메뉴 건너뛰기




Volumn 7, Issue 3, 2012, Pages

Optimization of time-course experiments for kinetic model discrimination

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE; HYDROXYACYLGLUTATHIONE HYDROLASE; LACTOYLGLUTATHIONE LYASE; METHYLGLYOXAL; DRUG DERIVATIVE; ENZYME; S LACTOYLGLUTATHIONE; S-LACTOYLGLUTATHIONE;

EID: 84857723721     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032749     Document Type: Article
Times cited : (17)

References (54)
  • 2
    • 4644301730 scopus 로고    scopus 로고
    • A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions
    • Kremling A, Fischer S, Gadkar K, Doyle FJ, Sauter T, et al. (2004) A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res 14: 1773-1785.
    • (2004) Genome Res , vol.14 , pp. 1773-1785
    • Kremling, A.1    Fischer, S.2    Gadkar, K.3    Doyle, F.J.4    Sauter, T.5
  • 3
    • 77951967006 scopus 로고    scopus 로고
    • An optimal experimental design approach to model discrimination in dynamic biochemical systems
    • Skanda D, Lebiedz D, (2010) An optimal experimental design approach to model discrimination in dynamic biochemical systems. Bioinformatics 26: 939-945.
    • (2010) Bioinformatics , vol.26 , pp. 939-945
    • Skanda, D.1    Lebiedz, D.2
  • 4
    • 77950535005 scopus 로고    scopus 로고
    • Discriminating between rival biochemical network models: three approaches to optimal experiment design
    • Melykuti B, August E, Papachristodoulou A, El-Samad H, (2010) Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Syst Biol 4: 38.
    • (2010) BMC Syst Biol , vol.4 , pp. 38
    • Melykuti, B.1    August, E.2    Papachristodoulou, A.3    El-Samad, H.4
  • 5
    • 0000477772 scopus 로고    scopus 로고
    • Optimal design: A computer program to study the best possible spacing of design points for model discrimination
    • Bardsley WG, Wood RMW, Melikhova EM, (1996) Optimal design: A computer program to study the best possible spacing of design points for model discrimination. Computers & Chemistry 20: 145-157.
    • (1996) Computers & Chemistry , vol.20 , pp. 145-157
    • Bardsley, W.G.1    Wood, R.M.W.2    Melikhova, E.M.3
  • 8
    • 0029551743 scopus 로고
    • Pharmacokinetic parameter estimations by minimum relative entropy method
    • Amisaki T, Eguchi S, (1995) Pharmacokinetic parameter estimations by minimum relative entropy method. J Pharmacokinet Biopharm 23: 479-494.
    • (1995) J Pharmacokinet Biopharm , vol.23 , pp. 479-494
    • Amisaki, T.1    Eguchi, S.2
  • 9
    • 4244040278 scopus 로고    scopus 로고
    • Glutathione-dependent detoxification of alpha-oxoaldehydes by the glyoxalase system: involvement in disease mechanisms and antiproliferative activity of glyoxalase I inhibitors
    • Thornalley PJ, (1998) Glutathione-dependent detoxification of alpha-oxoaldehydes by the glyoxalase system: involvement in disease mechanisms and antiproliferative activity of glyoxalase I inhibitors. Chem Biol Interact 111-112: 137-151.
    • (1998) Chem Biol Interact , vol.111-112 , pp. 137-151
    • Thornalley, P.J.1
  • 10
    • 0030597071 scopus 로고    scopus 로고
    • Glycoxidation and oxidative stress in Parkinson disease and diffuse Lewy body disease
    • Castellani R, Smith MA, Richey PL, Perry G, (1996) Glycoxidation and oxidative stress in Parkinson disease and diffuse Lewy body disease. Brain Res 737: 195-200.
