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Volumn 9, Issue 4, 2014, Pages

Affinity- and specificity-enhancing mutations are frequent in multispecific interactions between TIMP2 and MMPs

Author keywords

[No Author keywords available]

Indexed keywords

ADAM PROTEIN; GELATINASE B; MATRIX METALLOPROTEINASE; MATRIX METALLOPROTEINASE 14; TISSUE INHIBITOR OF METALLOPROTEINASE 2; MMP14 PROTEIN, HUMAN; PROTEIN BINDING; TIMP2 PROTEIN, HUMAN;

EID: 84899460613     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093712     Document Type: Article
Times cited : (38)

References (39)
  • 1
    • 79952093554 scopus 로고    scopus 로고
    • Multispecific recognition: Mechanism, evolution, and design
    • Erijman A, Aizner Y, Shifman JM (2011) Multispecific recognition: mechanism, evolution, and design. Biochemistry 50: 602-611.
    • (2011) Biochemistry , vol.50 , pp. 602-611
    • Erijman, A.1    Aizner, Y.2    Shifman, J.M.3
  • 3
    • 77049113770 scopus 로고    scopus 로고
    • The tissue inhibitors of metalloproteinases (TIMPs): An ancient family with structural and functional diversity
    • Brew K, Nagase H (2010) The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity. Biochim Biophys Acta 1803: 55-71.
    • (2010) Biochim Biophys Acta , vol.1803 , pp. 55-71
    • Brew, K.1    Nagase, H.2
  • 4
    • 81255188391 scopus 로고    scopus 로고
    • Tissue inhibitors of metalloproteinases
    • Murphy G (2011) Tissue inhibitors of metalloproteinases. Genome Biol 12: 233.
    • (2011) Genome Biol , vol.12 , pp. 233
    • Murphy, G.1
  • 5
    • 40349087284 scopus 로고    scopus 로고
    • Reappraising metalloproteinases in rheumatoid arthritis and osteoarthritis: Destruction or repair?
    • DOI 10.1038/ncprheum0727, PII NCPRHEUM0727
    • Murphy G, Nagase H (2008) Reappraising metalloproteinases in rheumatoid arthritis and osteoarthritis: destruction or repair? Nat Clin Pract Rheumatol 4: 128-135. (Pubitemid 351338627)
    • (2008) Nature Clinical Practice Rheumatology , vol.4 , Issue.3 , pp. 128-135
    • Murphy, G.1    Nagase, H.2
  • 6
    • 0036516460 scopus 로고    scopus 로고
    • Matrix metalloproteinases: A tail of a frog that became a prince
    • Brinckerhoff CE, Matrisian LM (2002) Matrix metalloproteinases: a tail of a frog that became a prince. Nat Rev Mol Cell Biol 3: 207-214.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 207-214
    • Brinckerhoff, C.E.1    Matrisian, L.M.2
  • 8
    • 0032167522 scopus 로고    scopus 로고
    • 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
    • DOI 10.1093/emboj/17.17.5238
    • Fernandez-Catalan C, Bode W, Huber R, Turk D, Calvete JJ, et al. (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: 5238-5248. (Pubitemid 28408489)
    • (1998) EMBO Journal , vol.17 , Issue.17 , pp. 5238-5248
    • Fernandez-Catalan, C.1    Bode, W.2    Huber, R.3    Turk, D.4    Calvete, J.J.5    Lichte, A.6    Tschesche, H.7    Maskos, K.8
  • 9
    • 33846675236 scopus 로고    scopus 로고
    • Flexibility and Variability of TIMP Binding: X-ray Structure of the Complex Between Collagenase-3/MMP-13 and TIMP-2
    • DOI 10.1016/j.jmb.2006.11.072, PII S0022283606016317
    • Maskos K, Lang R, Tschesche H, Bode W (2007) Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2. J Mol Biol 366: 1222-1231. (Pubitemid 46188638)
    • (2007) Journal of Molecular Biology , vol.366 , Issue.4 , pp. 1222-1231
    • Maskos, K.1    Lang, R.2    Tschesche, H.3    Bode, W.4
  • 10
    • 48749094943 scopus 로고    scopus 로고
    • Structural determinants of the ADAM inhibition by TIMP-3: Crystal structure of the TACE-N-TIMP-3 complex
    • Wisniewska M, Goettig P, Maskos K, Belouski E, Winters D, et al. (2008) Structural determinants of the ADAM inhibition by TIMP-3: crystal structure of the TACE-N-TIMP-3 complex. J Mol Biol 381: 1307-1319.
    • (2008) J Mol Biol , vol.381 , pp. 1307-1319
    • Wisniewska, M.1    Goettig, P.2    Maskos, K.3    Belouski, E.4    Winters, D.5
  • 11
    • 33847007324 scopus 로고    scopus 로고
    • Crystal structure of the catalytic domain of matrix metalloproteinase-1 in complex with the inhibitory domain of tissue inhibitor of metalloproteinase-1
    • DOI 10.1074/jbc.M607625200
