메뉴 건너뛰기




Volumn 21, Issue 11, 2012, Pages 1672-1681

Molecular dynamics simulation of the last step of a catalytic cycle: Product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis

Author keywords

Enzyme; Exit mechanism; Molecular dynamics simulation; Product

Indexed keywords

ARGININE; CHORISMATE MUTASE; CHORISMIC ACID; DIMER; MONOMER;

EID: 84867666999     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2143     Document Type: Article
Times cited : (2)

References (27)
  • 2
    • 0018168164 scopus 로고
    • Mechanism of chorismate mutase reaction
    • Gorisch H (1978) Mechanism of chorismate mutase reaction. Biochemistry 17:3700-3705.
    • (1978) Biochemistry , vol.17 , pp. 3700-3705
    • Gorisch, H.1
  • 3
    • 0000682795 scopus 로고
    • The uncatalyzed Claisen rearrangement of chorismate to prephenate prefers a transition-state of chairlike geometry
    • Copley SD, Knowles JR (1985) The uncatalyzed Claisen rearrangement of chorismate to prephenate prefers a transition-state of chairlike geometry. J Am Chem Soc 107:5306-5308.
    • (1985) J Am Chem Soc , vol.107 , pp. 5306-5308
    • Copley, S.D.1    Knowles, J.R.2
  • 4
    • 0015819741 scopus 로고
    • Kinetic and molecular orbital studies of the rearrangement of chorismate to prephenate
    • Andrews PR, Smith GD, Young IG (1973) Kinetic and molecular orbital studies of the rearrangement of chorismate to prephenate. Biochemistry 12:3492-3498.
    • (1973) Biochemistry , vol.12 , pp. 3492-3498
    • Andrews, P.R.1    Smith, G.D.2    Young, I.G.3
  • 5
    • 0032516484 scopus 로고    scopus 로고
    • A small, thermostable, and monofunctional chorismate mutase from the archeon Methanococcus jannaschii
    • DOI 10.1021/bi980449t
    • MacBeath G, Kast P, Hilvert D (1998) A small, thermostable, and monofunctional chorismate mutase from the archaeon Methanococcus jannaschii. Biochemistry 37:10062-73. (Pubitemid 28366360)
    • (1998) Biochemistry , vol.37 , Issue.28 , pp. 10062-10073
    • MacBeath, G.1    Kast, P.2    Hilvert, D.3
  • 6
    • 12544259906 scopus 로고    scopus 로고
    • Characterization of the secreted chorismate mutase from the pathogen Mycobacterium tuberculosis
    • Sasso S, Ramakrishnan C, Gamper M, Hilvert D, Kast P (2005) Characterization of the secreted chorismate mutase from the pathogen Mycobacterium tuberculosis. FEBS J 272:375-389.
    • (2005) FEBS J , vol.272 , pp. 375-389
    • Sasso, S.1    Ramakrishnan, C.2    Gamper, M.3    Hilvert, D.4    Kast, P.5
  • 7
    • 33645047892 scopus 로고    scopus 로고
    • 1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: Novel fold topology revealed
    • Okvist M, Dey R, Sasso S, Grahn E, Kast P, Krengel U (2006) 1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: Novel fold topology revealed. J Mol Biol 357:1483-1499.
    • (2006) J Mol Biol , vol.357 , pp. 1483-1499
    • Okvist, M.1    Dey, R.2    Sasso, S.3    Grahn, E.4    Kast, P.5    Krengel, U.6
  • 8
    • 37549047189 scopus 로고    scopus 로고
    • The two chorismate mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: Biochemical analysis and limited regulation of promoter activity by aromatic amino acids
    • Schneider CZ, Parish T, Basso LA, Santos DS (2008) The two chorismate mutases from both Mycobacterium tuberculosis and Mycobacterium smegmatis: biochemical analysis and limited regulation of promoter activity by aromatic amino acids. J Bact 190:122-134.
    • (2008) J Bact , vol.190 , pp. 122-134
    • Schneider, C.Z.1    Parish, T.2    Basso, L.A.3    Santos, D.S.4
  • 9
    • 0000167881 scopus 로고
    • Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction
    • Lyne PD, Mulholland AJ, Richards WG (1995) Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction. J Am Chem Soc 117:11345-11350.
    • (1995) J Am Chem Soc , vol.117 , pp. 11345-11350
    • Lyne, P.D.1    Mulholland, A.J.2    Richards, W.G.3
  • 10
    • 27644492410 scopus 로고    scopus 로고
    • Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: Correlation of barrier height with transition-state stabilization
    • DOI 10.1039/b508181e
    • Claeyssens F, Ranaghan KE, Manby FR, Harvey JN, Mulholland AJ (2005) Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transitionstate stabilization. Chem Commun 40:5068-5070. (Pubitemid 41566435)
    • (2005) Chemical Communications , Issue.40 , pp. 5068-5070
    • Claeyssens, F.1    Ranaghan, K.E.2    Manby, F.R.3    Harvey, J.N.4    Mulholland, A.J.5
