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Volumn 8, Issue 7, 2013, Pages

Computational and Experimental Insights into the Mechanism of Substrate Recognition and Feedback Inhibition of Protoporphyrinogen Oxidase

Author keywords

[No Author keywords available]

Indexed keywords

HEMATIN; PROTOPORPHYRINOGEN OXIDASE; THIOCTIC ACID;

EID: 84880723404     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0069198     Document Type: Article
Times cited : (25)

References (48)
  • 1
    • 79957445712 scopus 로고    scopus 로고
    • Porphyrins: One ring in the colors of life
    • Dayan FE, Dayan EA, (2011) Porphyrins: One ring in the colors of life. Am Sci 99: 236-243.
    • (2011) Am Sci , vol.99 , pp. 236-243
    • Dayan, F.E.1    Dayan, E.A.2
  • 2
    • 0016671103 scopus 로고
    • The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae
    • Poulson R, Polglase WJ, (1975) The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase activity in mitochondrial extracts of Saccharomyces cerevisiae. J Biol Chem 250: 1269-1274.
    • (1975) J Biol Chem , vol.250 , pp. 1269-1274
    • Poulson, R.1    Polglase, W.J.2
  • 3
    • 0017070102 scopus 로고
    • The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX in mammalian mitochondria
    • Poulson R, (1976) The enzymic conversion of protoporphyrinogen IX to protoporphyrin IX in mammalian mitochondria. J Biol Chem 251: 3730-3733.
    • (1976) J Biol Chem , vol.251 , pp. 3730-3733
    • Poulson, R.1
  • 4
    • 33747589914 scopus 로고    scopus 로고
    • A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase
    • Patzoldt WL, Hager AG, McCormick JS, Tranel PJ, (2006) A codon deletion confers resistance to herbicides inhibiting protoporphyrinogen oxidase. Proc Natl Acad Sci U S A 103: 12329-12334.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 12329-12334
    • Patzoldt, W.L.1    Hager, A.G.2    McCormick, J.S.3    Tranel, P.J.4
  • 5
    • 78049279741 scopus 로고    scopus 로고
    • Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803
    • Kato K, Tanaka R, Sano S, Tanaka A, Hosaka H, (2010) Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 107: 16649-16654.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 16649-16654
    • Kato, K.1    Tanaka, R.2    Sano, S.3    Tanaka, A.4    Hosaka, H.5
  • 6
    • 0041662029 scopus 로고    scopus 로고
    • A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen
    • Jeong E, Houn T, Kuk Y, Kim ES, Chandru HK, et al. (2003) A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen. Bioorg Chem 31: 389-397.
    • (2003) Bioorg Chem , vol.31 , pp. 389-397
    • Jeong, E.1    Houn, T.2    Kuk, Y.3    Kim, E.S.4    Chandru, H.K.5
  • 7
    • 0141872474 scopus 로고    scopus 로고
    • Kinetic and physical characterisation of recombinant wild-type and mutant human protoporphyrinogen oxidases
    • Maneli MH, Corrigall AV, Klump HH, Davids LM, Kirsch RE, et al. (2003) Kinetic and physical characterisation of recombinant wild-type and mutant human protoporphyrinogen oxidases. Biochim Biophys Acta 1650: 10-21.
    • (2003) Biochim Biophys Acta , vol.1650 , pp. 10-21
    • Maneli, M.H.1    Corrigall, A.V.2    Klump, H.H.3    Davids, L.M.4    Kirsch, R.E.5
  • 8
    • 77952419950 scopus 로고    scopus 로고
    • Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase
    • Dayan FE, Daga PR, Duke SO, Lee RM, Tranel PJ, et al. (2010) Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase. Biochim Biophys Acta 1804: 1548-1556.
    • (2010) Biochim Biophys Acta , vol.1804 , pp. 1548-1556
    • Dayan, F.E.1    Daga, P.R.2    Duke, S.O.3    Lee, R.M.4    Tranel, P.J.5
  • 9
    • 0032167638 scopus 로고    scopus 로고
    • The domain structure of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides
    • Arnould S, Camadro JM, (1998) The domain structure of protoporphyrinogen oxidase, the molecular target of diphenyl ether-type herbicides. Proc Natl Acad Sci U S A 95: 10553-10558.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 10553-10558
