Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses
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Tallant, 2010, Matrix metalloproteinases: fold and function of their catalytic domains, Biochim. Biophys. Acta, 1803, 20-8
Maskos, 2003, Structural basis of matrix metalloproteinases and tissue inhibitors of metalloproteinases, Mol. Biotechnol., 25, 241, 10.1385/MB:25:3:241
Murphy, 2008, Progress in matrix metalloproteinase research, Mol. Asp. Med., 29, 290, 10.1016/j.mam.2008.05.002
Nagase, 2006, Structure and function of matrix metalloproteinases and TIMPs, Cardiovasc. Res., 69, 562, 10.1016/j.cardiores.2005.12.002
Van Wart, 1990, The cysteine switch: a principle of regulation of metalloproteinase activity with potential applicability to the entire matrix metalloproteinase gene family, Proc. Natl. Acad. Sci. U. S. A., 87, 5578, 10.1073/pnas.87.14.5578
Butler, 2009, Updated biological roles for matrix metalloproteinases and new “intracellular” substrates revealed by degradomics, Biochemistry (Mosc), 48, 10830, 10.1021/bi901656f
Hynes, 2012, Overview of the matrisome—an inventory of extracellular matrix constituents and functions, Cold Spring Harb. Perspect. Biol., 4, a004903, 10.1101/cshperspect.a004903
Chen, 2007, Expression of extracellular matrix metalloproteinase inducer and matrix metalloproteinases during mouse embryonic development, Reprod. Camb. Engl., 133, 405, 10.1530/rep.1.01020
Deryugina, 2015, Tumor angiogenesis: MMP-mediated induction of intravasation- and metastasis-sustaining neovasculature, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 94, 10.1016/j.matbio.2015.04.004
Itoh, 2006, MT1-MMP: a key regulator of cell migration in tissue, IUBMB Life, 58, 589, 10.1080/15216540600962818
Aiken, 2010, Unraveling metalloproteinase function in skeletal biology and disease using genetically altered mice, Biochim. Biophys. Acta, 1803, 121, 10.1016/j.bbamcr.2009.07.002
Mott, 2004, Regulation of matrix biology by matrix metalloproteinases, Curr. Opin. Cell Biol., 16, 558, 10.1016/j.ceb.2004.07.010
Giannelli, 1997, Induction of cell migration by matrix metalloprotease-2 cleavage of laminin-5, Science, 277, 225, 10.1126/science.277.5323.225
Schenk, 2003, Binding to EGF receptor of a laminin-5 EGF-like fragment liberated during MMP-dependent mammary gland involution, J. Cell Biol., 161, 197, 10.1083/jcb.200208145
Xu, 2001, Proteolytic exposure of a cryptic site within collagen type IV is required for angiogenesis and tumor growth in vivo, J. Cell Biol., 154, 1069, 10.1083/jcb.200103111
Agnihotri, 2001, Osteopontin, a novel substrate for matrix metalloproteinase-3 (stromelysin-1) and matrix metalloproteinase-7 (matrilysin), J. Biol. Chem, 276, 28261, 10.1074/jbc.M103608200
Sage, 2003, Cleavage of the matricellular protein SPARC by matrix metalloproteinase 3 produces polypeptides that influence angiogenesis, J. Biol. Chem, 278, 37849, 10.1074/jbc.M302946200
Monboisse, 1840, Matrikines from basement membrane collagens: a new anti-cancer strategy, Biochim. Biophys. Acta, 2014, 2589
Ricard-Blum, 2014, Matricryptins and matrikines: biologically active fragments of the extracellular matrix, Exp. Dermatol., 23, 457, 10.1111/exd.12435
Butler, 2013, Matrix metalloproteinase processing of signaling molecules to regulate inflammation, Periodontol., 63, 123, 10.1111/prd.12035
Morrison, 2009, Matrix metalloproteinase proteomics: substrates, targets, and therapy, Curr. Opin. Cell Biol., 21, 645, 10.1016/j.ceb.2009.06.006
Schlage, 2015, Proteomic approaches to uncover MMP function, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 232, 10.1016/j.matbio.2015.01.003
Fortelny, 2014, Network analyses reveal pervasive functional regulation between proteases in the human protease web, PLoS Biol., 12, 10.1371/journal.pbio.1001869
Auf dem Keller, 2013, Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation, Sci. Signal., 6, 10.1126/scisignal.2003512
Bellac, 2014, Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis, Cell Rep., 9, 618, 10.1016/j.celrep.2014.09.006
Haro, 2000, Matrix metalloproteinase-7-dependent release of tumor necrosis factor-alpha in a model of herniated disc resorption, J. Clin. Invest., 105, 143, 10.1172/JCI7091
Suzuki, 1997, Matrix metalloproteinase-3 releases active heparin-binding EGF-like growth factor by cleavage at a specific juxtamembrane site, J. Biol. Chem., 272, 31730, 10.1074/jbc.272.50.31730
Zhang, 2003, HIV-induced metalloproteinase processing of the chemokine stromal cell derived factor-1 causes neurodegeneration, Nat. Neurosci., 6, 1064, 10.1038/nn1127
