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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.

Iyer S, Wei S, Brew K, Acharya KR
J Biol Chem 282 364-71 (2007)
Cited: 55 times
EuropePMC logo PMID: 17050530

Abstract

The mammalian collagenases are a subgroup of the matrix metalloproteinases (MMPs) that are uniquely able to cleave triple helical fibrillar collagens. Collagen breakdown is an essential part of extracellular matrix turnover in key physiological processes including morphogenesis and wound healing; however, unregulated collagenolysis is linked to important diseases such as arthritis and cancer. The tissue inhibitors of metalloproteinases (TIMPs) function in controlling the activity of MMPs, including collagenases. We report here the structure of a complex of the catalytic domain of fibroblast collagenase (MMP-1) with the N-terminal inhibitory domain of human TIMP-1 (N-TIMP-1) at 2.54 A resolution. Comparison with the previously reported structure of the TIMP-1/stromelysin-1 (MMP-3) complex shows that the mechanisms of inhibition of both MMPs are generally similar, yet there are significant differences in the protein-protein interfaces in the two complexes. Specifically, the loop between beta-strands A and B of TIMP-1 makes contact with MMP-3 but not with MMP-1, and there are marked differences in the roles of individual residues in the C-D connector of TIMP-1 in binding to the two MMPs. Structural rearrangements in the bound MMPs are also strikingly different. This is the first crystallographic structure that contains the truncated N-terminal domain of a TIMP, which shows only minor differences from the corresponding region of the full-length protein. Differences in the interactions in the two TIMP-1 complexes provide a structural explanation for the results of previous mutational studies and a basis for designing new N-TIMP-1 variants with restricted specificity.

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  1. Protein-protein docking benchmark version 4.0. Hwang H, Vreven T, Janin J, Weng Z. Proteins 78 3111-3114 (2010)
  2. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. Bourgeas R, Basse MJ, Morelli X, Roche P. PLoS One 5 e9598 (2010)
  3. How structure defines affinity in protein-protein interactions. Erijman A, Rosenthal E, Shifman JM. PLoS One 9 e110085 (2014)
  4. Reactive-site mutants of N-TIMP-3 that selectively inhibit ADAMTS-4 and ADAMTS-5: biological and structural implications. Lim NH, Kashiwagi M, Visse R, Jones J, Enghild JJ, Brew K, Nagase H. Biochem J 431 113-122 (2010)
  5. Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): identification of selective inhibitors of collagenase-1 (metalloproteinase 1 (MMP-1)). Bahudhanapati H, Zhang Y, Sidhu SS, Brew K. J Biol Chem 286 31761-31770 (2011)
  6. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data. Ohue M, Matsuzaki Y, Uchikoga N, Ishida T, Akiyama Y. Protein Pept Lett 21 766-778 (2014)
  7. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. Engin HB, Guney E, Keskin O, Oliva B, Gursoy A. PLoS One 8 e81035 (2013)
  8. Protein-protein binding site identification by enumerating the configurations. Guo F, Li SC, Wang L, Zhu D. BMC Bioinformatics 13 158 (2012)
  9. Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach. Martin OA, Villegas ME, Vila JA, Scheraga HA. J Biomol NMR 46 217-225 (2010)
  10. Prediction of Protein-Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets. Xie Z, Deng X, Shu K. Int J Mol Sci 21 E467 (2020)
  11. Changes in protein structure at the interface accompanying complex formation. Chakravarty D, Janin J, Robert CH, Chakrabarti P. IUCrJ 2 643-652 (2015)
  12. Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction. Liu J, Gong X. BMC Bioinformatics 20 609 (2019)
  13. TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets. Cantacessi C, Hofmann A, Pickering D, Navarro S, Mitreva M, Loukas A. Parasit Vectors 6 156 (2013)
  14. 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. Wu Y, Wei S, Van Doren SR, Brew K. J Biol Chem 286 16891-16899 (2011)
  15. Anti-liver fibrosis activity of curcumin/chitosan-coated green silver nanoparticles. Elzoheiry A, Ayad E, Omar N, Elbakry K, Hyder A. Sci Rep 12 18403 (2022)
  16. Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. Sudha G, Singh P, Swapna LS, Srinivasan N. Protein Sci 24 1856-1873 (2015)
  17. Accurate Prediction of Docked Protein Structure Similarity. Akbal-Delibas B, Pomplun M, Haspel N. J Comput Biol 22 892-904 (2015)
  18. Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering. Giangreco I, Nicolotti O, Carotti A, De Carlo F, Gargano G, Bellotti R. BMC Bioinformatics 11 500 (2010)
  19. Protein docking with predicted constraints. Krippahl L, Barahona P. Algorithms Mol Biol 10 9 (2015)
  20. Classification of protein-protein association rates based on biophysical informatics. Dhusia K, Wu Y. BMC Bioinformatics 22 408 (2021)
  21. PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? Rebollo A, Fliedel L, Tuffery P. Biomolecules 12 178 (2022)
  22. Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble. Sung E, Kim S, Shin W. BMC Bioinformatics 11 256 (2010)
  23. Bioinformatics screening of colorectal-cancer causing molecular signatures through gene expression profiles to discover therapeutic targets and candidate agents. Horaira MA, Islam MA, Kibria MK, Alam MJ, Kabir SR, Mollah MNH. BMC Med Genomics 16 64 (2023)