    • Arnould, S.1    Camadro, J.M.2
  • 10
    • 0024970331 scopus 로고
    • Protoporphyrinogen oxidase as a molecular target for diphenyl ether herbicides
    • Matringe M, Camadro JM, Labbe P, Scalla R, (1989) Protoporphyrinogen oxidase as a molecular target for diphenyl ether herbicides. Biochem J 260: 231-235.
    • (1989) Biochem J , vol.260 , pp. 231-235
    • Matringe, M.1    Camadro, J.M.2    Labbe, P.3    Scalla, R.4
  • 11
    • 9644290818 scopus 로고    scopus 로고
    • Synthesis and herbicidal activity of novel heterocyclic protoporphyrinogen oxidase inhibitors
    • Meazza G, Bettarini F, La Porta P, Piccardi P, Signorini E, et al. (2004) Synthesis and herbicidal activity of novel heterocyclic protoporphyrinogen oxidase inhibitors. Pest Manag Sci 60: 1178-1188.
    • (2004) Pest Manag Sci , vol.60 , pp. 1178-1188
    • Meazza, G.1    Bettarini, F.2    La Porta, P.3    Piccardi, P.4    Signorini, E.5
  • 13
    • 70449642877 scopus 로고    scopus 로고
    • Photofrin PDT for early stage oesophageal cancer: long term results in 40 patients and literature review
    • Moghissi K, Dixon K, Stringer M, Thorpe JA, (2009) Photofrin PDT for early stage oesophageal cancer: long term results in 40 patients and literature review. Photodiagnosis Photodyn Ther 6: 159-166.
    • (2009) Photodiagnosis Photodyn Ther , vol.6 , pp. 159-166
    • Moghissi, K.1    Dixon, K.2    Stringer, M.3    Thorpe, J.A.4
  • 14
    • 67349201695 scopus 로고    scopus 로고
    • Photodynamic therapy (PDT): a short review on cellular mechanisms and cancer research applications for PDT
    • Robertson CA, Evans DH, Abrahamse H, (2009) Photodynamic therapy (PDT): a short review on cellular mechanisms and cancer research applications for PDT. J Photochem Photobiol B 96: 1-8.
    • (2009) J Photochem Photobiol B , vol.96 , pp. 1-8
    • Robertson, C.A.1    Evans, D.H.2    Abrahamse, H.3
  • 16
    • 33644938813 scopus 로고    scopus 로고
    • Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain
    • Zhang D, Gullingsrud J, McCammon JA, (2006) Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc 128: 3019-3026.
    • (2006) J Am Chem Soc , vol.128 , pp. 3019-3026
    • Zhang, D.1    Gullingsrud, J.2    McCammon, J.A.3
  • 17
    • 79960007037 scopus 로고    scopus 로고
    • Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
    • Buch I, Giorgino T, De Fabritiis G, (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A 108: 10184-10189.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 19
    • 2442563409 scopus 로고    scopus 로고
    • Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis
    • Koch M, Breithaupt C, Kiefersauer R, Freigang J, Huber R, et al. (2004) Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis. EMBO J 23: 1720-1728.
    • (2004) EMBO J , vol.23 , pp. 1720-1728
    • Koch, M.1    Breithaupt, C.2    Kiefersauer, R.3    Freigang, J.4    Huber, R.5
  • 20
    • 33947230298 scopus 로고    scopus 로고
    • Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site
    • Heinemann IU, Diekmann N, Masoumi A, Koch M, Messerschmidt A, et al. (2007) Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site. Biochem J 402: 575-580.
    • (2007) Biochem J , vol.402 , pp. 575-580
    • Heinemann, I.U.1    Diekmann, N.2    Masoumi, A.3    Koch, M.4    Messerschmidt, A.5
  • 21
    • 79551625890 scopus 로고    scopus 로고
    • Structural insight into human variegate porphyria disease
    • Qin X, Tan Y, Wang L, Wang Z, Wang B, et al. (2010) Structural insight into human variegate porphyria disease. FASEB J 25: 653-664.
    • (2010) FASEB J , vol.25 , pp. 653-664
    • Qin, X.1    Tan, Y.2    Wang, L.3    Wang, Z.4    Wang, B.5
  • 22
    • 79955983984 scopus 로고    scopus 로고
    • Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations
