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Volumn 78, Issue 1, 2010, Pages 1-11

Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

Author keywords

Enzyme catalysis; Hydrolysis; Metalloenzymes; Molecular modelling; Structural biology

Indexed keywords

GELATINASE A; PEPTIDE;

EID: 77949416782     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22493     Document Type: Article
Times cited : (17)

References (38)
  • 2
    • 0035479845 scopus 로고    scopus 로고
    • Matrix metalloproteinases: They're not just for matrix anymore!
    • McCawley LJ, Matrisian LM. Matrix metalloproteinases: they're not just for matrix anymore! Curr Opin Cell Biol 2001;13:534-540.
    • (2001) Curr Opin Cell Biol , vol.13 , pp. 534-540
    • McCawley, L.J.1    Matrisian, L.M.2
  • 3
    • 15244350894 scopus 로고    scopus 로고
    • Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs
    • DOI 10.1016/j.biochi.2004.09.025
    • Cuniasse P, Devel L, Makaritis A, Beau F, Georgiadis D, Matziari M, Yiotakis A, Dive V. Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs. Biochimie 2005;87:393-402. (Pubitemid 40387619)
    • (2005) Biochimie , vol.87 , pp. 393-402
    • Cuniasse, P.1    Devel, L.2    Makaritis, A.3    Beau, F.4    Georgiadis, D.5    Matziari, M.6    Yiotakis, A.7    Dive, V.8
  • 4
    • 14044274265 scopus 로고    scopus 로고
    • Recent developments in the design of specific matrix metalloproteinase inhibitors aided by structural and computational studies
    • Rao BG. Recent developments in the design of specific matrix metalloproteinase inhibitors aided by structural and computational studies. Curr Pharm Des 2005;11:295-322.
    • (2005) Curr Pharm des , vol.11 , pp. 295-322
    • Rao, B.G.1
  • 5
    • 34447269445 scopus 로고    scopus 로고
    • Matrix metalloproteinase inhibitors: New challenges in the era of post broad-spectrum inhibitors
    • DOI 10.2174/138161207781039706
    • Nuti E, Tuccinardi T, Rossello A. Matrix metalloproteinase inhibitors: new challenges in the era of post broad-spectrum inhibitors. Curr Pharm Des 2007;13:2087-2100. (Pubitemid 47040490)
    • (2007) Current Pharmaceutical Design , vol.13 , Issue.20 , pp. 2087-2100
    • Nuti, E.1    Tuccinardi, T.2    Rossello, A.3
  • 6
    • 33644545381 scopus 로고    scopus 로고
    • Validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy
    • DOI 10.1038/nrc1821, PII N1821
    • Overall CM, Kleifeld O. Validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Nat Rev Cancer 2006;6:227-239. (Pubitemid 43292566)
    • (2006) Nature Reviews Cancer , vol.6 , Issue.3 , pp. 227-239
    • Overall, C.M.1    Kleifeld, O.2
  • 7
    • 33645738383 scopus 로고    scopus 로고
    • Towards third generation matrix matelloproteinase inhibitors for cancer therapy
    • Overall CM, Kleifeld O. Towards third generation matrix matelloproteinase inhibitors for cancer therapy. Brit J Cancer 2006; 94:941-946.
    • (2006) Brit J Cancer , vol.94 , pp. 941-946
    • Overall, C.M.1    Kleifeld, O.2
  • 8
    • 15244343490 scopus 로고    scopus 로고
    • Crystal structures of MMPs in complex with physiological and pharmacological inhibitors
    • DOI 10.1016/j.biochi.2004.11.019
    • Maskos K. Crystal structures of MMPs in complex with physiological and pharmacological inhibitors. Biochimie 2005;87:249-263. (Pubitemid 40387604)
    • (2005) Biochimie , vol.87 , pp. 249-263
    • Maskos, K.1
  • 9
    • 0027257103 scopus 로고
    • Comparative sequence specificities of human 72- And 92-kDa gelatinases (type IV collagenases) and PUMP (matrilysin)
    • Netzel-ArnettS,SangQ-X,MooreWGI,NavreM,Birkedal-HansenH,VanWartHE. Comparativesequencesspecificitiesofhuman72and92- kDagelatinases(typeIVcollagenases)andPUMP(matrilysin).Biochemistry1993;32: 6427-6432.(Pubitemid23208826)
    • (1993) Biochemistry , vol.32 , Issue.25 , pp. 6427-6432
    • Netzel-Arnett, S.1    Sang, Q.-X.2    Moore, W.G.I.3    Navre, M.4    Birkedal-Hansen, H.5    Van Wart, H.E.6
  • 10
    • 0028918852 scopus 로고
    • Rapid identification of highly active and selective substrates for stromelysin and matrilysin using bacteriophage peptide display libraries
    • Smith MM, Shi L, Navre M. Rapid identification of highly active and selective substrates for stromelysin and matrilysin using bacteriophage peptide display libraries. J Biol Chem 1995;270:6440-6449.
    • (1995) J Biol Chem , vol.270 , pp. 6440-6449
    • Smith, M.M.1    Shi, L.2    Navre, M.3
  • 11
    • 0034946412 scopus 로고    scopus 로고