McQuibban, 2000, Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3, Science, 289, 1202, 10.1126/science.289.5482.1202
Wilson, 1999, Regulation of intestinal alpha-defensin activation by the metalloproteinase matrilysin in innate host defense, Science, 286, 113, 10.1126/science.286.5437.113
Poulalhon, 2006, Modulation of collagen and MMP-1 gene expression in fibroblasts by the immunosuppressive drug rapamycin. A direct role as an antifibrotic agent?, J. Biol. Chem., 281, 33045, 10.1074/jbc.M606366200
Dufour, 2013, Missing the target: matrix metalloproteinase antitargets in inflammation and cancer, Trends Pharmacol. Sci., 34, 233, 10.1016/j.tips.2013.02.004
Shay, 2015, Moving targets: emerging roles for MMPs in cancer progression and metastasis, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 200, 10.1016/j.matbio.2015.01.019
Bonnans, 2014, Remodelling the extracellular matrix in development and disease, Nat. Rev. Mol. Cell Biol., 15, 786, 10.1038/nrm3904
Cox, 2011, Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer, Dis. Model. Mech., 4, 165, 10.1242/dmm.004077
Lu, 2011, Extracellular matrix degradation and remodeling in development and disease, Cold Spring Harb. Perspect. Biol., 3, 10.1101/cshperspect.a005058
Kessenbrock, 2015, Matrix metalloproteinases in stem cell regulation and cancer, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 184, 10.1016/j.matbio.2015.01.022
Itoh, 2015, Membrane-type matrix metalloproteinases: their functions and regulations, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 207, 10.1016/j.matbio.2015.03.004
Overall, 2002, Molecular determinants of metalloproteinase substrate specificity: matrix metalloproteinase substrate binding domains, modules, and exosites, Mol. Biotechnol., 22, 51, 10.1385/MB:22:1:051
Patterson, 2001, Specific collagenolysis by gelatinase A, MMP-2, is determined by the hemopexin domain and not the fibronectin-like domain, FEBS Lett., 503, 158, 10.1016/S0014-5793(01)02723-5
Steffensen, 1995, Extracellular matrix binding properties of recombinant fibronectin type II-like modules of human 72-kDa gelatinase/type IV collagenase. High affinity binding to native type I collagen but not native type IV collagen, J. Biol. Chem., 270, 11555, 10.1074/jbc.270.19.11555
Gomis-Rüth, 1824, A standard orientation for metallopeptidases, Biochim. Biophys. Acta, 2012, 157
Harris, 2000, Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries, Proc. Natl. Acad. Sci., 97, 7754, 10.1073/pnas.140132697
Kasperkiewicz, 2012, Current and prospective applications of non-proteinogenic amino acids in profiling of proteases substrate specificity, Biol. Chem., 393, 843, 10.1515/hsz-2012-0167
Schilling, 2007, Proteomic discovery of protease substrates, Curr. Opin. Chem. Biol., 11, 36, 10.1016/j.cbpa.2006.11.037
Schilling, 2008, Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites, Nat. Biotechnol., 26, 685, 10.1038/nbt1408
Schilling, 2011, Characterization of the prime and non-prime active site specificities of proteases by proteome-derived peptide libraries and tandem mass spectrometry, Nat. Protoc., 6, 111, 10.1038/nprot.2010.178
Barré, 2014, Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries, PLoS One, 9, 10.1371/journal.pone.0105984
Becker-Pauly, 2011, Proteomic analyses reveal an acidic prime side specificity for the astacin metalloprotease family reflected by physiological substrates, Mol. Cell Proteomics, 10, 10.1074/mcp.M111.009233
Cruz, 2014, RC1339/APRc from Rickettsia conorii is a novel aspartic protease with properties of retropepsin-like enzymes, PLoS Pathog., 10, 10.1371/journal.ppat.1004324
Eckhard, 2014, Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen, J. Proteome, 100, 102, 10.1016/j.jprot.2013.10.004
Marino, 2014, Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity, Biochem. J., 457, 335, 10.1042/BJ20130196
Turk, 2001, Determination of protease cleavage site motifs using mixture-based oriented peptide libraries, Nat. Biotechnol., 19, 661, 10.1038/90273
Chen, 2003, A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9, J. Biol. Chem, 278, 17158, 10.1074/jbc.M210324200
Kridel, 2001, Substrate hydrolysis by matrix metalloproteinase-9, J. Biol. Chem, 276, 20572, 10.1074/jbc.M100900200
Reiter, 1999, Inhibition of MMP-1 and MMP-13 with phosphinic acids that exploit binding in the S2 pocket, Bioorg. Med. Chem. Lett., 9, 127, 10.1016/S0960-894X(98)00729-X
Deng, 2000, Substrate specificity of human collagenase 3 assessed using a phage-displayed peptide library, J. Biol. Chem., 275, 31422, 10.1074/jbc.M004538200