Reviews citing this publication (7)

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  2. Tissue inhibitor of metalloproteinases-4. The road less traveled. Melendez-Zajgla J, Del Pozo L, Ceballos G, Maldonado V. Mol Cancer 7 85 (2008)
  3. Matrix metalloproteinases as potential targets in the venous dilation associated with varicose veins. Kucukguven A, Khalil RA. Curr Drug Targets 14 287-324 (2013)
  4. Metalloproteinases as mediators of inflammation and the eyes: molecular genetic underpinnings governing ocular pathophysiology. Singh M, Tyagi SC. Int J Ophthalmol 10 1308-1318 (2017)
  5. Role of matrix metalloproteinases in cholestasis and hepatic ischemia/reperfusion injury: A review. Palladini G, Ferrigno A, Richelmi P, Perlini S, Vairetti M. World J Gastroenterol 21 12114-12124 (2015)
  6. Reflections on the evolution of the vertebrate tissue inhibitors of metalloproteinases. Brew K. FASEB J 33 71-87 (2019)
  7. The Repertoire of Tissue Inhibitors of Metalloproteases: Evolution, Regulation of Extracellular Matrix Proteolysis, Engineering and Therapeutic Challenges. Costa S, Ragusa MA, Lo Buglio G, Scilabra SD, Nicosia A. Life (Basel) 12 1145 (2022)