    • Iyer S, Wei S, Brew K, Acharya KR (2007) Crystal structure of the catalytic domain of matrix metalloproteinase-1 in complex with the inhibitory domain of tissue inhibitor of metalloproteinase-1. J Biol Chem 282: 364-371. (Pubitemid 47076625)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.1 , pp. 364-371
    • Iyer, S.1    Wei, S.2    Brew, K.3    Acharya, K.R.4
  • 12
    • 77954827231 scopus 로고    scopus 로고
    • The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function
    • Grossman M, Tworowski D, Dym O, Lee MH, Levy Y, et al. (2010) The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function. Biochemistry 49: 6184-6192.
    • (2010) Biochemistry , vol.49 , pp. 6184-6192
    • Grossman, M.1    Tworowski, D.2    Dym, O.3    Lee, M.H.4    Levy, Y.5
  • 13
    • 84884490364 scopus 로고    scopus 로고
    • 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 (2013) Matrix metalloproteinase-10/TIMP-2 structure and analyses define conserved core interactions and diverse exosite interactions in MMP/TIMP complexes. PLoS One 8: e75836.
    • (2013) PLoS One , vol.8
    • Batra, J.1    Soares, A.S.2    Mehner, C.3    Radisky, E.S.4
  • 14
    • 0029876136 scopus 로고    scopus 로고
    • Folding and characterization of the amino-terminal domain of human tissue inhibitor of metalloproteinases-1 (TIMP-1) expressed at high yield in E. coli
    • DOI 10.1016/0014-5793(96)00304-3
    • Huang W, Suzuki K, Nagase H, Arumugam S, Van Doren SR, et al. (1996) Folding and characterization of the amino-terminal domain of human tissue inhibitor of metalloproteinases-1 (TIMP-1) expressed at high yield in E. coli. FEBS Lett 384: 155-161. (Pubitemid 26139794)
    • (1996) FEBS Letters , vol.384 , Issue.2 , pp. 155-161
    • Huang, W.1    Suzuki, K.2    Nagase, H.3    Arumugam, S.4    Van Doren, S.R.5    Brew, K.6
  • 15
    • 55349094310 scopus 로고    scopus 로고
    • Activation of matrix metalloproteinase-2 (MMP-2) by membrane type 1 matrix metalloproteinase through an artificial receptor for proMMP-2 generates active MMP-2
    • Nishida Y, Miyamori H, Thompson EW, Takino T, Endo Y, et al. (2008) Activation of matrix metalloproteinase-2 (MMP-2) by membrane type 1 matrix metalloproteinase through an artificial receptor for proMMP-2 generates active MMP-2. Cancer Res 68: 9096-9104.
    • (2008) Cancer Res , vol.68 , pp. 9096-9104
    • Nishida, Y.1    Miyamori, H.2    Thompson, E.W.3    Takino, T.4    Endo, Y.5
  • 16
    • 0037561804 scopus 로고    scopus 로고
    • Protein engineering of the tissue inhibitor of metalloproteinase 1 (TIMP-1) inhibitory domain: In search of selective matrix metalloproteinase inhibitors
    • DOI 10.1074/jbc.M211793200
    • Wei S, Chen Y, Chung L, Nagase H, Brew K (2003) Protein engineering of the tissue inhibitor of metalloproteinase 1 (TIMP-1) inhibitory domain. In search of selective matrix metalloproteinase inhibitors. J Biol Chem 278: 9831-9834. (Pubitemid 36800485)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.11 , pp. 9831-9834
    • Wei, S.1    Chen, Y.2    Chung, L.3    Nagase, H.4    Brew, K.5
  • 17
    • 34548436604 scopus 로고    scopus 로고
    • Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1; gelatinase-selective inhibitors
    • DOI 10.1110/ps.072978507
    • Hamze AB, Wei S, Bahudhanapati H, Kota S, Acharya KR, et al. (2007) Constraining specificity in the N-domain of tissue inhibitor of metalloproteinases-1; gelatinase-selective inhibitors. Protein Sci 16: 1905-1913. (Pubitemid 47367113)
    • (2007) Protein Science , vol.16 , Issue.9 , pp. 1905-1913
    • Hamze, A.B.1    Wei, S.2    Bahudhanapati, H.3    Kota, S.4    Acharya, K.R.5    Brew, K.6
  • 18
    • 25444445358 scopus 로고    scopus 로고
    • Reactive site mutations in tissue inhibitor of metalloproteinase-3 disrupt inhibition of matrix metalloproteinases but not tumor necrosis factor-alpha-converting enzyme
    • DOI 10.1074/jbc.C500220200
    • Wei S, Kashiwagi M, Kota S, Xie Z, Nagase H, et al. (2005) Reactive site mutations in tissue inhibitor of metalloproteinase-3 disrupt inhibition of matrix metalloproteinases but not tumor necrosis factor-alpha-converting enzyme. J Biol Chem 280: 32877-32882. (Pubitemid 41368336)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.38 , pp. 32877-32882