McGeehan, 1994, Characterization of the peptide substrate specificities of interstitial collagenase and 92-kDa gelatinase. Implications for substrate optimization, J. Biol. Chem., 269, 32814, 10.1016/S0021-9258(20)30064-8
Smith, 1995, Rapid identification of highly active and selective substrates for stromelysin and matrilysin using bacteriophage peptide display libraries, J. Biol. Chem., 270, 6440, 10.1074/jbc.270.12.6440
Nagase, 1994, Design and characterization of a fluorogenic substrate selectively hydrolyzed by stromelysin 1 (matrix metalloproteinase-3), J. Biol. Chem., 269, 20952, 10.1016/S0021-9258(17)31914-2
Nagase, 1996, Human matrix metalloproteinase specificity studies using collagen sequence-based synthetic peptides, Biopolymers, 40, 399, 10.1002/(SICI)1097-0282(1996)40:4<399::AID-BIP5>3.0.CO;2-R
Netzel-Arnett, 1993, Comparative sequence specificities of human 72- and 92-kDa gelatinases (type IV collagenases) and PUMP (matrilysin), Biochemistry (Mosc), 32, 6427, 10.1021/bi00076a016
Bode, 1999, Structural properties of matrix metalloproteinases, Cell Mol. Life Sci., 55, 639, 10.1007/s000180050320
Ratnikov, 2014, Basis for substrate recognition and distinction by matrix metalloproteinases, Proc. Natl. Acad. Sci. U. S. A., 111, E4148, 10.1073/pnas.1406134111
Dean, 2008, Macrophage-specific metalloelastase (MMP-12) truncates and inactivates ELR+ CXC chemokines and generates CCL2, -7, -8, and -13 antagonists: potential role of the macrophage in terminating polymorphonuclear leukocyte influx, Blood, 112, 3455, 10.1182/blood-2007-12-129080
Rawlings, 2014, MEROPS: the database of proteolytic enzymes, their substrates and inhibitors, Nucleic Acids Res., 42, D503, 10.1093/nar/gkt953
Overall, 2002, Discovery of chemokine substrates for matrix metalloproteinases by exosite scanning: a new tool for degradomics, Biol. Chem., 383, 1059, 10.1515/BC.2002.114
Li, 2002, Matrilysin shedding of syndecan-1 regulates chemokine mobilization and transepithelial efflux of neutrophils in acute lung injury, Cell, 111, 635, 10.1016/S0092-8674(02)01079-6
Knight, 1992, A novel coumarin-labelled peptide for sensitive continuous assays of the matrix metalloproteinases, FEBS Lett., 296, 263, 10.1016/0014-5793(92)80300-6
London, 2011, Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions, Nucleic Acids Res., 39, W249, 10.1093/nar/gkr431
Kukreja, 2015, High-throughput multiplexed peptide-centric profiling illustrates both substrate cleavage redundancy and specificity in the MMP family, Chem. Biol., 22, 1122, 10.1016/j.chembiol.2015.07.008
Prudova, 2010, Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics, Mol. Cell Proteomics, 9, 894, 10.1074/mcp.M000050-MCP201
Kohno, 2006, Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453, Biochem. Biophys. Res. Commun., 344, 315, 10.1016/j.bbrc.2006.03.098
Kleifeld, 2010, Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products, Nat. Biotechnol., 28, 281, 10.1038/nbt.1611
Kleifeld, 2011, Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates, Nat. Protoc., 6, 1578, 10.1038/nprot.2011.382
Fields, 2015, New strategies for targeting matrix metalloproteinases, Matrix Biol. J. Int. Soc. Matrix Biol., 44–46, 239, 10.1016/j.matbio.2015.01.002
Sela-Passwell, 2011, New opportunities in drug design of metalloproteinase inhibitors: combination between structure–function experimental approaches and systems biology, Expert Opin. Drug Discov., 6, 527, 10.1517/17460441.2011.560936
Morrison, 2006, TIMP independence of matrix metalloproteinase (MMP)-2 activation by membrane type 2 (MT2)-MMP is determined by contributions of both the MT2-MMP catalytic and hemopexin C domains, J. Biol. Chem., 281, 26528, 10.1074/jbc.M603331200
Butler, 2004, The canonical methionine 392 of matrix metalloproteinase 2 (gelatinase A) is not required for catalytic efficiency or structural integrity: probing the role of the methionine-turn in the metzincin metalloprotease superfamily, J. Biol. Chem., 279, 15615, 10.1074/jbc.M312727200
Rozanov, 2003, Membrane type-1 matrix metalloproteinase functions as a proprotein self-convertase. Expression of the latent zymogen in Pichia pastoris, autolytic activation, and the peptide sequence of the cleavage forms, J. Biol. Chem, 278, 8257, 10.1074/jbc.M213246200
The UniProt Consortium, 2014, Activities at the Universal Protein Resource (UniProt), Nucleic Acids Res., 42, D191, 10.1093/nar/gku469
Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinforma Oxf. Engl. 2004;20:1466–7. doi:http://dx.doi.org/10.1093/bioinformatics/bth092.