    • Hao GF, Tan Y, Yu NX, Yang GF, (2011) Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations. J Comput Aided Mol Des 25: 213-222.
    • (2011) J Comput Aided Mol Des , vol.25 , pp. 213-222
    • Hao, G.F.1    Tan, Y.2    Yu, N.X.3    Yang, G.F.4
  • 23
    • 80053106260 scopus 로고    scopus 로고
    • Human butyrylcholinesterase-cocaine binding pathway and free energy profiles by molecular dynamics and potential of mean force simulations
    • Huang X, Zheng F, Zhan CG, (2011) Human butyrylcholinesterase-cocaine binding pathway and free energy profiles by molecular dynamics and potential of mean force simulations. J Phys Chem B 115: 11254-11260.
    • (2011) J Phys Chem B , vol.115 , pp. 11254-11260
    • Huang, X.1    Zheng, F.2    Zhan, C.G.3
  • 24
    • 84863834582 scopus 로고    scopus 로고
    • Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex
    • Hao GF, Wang F, Li H, Zhu XL, Yang WC, et al. (2012) Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J Am Chem Soc 134: 11168-11176.
    • (2012) J Am Chem Soc , vol.134 , pp. 11168-11176
    • Hao, G.F.1    Wang, F.2    Li, H.3    Zhu, X.L.4    Yang, W.C.5
  • 25
    • 37049059539 scopus 로고
    • Prevalence and significance of the product inhibition of enzymes
    • Frieden E, Walter C, (1963) Prevalence and significance of the product inhibition of enzymes. Nature 198: 834-837.
    • (1963) Nature , vol.198 , pp. 834-837
    • Frieden, E.1    Walter, C.2
  • 26
    • 74349118194 scopus 로고    scopus 로고
    • GDP-mannose pyrophosphorylase is essential in the bloodstream form of Trypanosoma brucei
    • Denton H, Fyffe S, Smith TK, (2010) GDP-mannose pyrophosphorylase is essential in the bloodstream form of Trypanosoma brucei. Biochem J 425: 603-614.
    • (2010) Biochem J , vol.425 , pp. 603-614
    • Denton, H.1    Fyffe, S.2    Smith, T.K.3
  • 27
    • 70349376092 scopus 로고    scopus 로고
    • Two forms of feedback inhibition determine the dynamical state of a small hippocampal network
    • Zeldenrust F, Wadman WJ (2009) Two forms of feedback inhibition determine the dynamical state of a small hippocampal network. Neural Netw. 1139-1158.
    • (2009) Neural Netw , pp. 1139-1158
    • Zeldenrust, F.1    Wadman, W.J.2
  • 29
    • 33947716119 scopus 로고    scopus 로고
    • A semiempirical free energy force field with charge-based desolvation
    • Huey R, Morris GM, Olson AJ, Goodsell DS, (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28: 1145-1152.
    • (2007) J Comput Chem , vol.28 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 30
    • 14844293471 scopus 로고    scopus 로고
    • A component-based software environment for visualizing large macromolecular assemblies
    • Sanner MF, (2005) A component-based software environment for visualizing large macromolecular assemblies. Structure 13: 447-462.
    • (2005) Structure , vol.13 , pp. 447-462
    • Sanner, M.F.1
  • 32
    • 84986468608 scopus 로고
    • An approach to computing electrostatic charges for molecules
    • Singh UC, Kollman PA, (1984) An approach to computing electrostatic charges for molecules. J Comput Chem 5: 129-145.
    • (1984) J Comput Chem , vol.5 , pp. 129-145
    • Singh, U.C.1    Kollman, P.A.2
  • 33
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler BH, Merz KM, Kollman PA, (1990) Atomic charges derived from semiempirical methods. J Comput Chem 11: 431-439.
    • (1990) J Comput Chem , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 34
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA, (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97: 10269-10280.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 35
    • 0000667030 scopus 로고
    • Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
    • Cornell WD, Cieplak P, Bayly CI, Kollman PA, (1993) Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc 115: 9620-9631.
    • (1993) J Am Chem Soc , vol.115 , pp. 9620-9631
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Kollman, P.A.4