    • Wei, S.1    Kashiwagi, M.2    Kota, S.3    Xie, Z.4    Nagase, H.5    Brew, K.6
  • 19
    • 0141959313 scopus 로고    scopus 로고
    • Unveiling the surface epitopes that render tissue inhibitor of metalloproteinase-1 inactive against membrane type 1-matrix metalloproteinase
    • DOI 10.1074/jbc.M305678200
    • Lee MH, Rapti M, Murphy G (2003) Unveiling the surface epitopes that render tissue inhibitor of metalloproteinase-1 inactive against membrane type 1-matrix metalloproteinase. J Biol Chem 278: 40224-40230. (Pubitemid 37248590)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.41 , pp. 40224-40230
    • Lee, M.-H.1    Rapti, M.2    Murphy, G.3
  • 20
    • 80053564539 scopus 로고    scopus 로고
    • Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches
    • Grossman M, Sela-Passwell N, Sagi I (2011) Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches. Curr Opin Struct Biol 21: 678-685.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 678-685
    • Grossman, M.1    Sela-Passwell, N.2    Sagi, I.3
  • 21
    • 80052401858 scopus 로고    scopus 로고
    • 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 (2011) Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): identification of selective inhibitors of collagenase-1 (metalloproteinase 1 (MMP-1)). J Biol Chem 286: 31761-31770.
    • (2011) J Biol Chem , vol.286 , pp. 31761-31770
    • Bahudhanapati, H.1    Zhang, Y.2    Sidhu, S.S.3    Brew, K.4
  • 22
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • DOI 10.1016/S0022-2836(03)00670-3
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331: 281-299. (Pubitemid 36870793)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.1 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 23
    • 84874036031 scopus 로고    scopus 로고
    • Computational methods for controlling binding specificity
    • Sharabi O, Erijman A, Shifman JM (2013) Computational methods for controlling binding specificity. Methods Enzymol 523: 41-59.
    • (2013) Methods Enzymol , vol.523 , pp. 41-59
    • Sharabi, O.1    Erijman, A.2    Shifman, J.M.3
  • 24
    • 79954603143 scopus 로고    scopus 로고
    • Triathlon for energy functions: Who is the winner for design of protein-protein interactions?
    • Sharabi O, Dekel A, Shifman JM (2011) Triathlon for energy functions: who is the winner for design of protein-protein interactions? Proteins 79: 1487-1498.
    • (2011) Proteins , vol.79 , pp. 1487-1498
    • Sharabi, O.1    Dekel, A.2    Shifman, J.M.3
  • 25
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Applications to side-chain predictions
    • Dunbrack RL, Karplus M (1993) Backbone-dependent rotamer library for proteins. Applications to side-chain predictions. J Mol Biol 230: 543-574.
    • (1993) J Mol Biol , vol.230 , pp. 543-574
    • Dunbrack, R.L.1    Karplus, M.2
  • 26
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in side chain packing problem
    • Desmet J, De Maeyer M, Hazes B, Lasters I (1992) The dead-end elimination theorem and its use in side chain packing problem. Nature 356: 539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    De Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 28
    • 79959999002 scopus 로고    scopus 로고
    • Transfer-PCR (TPCR): A highway for DNA cloning and protein engineering
    • Erijman A, Dantes A, Bernheim R, Shifman JM, Peleg Y (2011) Transfer-PCR (TPCR): a highway for DNA cloning and protein engineering. J Struct Biol 175: 171-177.
    • (2011) J Struct Biol , vol.175 , pp. 171-177
    • Erijman, A.1    Dantes, A.2    Bernheim, R.3    Shifman, J.M.4    Peleg, Y.5
  • 29
    • 84884653264 scopus 로고    scopus 로고
    • Predicting affinity- and specificity-enhancing mutations at protein-protein interfaces
    • Sharabi O, Shirian J, Shifman JM (2013) Predicting affinity- and specificity-enhancing mutations at protein-protein interfaces. Biochem Soc Trans 41: 1166-1169.
    • (2013) Biochem Soc Trans , vol.41 , pp. 1166-1169
    • Sharabi, O.1    Shirian, J.2    Shifman, J.M.3
  • 30
    • 0033575223 scopus 로고    scopus 로고
    • The specificity of TIMP-2 for matrix metalloproteinases can be modified by single amino acid mutations