Keller, 2002, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Anal. Chem., 74, 5383, 10.1021/ac025747h
Keller, 2005, A uniform proteomics MS/MS analysis platform utilizing open XML file formats, Mol. Syst. Biol., 1, 2005.0017, 10.1038/msb4100024
Schilling, 2011, Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites, Biol. Chem., 392, 1031, 10.1515/BC.2011.158
Kersey, 2004, The International Protein Index: an integrated database for proteomics experiments, Proteomics, 4, 1985, 10.1002/pmic.200300721
Colaert, 2009, Improved visualization of protein consensus sequences by iceLogo, Nat. Methods, 6, 786, 10.1038/nmeth1109-786
Vizcaíno, 2013, The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013, Nucleic Acids Res., 41, D1063, 10.1093/nar/gks1262
Abel, 2003, Pre-steady-state kinetics of Bacillus licheniformis 1,3–1,4-beta-glucanase: evidence for a regulatory binding site, Biochem. J., 371, 997, 10.1042/bj20021504
Antoni, 2013, Crystallization of bi-functional ligand protein complexes, J. Struct. Biol., 182, 246, 10.1016/j.jsb.2013.03.015
Browner, 1995, Matrilysin-inhibitor complexes: common themes among metalloproteases, Biochemistry (Mosc), 34, 6602, 10.1021/bi00020a004
Fernandez-Catalan, 1998, Crystal structure of the complex formed by the membrane type 1-matrix metalloproteinase with the tissue inhibitor of metalloproteinases-2, the soluble progelatinase A receptor, EMBO J., 17, 5238, 10.1093/emboj/17.17.5238
Hashimoto, 2011, Structural basis for matrix metalloproteinase-2 (MMP-2)-selective inhibitory action of β-amyloid precursor protein-derived inhibitor, J. Biol. Chem., 286, 33236, 10.1074/jbc.M111.264176
Iyer, 2006, Crystal structure of an active form of human MMP-1, J. Mol. Biol., 362, 78, 10.1016/j.jmb.2006.06.079
Matter, 1999, Quantitative structure–activity relationship of human neutrophil collagenase (MMP-8) inhibitors using comparative molecular field analysis and X-ray structure analysis, J. Med. Chem., 42, 1908, 10.1021/jm980631s
Nar, 2001, Crystal structure of human macrophage elastase (MMP-12) in complex with a hydroxamic acid inhibitor, J. Mol. Biol., 312, 743, 10.1006/jmbi.2001.4953
Steele, 2000, Expression, characterization and structure determination of an active site mutant (Glu202-Gln) of mini-stromelysin-1, Protein Eng., 13, 397, 10.1093/protein/13.6.397
Bordoli, 2012, Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal, Methods Mol. Biol., 857, 107, 10.1007/978-1-61779-588-6_5
DeLano, 2005, The case for open-source software in drug discovery, Drug Discov. Today, 10, 213, 10.1016/S1359-6446(04)03363-X
Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211
Yang, 2012, UCSF chimera, MODELLER, and IMP: an integrated modeling system, J. Struct. Biol., 179, 269, 10.1016/j.jsb.2011.09.006
Dolinsky, 2004, PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations, Nucleic Acids Res., 32, W665, 10.1093/nar/gkh381
Olsson, 2011, PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions, J. Chem. Theory Comput., 7, 525, 10.1021/ct100578z
Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc. Natl. Acad. Sci. U. S. A., 98, 10037, 10.1073/pnas.181342398
Lerner, 2008
Bond, 2003, TopDraw: a sketchpad for protein structure topology cartoons, Bioinforma Oxf. Engl., 19, 311, 10.1093/bioinformatics/19.2.311
Winn, 2011, Overview of the CCP4 suite and current developments, Acta Crystallogr. D Biol. Crystallogr., 67, 235, 10.1107/S0907444910045749
Wessel, 1984, A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids, Anal. Biochem., 138, 141, 10.1016/0003-2697(84)90782-6