitor of Metalloproteinase-1

Cited by 62 publications

References 38 publications

Entropy Increases from Different Sources Support the High-affinity Binding of the N-terminal Inhibitory Domains of Tissue Inhibitors of Metalloproteinases to the Catalytic Domains of Matrix Metalloproteinases-1 and -3

Entropy Increases from Different Sources Support the High-affinity Binding of the N-terminal Inhibitory Domains of Tissue Inhibitors of Metalloproteinases to the Catalytic Domains of Matrix Metalloproteinases-1 and -3

Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14

Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP‐9 and MMP‐14

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