    • Butler GS, Hutton M, Wattam BA, Williamson RA, Knauper V, et al. (1999) The specificity of TIMP-2 for matrix metalloproteinases can be modified by single amino acid mutations. J Biol Chem 274: 20391-20396.
    • (1999) J Biol Chem , vol.274 , pp. 20391-20396
    • Butler, G.S.1    Hutton, M.2    Wattam, B.A.3    Williamson, R.A.4    Knauper, V.5
  • 31
    • 74549136698 scopus 로고    scopus 로고
    • Tradeoff between stability and multispecificity in the design of promiscuous proteins
    • Fromer M, Shifman JM (2009) Tradeoff between stability and multispecificity in the design of promiscuous proteins. PLoS Comput Biol 5: e1000627.
    • (2009) PLoS Comput Biol , vol.5
    • Fromer, M.1    Shifman, J.M.2
  • 32
    • 34548383489 scopus 로고    scopus 로고
    • Design of multi-specificity in protein interfaces
    • Humphris EL, Kortemme T (2007) Design of multi-specificity in protein interfaces. PLoS Comput Biol 3: e164.
    • (2007) PLoS Comput Biol , vol.3
    • Humphris, E.L.1    Kortemme, T.2
  • 33
    • 84873085753 scopus 로고    scopus 로고
    • A strategy for modulation of enzymes in the ubiquitin system
    • Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, et al. (2013) A strategy for modulation of enzymes in the ubiquitin system. Science 339: 590-595.
    • (2013) Science , vol.339 , pp. 590-595
    • Ernst, A.1    Avvakumov, G.2    Tong, J.3    Fan, Y.4    Zhao, Y.5
  • 34
    • 84898431842 scopus 로고    scopus 로고
    • Mapping the binding landscape of a picomolar protein-protein complex through computation and experiment
    • Aizner Y, Sharabi O, Shirian J, Dakwar G, Abvraham O, et al. (2014) Mapping the binding landscape of a picomolar protein-protein complex through computation and experiment. Structure 22, 1-10.
    • (2014) Structure , vol.22 , pp. 1-10
    • Aizner, Y.1    Sharabi, O.2    Shirian, J.3    Dakwar, G.4    Abvraham, O.5
  • 35
    • 35148855712 scopus 로고    scopus 로고
    • Computational design of antibody-affinity improvement beyond in vivo maturation
    • DOI 10.1038/nbt1336, PII NBT1336
    • Lippow SM, Wittrup KD, Tidor B (2007) Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol 25: 1171-1176. (Pubitemid 47538113)
    • (2007) Nature Biotechnology , vol.25 , Issue.10 , pp. 1171-1176
    • Lippow, S.M.1    Wittrup, K.D.2    Tidor, B.3
  • 36
    • 34547571461 scopus 로고    scopus 로고
    • Structure-based Protocol for Identifying Mutations that Enhance Protein-Protein Binding Affinities
    • DOI 10.1016/j.jmb.2007.05.096, PII S0022283607007668
    • Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, et al. (2007) Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. Journal of Molecular Biology 371: 1392-1404. (Pubitemid 47198253)
    • (2007) Journal of Molecular Biology , vol.371 , Issue.5 , pp. 1392-1404
    • Sammond, D.W.1    Eletr, Z.M.2    Purbeck, C.3    Kimple, R.J.4    Siderovski, D.P.5    Kuhlman, B.6
  • 37
    • 0031450506 scopus 로고    scopus 로고
    • Hydrogen bonds and salt bridges across protein-protein interfaces
    • Xu D, Tsai CJ, Nussinov R (1997) Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng 10: 999-1012. (Pubitemid 28004646)
    • (1997) Protein Engineering , vol.10 , Issue.9 , pp. 999-1012
    • Xu, D.1    Tsai, C.-J.2    Nussinov, R.3
  • 38
    • 33750075732 scopus 로고    scopus 로고
    • Specificity of molecular interactions in transient protein-protein interaction interfaces
    • DOI 10.1002/prot.21056
    • Cho KI, Lee K, Lee KH, Kim D, Lee D (2006) Specificity of molecular interactions in transient protein-protein interaction interfaces. Proteins 65: 593-606. (Pubitemid 44583210)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.3 , pp. 593-606
    • Cho, K.-I.1    Lee, K.2    Lee, K.H.3    Kim, D.4    Lee, D.5
  • 39
    • 0003819359 scopus 로고
    • Shannon information as a measure of amino acid diversity
    • A.S P, Weisbuch G, editors. Berlin: Springer-Verlag
    • Litwin S, Jores R (1992) Shannon information as a measure of amino acid diversity. In: A.S P, Weisbuch G, editors. Theoretical and Experimental Insights into Immunology. Berlin: Springer-Verlag. pp. 289-296.
    • (1992) Theoretical and Experimental Insights into Immunology , pp. 289-296
    • Litwin, S.1    Jores, R.2


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