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  2. Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1; gelatinase-selective inhibitors. Hamze AB, Wei S, Bahudhanapati H, Kota S, Acharya KR, Brew K. Protein Sci 16 1905-1913 (2007)
  3. Development of High Affinity and High Specificity Inhibitors of Matrix Metalloproteinase 14 through Computational Design and Directed Evolution. Arkadash V, Yosef G, Shirian J, Cohen I, Horev Y, Grossman M, Sagi I, Radisky ES, Shifman JM, Papo N. J Biol Chem 292 3481-3495 (2017)
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  5. Affinity- and specificity-enhancing mutations are frequent in multispecific interactions between TIMP2 and MMPs. Sharabi O, Shirian J, Grossman M, Lebendiker M, Sagi I, Shifman J. PLoS One 9 e93712 (2014)
  6. Activity of matrix metallo proteinases (MMPs) and the tissue inhibitor of MMP (TIMP)-1 in electromagnetic field-exposed THP-1 cells. Patruno A, Pesce M, Marrone A, Speranza L, Grilli A, De Lutiis MA, Felaco M, Reale M. J Cell Physiol 227 2767-2774 (2012)
  7. Unraveling hidden regulatory sites in structurally homologous metalloproteases. Udi Y, Fragai M, Grossman M, Mitternacht S, Arad-Yellin R, Calderone V, Melikian M, Toccafondi M, Berezovsky IN, Luchinat C, Sagi I. J Mol Biol 425 2330-2346 (2013)
  8. Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes. Batra J, Soares AS, Mehner C, Radisky ES. PLoS One 8 e75836 (2013)
  9. Selective function-blocking monoclonal human antibody highlights the important role of membrane type-1 matrix metalloproteinase (MT1-MMP) in metastasis. Remacle AG, Cieplak P, Nam DH, Shiryaev SA, Ge X, Strongin AY. Oncotarget 8 2781-2799 (2017)
  10. Converting a broad matrix metalloproteinase family inhibitor into a specific inhibitor of MMP-9 and MMP-14. Shirian J, Arkadash V, Cohen I, Sapir T, Radisky ES, Papo N, Shifman JM. FEBS Lett 592 1122-1134 (2018)
  11. Site specific cleavage mediated by MMPs regulates function of agrin. Patel TR, Butler G, McFarlane A, Xie I, Overall CM, Stetefeld J. PLoS One 7 e43669 (2012)
  12. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. Melo R, Fieldhouse R, Melo A, Correia JD, Cordeiro MN, Gümüş ZH, Costa J, Bonvin AM, Moreira IS. Int J Mol Sci 17 E1215 (2016)
  13. Conditioned Medium from Human Amnion-Derived Mesenchymal Stem Cells Regulates Activation of Primary Hepatic Stellate Cells. Fu Q, Ohnishi S, Sakamoto N. Stem Cells Int 2018 4898152 (2018)
  14. Protective effects of butanol fraction from Betula platyphyla var. japonica on cartilage alterations in a rabbit collagenase-induced osteoarthritis. Huh JE, Baek YH, Kim YJ, Lee JD, Choi DY, Park DS. J Ethnopharmacol 123 515-521 (2009)
  15. Collagenolytic activity is suppressed in organ-cultured human skin exposed to a gadolinium-based MRI contrast agent. Perone PA, Weber SL, DaSilva M, Paruchuri T, Bhagavathula N, Aslam MN, Dame MK, Johnson KJ, Swartz RD, Varani J. Invest Radiol 45 42-48 (2010)
  16. Inactivation of N-TIMP-1 by N-terminal acetylation when expressed in bacteria. Van Doren SR, Wei S, Gao G, DaGue BB, Palmier MO, Bahudhanapati H, Brew K. Biopolymers 89 960-968 (2008)
  17. Dynamic interdomain interactions contribute to the inhibition of matrix metalloproteinases by tissue inhibitors of metalloproteinases. Remacle AG, Shiryaev SA, Radichev IA, Rozanov DV, Stec B, Strongin AY. J Biol Chem 286 21002-21012 (2011)
  18. Combinatorial engineering of N-TIMP2 variants that selectively inhibit MMP9 and MMP14 function in the cell. Arkadash V, Radisky ES, Papo N. Oncotarget 9 32036-32053 (2018)
  19. Potential clinical applications of matrix metalloproteinase inhibitors and their future prospects. Li W, Saji S, Sato F, Noda M, Toi M. Int J Biol Markers 28 117-130 (2013)
  20. Engineered sarafotoxins as tissue inhibitor of metalloproteinases-like matrix metalloproteinase inhibitors. Lauer-Fields JL, Cudic M, Wei S, Mari F, Fields GB, Brew K. J Biol Chem 282 26948-26955 (2007)
  21. Selective inhibition of matrix metalloproteinase 10 (MMP10) with a single-domain antibody. Razai AS, Eckelman BP, Salvesen GS. J Biol Chem 295 2464-2472 (2020)
  22. Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14. Zou H, Wu Y, Brew K. J Biol Chem 291 11348-11358 (2016)
  23. The efficient expression of human fibroblast collagenase in Escherichia coli and the discovery of flavonoid inhibitors. Lu W, Zhu J, Zou S, Li X, Huang J. J Enzyme Inhib Med Chem 28 741-746 (2013)
  24. New biochemical insight of conserved water molecules at catalytic and structural Zn2+ ions in human matrix metalloproteinase-I: a study by MD-simulation. Chakrabarti B, Bairagya HR, Mukhopadhyay BP, Sekar K. J Mol Model 23 57 (2017)
  25. Serpin A1 C-Terminal Peptides as Collagen Turnover Modulators. Pascarella S, Tiberi C, Sabatino G, Nuti F, Papini AM, Giovannelli L, Rovero P. ChemMedChem 11 1850-1855 (2016)


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