  • 36
    • 65249103492 scopus 로고    scopus 로고
    • Understanding the mechanism of drug resistance due to a codon deletion in protoporphyrinogen oxidase through computational modeling
    • Hao GF, Zhu XL, Ji FQ, Zhang L, Yang GF, et al. (2009) Understanding the mechanism of drug resistance due to a codon deletion in protoporphyrinogen oxidase through computational modeling. J Phys Chem B 113: 4865-4875.
    • (2009) J Phys Chem B , vol.113 , pp. 4865-4875
    • Hao, G.F.1    Zhu, X.L.2    Ji, F.Q.3    Zhang, L.4    Yang, G.F.5
  • 37
    • 0034702646 scopus 로고    scopus 로고
    • Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath
    • Morishita T, (2000) Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath. J Chem Phys 113: 2976-2982.
    • (2000) J Chem Phys , vol.113 , pp. 2976-2982
    • Morishita, T.1
  • 38
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 39
  • 40
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of mot ion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical integration of the Cartesian equations of mot ion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 41
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
    • (2000) Acc Chem Res , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5
  • 42
    • 77954949788 scopus 로고    scopus 로고
    • Computational mutation scanning and drug resistance mechanisms of HIV-1 protease inhibitors
    • Hao GF, Yang GF, Zhan CG, (2010) Computational mutation scanning and drug resistance mechanisms of HIV-1 protease inhibitors. J Phys Chem B 114: 9663-9676.
    • (2010) J Phys Chem B , vol.114 , pp. 9663-9676
    • Hao, G.F.1    Yang, G.F.2    Zhan, C.G.3
  • 43
    • 77956288365 scopus 로고    scopus 로고
    • The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations
    • Hao GF, Yang GF, (2010) The role of Phe82 and Phe351 in auxin-induced substrate perception by TIR1 ubiquitin ligase: a novel insight from molecular dynamics simulations. PLoS One 5: e10742.
    • (2010) PLoS One , vol.5
    • Hao, G.F.1    Yang, G.F.2
  • 44
    • 0342929614 scopus 로고
    • Nonphysical sampling distribution in Monte Carlo free-energy estimation: umbrella sampling
    • Torrie GM, Valleau JP, (1977) Nonphysical sampling distribution in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys 23: 187-199.
    • (1977) J Comput Phys , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 45
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg J, (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method. J Comput Chem 13: 1011-1021.
    • (1992) J Comput Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.5
  • 46
    • 28044458963 scopus 로고    scopus 로고
    • Computational redesign of human butyrylcholinesterase for anticocaine medication
    • Pan Y, Gao D, Yang W, Cho H, Yang G, et al. (2005) Computational redesign of human butyrylcholinesterase for anticocaine medication. Proc Natl Acad Sci U S A 102: 16656-16661.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 16656-16661
    • Pan, Y.1    Gao, D.2    Yang, W.3    Cho, H.4    Yang, G.5
  • 47
    • 31044435861 scopus 로고    scopus 로고
    • Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation
    • Gao D, Cho H, Yang W, Pan Y, Yang G, et al. (2006) Computational design of a human butyrylcholinesterase mutant for accelerating cocaine hydrolysis based on the transition-state simulation. Angew Chem-Int Edit 45: 653-657.
    • (2006) Angew Chem -Int Edit , vol.45 , pp. 653-657
    • Gao, D.1    Cho, H.2    Yang, W.3    Pan, Y.4    Yang, G.5
  • 48
    • 42149093718 scopus 로고    scopus 로고
    • Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers
    • Pan Y, Gao D, Zhan CG, (2008) Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers. J Am Chem Soc 130: 5140-5149.
    • (2008) J Am Chem Soc , vol.130 , pp. 5140-5149
    • Pan, Y.1    Gao, D.2    Zhan, C.G.3


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