    • Determination of protease cleavage site motifs using mixture-based oriented peptide libraries
    • Turk BE, Huang LL, Piro ET, Cantley LC. Determination of protease cleavage site motifs using mixture-based oriented peptide libraries. Nat Biotech 2001;19:661-667.
    • (2001) Nat Biotech , vol.19 , pp. 661-667
    • Turk, B.E.1    Huang, L.L.2    Piro, E.T.3    Cantley, L.C.4
  • 14
    • 0038269103 scopus 로고    scopus 로고
    • A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase2 and matrix metalloproteinase-9
    • Chen EI, Li W, Godzik A, Howard EW, Smith JW. A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase2 and matrix metalloproteinase-9. J Biol Chem 2003;278:1715817163.
    • (2003) J Biol Chem , vol.278 , pp. 1715817163
    • Chen, E.I.1    Li, W.2    Godzik, A.3    Howard, E.W.4    Smith, J.W.5
  • 15
    • 33846092077 scopus 로고    scopus 로고
    • Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases
    • DOI 10.1021/jp0656882
    • Diaz N, Suárez D, Sordo TL. Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases. J Phys Chem B 2006;110:24222-24230. (Pubitemid 46065863)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.47 , pp. 24222-24230
    • Diaz, N.1    Suarez, D.2    Sordo, T.L.3
  • 16
    • 34547787057 scopus 로고    scopus 로고
    • Molecular dynamics simulations of matrix metalloproteinase 2: Role of the structural metal ions
    • DOI 10.1021/bi700541p
    • Diaz N, Suárez D. Molecular dynamics simulations of matrix metailoproteinase 2: the role of the structural metal ions. Biochemistry 2007;46:8943-8952. (Pubitemid 47237369)
    • (2007) Biochemistry , vol.46 , Issue.31 , pp. 8943-8952
    • Diaz, N.1    Suarez, D.2
  • 17
    • 44949110147 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the active matrix metalloproteinase-2: Positioning of the N-terminal fragment and binding of a small peptide substrate
    • DOI 10.1002/prot.21894
    • Diaz N, Suárez D. Molecular dynamics simulations of the active matrix metalloproteinase-2: positioning of the N-terminal fragment and binding of a small peptide substrate. Proteins: Struct Punct Bioinf 2008;72:50-61. (Pubitemid 351809147)
    • (2008) Proteins: Structure, Function and Genetics , vol.72 , Issue.1 , pp. 50-61
    • Diaz, N.1    Suarez, D.2
  • 19
    • 0142236572 scopus 로고    scopus 로고
    • Low mode search. An efficient, automated computational method for conformational analysis: Application to cyclic and acyclic alkanes and cyclic peptides
    • Kolossváry I, Guida WC, Low mode search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides J Am Chem Soc 1996;118:5011-5019.
    • (1996) J Am Chem Soc , vol.118 , pp. 5011-5019
    • Kolossváry, I.1    Guida, W.C.2
  • 20
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Ace Chem Res 2000;33:889-897. (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 22
    • 0344796204 scopus 로고
    • Ion-water interaction potentials derived from free energy perturbation simulations
    • Aqvist J. Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem 1990;94:8021-8024.
    • (1990) J Phys Chem , vol.94 , pp. 8021-8024
    • Aqvist, J.1
  • 23
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • DOI 10.1016/j.jmgm.2003.12.005, PII S1093326303001943
    • Feig M, Karanicoias J, Brooks CL. MMTSB tool set: Enhanced sampling and multiscale modelling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395. (Pubitemid 38510304)
    • (2004) Journal of Molecular Graphics and Modelling , vol.22 , Issue.5 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 24
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MMPB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke H, Case DA. Converging free energy estimates: MMPB(GB)SA studies on the protein-protein complex Ras-Raf. J Cornput Chem 2003;25:238-250.
    • (2003) J Cornput Chem , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 25
    • 0037079570 scopus 로고    scopus 로고
    • Computational alanine scanning of the 1:1 human growth hormone-receptor complex
    • DOI 10.1002/jcc.1153
    • Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem 2002;23:15-27. (Pubitemid 34063126)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.1 , pp. 15-27
    • Huo, S.1    Massova, I.2    Kollman, P.A.3
  • 26
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • DOI 10.1021/ja990935j
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem. Soc 1999;121:8133-8143. (Pubitemid 29444447)
    • (1999) Journal of the American Chemical Society , vol.121 , Issue.36 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 27