  • 11
    • 52949128744 scopus 로고    scopus 로고
    • On the relationship between folding and chemical landscapes in enzyme catalysis
    • Roca M, Messer B, Hilvert D, Warshel A (2008) On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Nat Acad Sci USA 105:13877-13882.
    • (2008) Proc Nat Acad Sci USA , vol.105 , pp. 13877-13882
    • Roca, M.1    Messer, B.2    Hilvert, D.3    Warshel, A.4
  • 12
    • 0027274818 scopus 로고
    • Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog
    • Chook YM, Ke HM, Lipscomb WN (1993) Crystal structures of the monofunctional chorismate mutase from Bacillus subtilis and its complex with a transition state analog. Proc Nat Acad Sci USA 90:8600-8603.
    • (1993) Proc Nat Acad Sci USA , vol.90 , pp. 8600-8603
    • Chook, Y.M.1    Ke, H.M.2    Lipscomb, W.N.3
  • 13
    • 0029109922 scopus 로고
    • Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase
    • Lee AY, Karplus PA, Ganem B, Clardy J (1995) Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase. J Am Chem Soc 117:3627-3628.
    • (1995) J Am Chem Soc , vol.117 , pp. 3627-3628
    • Lee, A.Y.1    Karplus, P.A.2    Ganem, B.3    Clardy, J.4
  • 14
    • 0034634393 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    • Ludemann SK, Lounnas V, Wade RC (2000) How do substrates enter and products exit the buried active site of cytochrome P450cam? Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J Mol Biol 303:797-811.
    • (2000) J Mol Biol , vol.303 , pp. 797-811
    • Ludemann, S.K.1    Lounnas, V.2    Wade, R.C.3
  • 15
    • 0037073487 scopus 로고    scopus 로고
    • Navigation inside a protease: Substrate selection and product exit in the tricorn protease from Thermoplasma acidophilum
    • DOI 10.1016/S0022-2836(02)01153-1
    • Kim JS, Groll M, Musiol HA, Behrendt R, Kaiser M, Moroder L, Huber R, Brandstetter H (2002) Navigation inside a protease: substrate selection and product exit in the tricorn protease from Thermoplasma acidophilum. J Mol Biol 324:1041-1050. (Pubitemid 41782992)
    • (2002) Journal of Molecular Biology , vol.324 , Issue.5 , pp. 1041-1050
    • Kim, J.-S.1    Groll, M.2    Musiol, H.-J.3    Behrendt, R.4    Kaiser, M.5    Moroder, L.6    Huber, R.7    Brandstetter, H.8
  • 16
    • 70349509736 scopus 로고    scopus 로고
    • Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: Involvement of phenylalanine residues in the gating mechanism
    • Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R (2009) Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B 113:13018-13025.
    • (2009) J Phys Chem B , vol.113 , pp. 13018-13025
    • Fishelovitch, D.1    Shaik, S.2    Wolfson, H.J.3    Nussinov, R.4
  • 18
    • 0030058137 scopus 로고    scopus 로고
    • Electrostatic catalysis of the claisen rearrangement: Probing the role of Glu78 in Bacillus subtilis chorismate mutase by genetic selection
    • DOI 10.1021/ja953701i
    • Kast P, Hartgerink JD, Asifullah M, Hilvert D (1996) Electrostatic catalysis of the Claisen rearrangement: probing the role of Glu78 in Bacillus subtilis chorismate mutase by genetic selection. J Am Chem Soc 118:3069-3070. (Pubitemid 3044283)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.12 , pp. 3069-3070
    • Kast, P.1    Hartgerink, J.D.2    Asif-Ullah, M.3    Hilvert, D.4
  • 21
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • DOI 10.1002/jcc.1078
    • Schuler LD, Daura X, van Gunsteren WF (2001) An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J Comp Chem 22:1205-1218. (Pubitemid 32662797)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.11 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    Van Gunsteren, W.F.3
  • 22
  • 23
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 23:327-341.
    • (1977) J Comp Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 26
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451-5459.
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 27
    • 0035878765 scopus 로고    scopus 로고
    • Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
    • DOI 10.1063/1.1379764
    • Heinz TN, van Gunsteren WF, Hünenberger PH (2001) Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J Chem Phys 115:1125-1136. (Pubitemid 32699300)
    • (2001) Journal of Chemical Physics , vol.115 , Issue.3 , pp. 1125-1136
    • Heinz, T.N.1    Van Gunsteren, W.F.2    Hunenberger, P.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.