    • 0001444487 scopus 로고    scopus 로고
    • Modeling unusual nucleic acid structures
    • Leontes NB, SantaLucia JJ, editors. Washington, DC: American Chemical Society
    • Macke T, Case DA. Modeling unusual nucleic acid structures. In: Leontes NB, SantaLucia JJ, editors. Molecular modeling of nucleic acids. Washington, DC: American Chemical Society; 1998. pp 379393.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379393
    • Macke, T.1    Case, D.A.2
  • 28
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus M, Ichiye T, Pettit BM. Configurational entropy of native proteins. Biophys J 1987;52:1083-1085.
    • (1987) Biophys J , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettit, B.M.3
  • 29
    • 0034271164 scopus 로고    scopus 로고
    • Physical nature of higher-order mutual information: Intrinsic correlations and frustration
    • Matsuda H. Physical nature of higher-order mutual information: intrinsic correlations and frustration. Phys Rev E 2000;62:30983102.
    • (2000) Phys Rev e , vol.62 , pp. 30983102
    • Matsuda, H.1
  • 30
    • 57449110766 scopus 로고    scopus 로고
    • Entropie control of the relative stability of triple-helical collagen peptide models
    • Suárez E, Díaz N, Suárez D, Entropie control of the relative stability of triple-helical collagen peptide models. J Phys Chem B 2008;112: 15248-15255.
    • (2008) J Phys Chem B , vol.112 , pp. 15248-15255
    • Suárez, E.1    Díaz, N.2    Suárez, D.3
  • 31
    • 84860129313 scopus 로고    scopus 로고
    • version 4.0, Schrödinger, LLC, New York, NY
    • QSite, version 4.0, Schrödinger, LLC, New York, NY, 2005.
    • (2005) QSite
  • 32
    • 0033523040 scopus 로고    scopus 로고
    • Structure of human pro-matrix metalloproteinase-2: Activation mechanism revealed
    • DOI 10.1126/science.284.5420.1667
    • Morgunova E, Tuuttila A, Bergmann U, Isupov M, Lindqvist Y, Schneider G, Tryggvason K. Structure of human pro-matrix metalloproteinase-2: activation mechanism revealed. Science 1999;284: 1667-1670. (Pubitemid 29291376)
    • (1999) Science , vol.284 , Issue.5420 , pp. 1667-1670
    • Morgunova, E.1    Tuuttila, A.2    Bergmann, U.3    Isupov, M.4    Lindqvist, Y.5    Schneider, G.6    Tryggvason, K.7
  • 33
    • 0000757079 scopus 로고
    • Exchange-correlation approximation in density-functional theory
    • Yarkony DR, editor. Singapore: World Scientific
    • Becke AD. Exchange-correlation approximation in density-functional theory. In: Yarkony DR, editor. Modern electronic structure theory part II. Singapore: World Scientific; 1995.
    • (1995) Modern Electronic Structure Theory Part II
    • Becke, A.D.1
  • 34
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • DOI 10.1021/jp003919d
    • Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001;105:6474-6487. (Pubitemid 35339015)
    • (2001) Journal of Physical Chemistry B , vol.105 , Issue.28 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 35
    • 0001664118 scopus 로고    scopus 로고
    • A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
    • Murphy RB, Philipp DM, Friesner RA. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. J Comput Chem 2000;21:1442-1457.
    • (2000) J Comput Chem , vol.21 , pp. 1442-1457
    • Murphy, R.B.1    Philipp, D.M.2    Friesner, R.A.3
  • 36
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
    • DOI 10.1021/jp010454y
    • Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear Poisson-Boitzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 2001;105:6507-6514. (Pubitemid 35339019)
    • (2001) Journal of Physical Chemistry B , vol.105 , Issue.28 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 37
    • 33748278773 scopus 로고    scopus 로고
    • Molecular dynamics simulation of peptide folding
    • DOI 10.1007/s00214-005-0070-4
    • Daura X. Molecular dynamics simulation of peptide folding. Theor Chem Acta 2006;116:297-306. (Pubitemid 44318432)
    • (2006) Theoretical Chemistry Accounts , vol.116 , Issue.1-3 , pp. 297-306
    • Daura, X.1
  • 38
    • 50249107450 scopus 로고    scopus 로고
    • Peptide hydrolysis catalyzed by matrix metalloproteinase 2: A computational study
    • Diaz N, Suárez D. Peptide hydrolysis catalyzed by matrix metalloproteinase 2: a computational study. J Phys Chem B 2008;112: 8412-8424.
    • (2008) J Phys Chem B , vol.112 , pp. 8412-8424
    • Diaz, N.1    Suárez, D.2


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