    • (1996) Brain Res , vol.737 , pp. 195-200
    • Castellani, R.1    Smith, M.A.2    Richey, P.L.3    Perry, G.4
  • 12
    • 19944432234 scopus 로고    scopus 로고
    • Argpyrimidine, a methylglyoxal-derived advanced glycation end-product in familial amyloidotic polyneuropathy
    • Gomes R, Sousa Silva M, Quintas A, Cordeiro C, Freire A, et al. (2005) Argpyrimidine, a methylglyoxal-derived advanced glycation end-product in familial amyloidotic polyneuropathy. Biochem J 385: 339-345.
    • (2005) Biochem J , vol.385 , pp. 339-345
    • Gomes, R.1    Sousa Silva, M.2    Quintas, A.3    Cordeiro, C.4    Freire, A.5
  • 13
    • 0026482265 scopus 로고
    • Advanced glycosylation: chemistry, biology, and implications for diabetes and aging
    • Bucala R, Cerami A, (1992) Advanced glycosylation: chemistry, biology, and implications for diabetes and aging. Adv Pharmacol 23: 1-34.
    • (1992) Adv Pharmacol , vol.23 , pp. 1-34
    • Bucala, R.1    Cerami, A.2
  • 14
    • 0042820029 scopus 로고    scopus 로고
    • Enhancement of chaperone function of alpha-crystallin by methylglyoxal modification
    • Nagaraj RH, Oya-Ito T, Padayatti PS, Kumar R, Mehta S, et al. (2003) Enhancement of chaperone function of alpha-crystallin by methylglyoxal modification. Biochemistry 42: 10746-10755.
    • (2003) Biochemistry , vol.42 , pp. 10746-10755
    • Nagaraj, R.H.1    Oya-Ito, T.2    Padayatti, P.S.3    Kumar, R.4    Mehta, S.5
  • 15
    • 80055057809 scopus 로고    scopus 로고
    • Beyond Genetic Factors in Familial Amyloidotic Polyneuropathy: Protein Glycation and the Loss of Fibrinogen's Chaperone Activity
    • da Costa G, Gomes RA, Guerreiro A, Mateus E, Monteiro E, et al. (2011) Beyond Genetic Factors in Familial Amyloidotic Polyneuropathy: Protein Glycation and the Loss of Fibrinogen's Chaperone Activity. PLoS One 6: e24850.
    • (2011) PLoS One , vol.6
    • da Costa, G.1    Gomes, R.A.2    Guerreiro, A.3    Mateus, E.4    Monteiro, E.5
  • 17
    • 47249109476 scopus 로고    scopus 로고
    • Evolutionary Algorithms for Solving Multi-Objective Problems
    • In: Goldberg DE, Koza JR, editors, New York, Springer
    • Coello Coello CA, Lamont GB, Van Veldhuizen DA, (2007) Evolutionary Algorithms for Solving Multi-Objective Problems; In: Goldberg DE, Koza JR, editors. New York Springer.
    • (2007)
    • Coello Coello, C.A.1    Lamont, G.B.2    Van Veldhuizen, D.A.3
  • 20
    • 0001371953 scopus 로고
    • The mechanism of the glyoxalase I reaction, and the effect of ophthalmic acid as an inhibitor
    • Cliffe EE, Waley SG, (1961) The mechanism of the glyoxalase I reaction, and the effect of ophthalmic acid as an inhibitor. Biochem J 79: 475-482.
    • (1961) Biochem J , vol.79 , pp. 475-482
    • Cliffe, E.E.1    Waley, S.G.2
  • 21
    • 70449154891 scopus 로고
    • The effects of some analogues of glutathione on the glyoxalase system
    • Kermack WO, Matheson NA, (1957) The effects of some analogues of glutathione on the glyoxalase system. Biochem J 65: 48-58.
    • (1957) Biochem J , vol.65 , pp. 48-58
    • Kermack, W.O.1    Matheson, N.A.2
  • 22
    • 0024207748 scopus 로고
    • Diffusion-dependent rates for the hydrolysis reaction catalyzed by glyoxalase II from rat erythrocytes
    • Guha MK, Vander Jagt DL, Creighton DJ, (1988) Diffusion-dependent rates for the hydrolysis reaction catalyzed by glyoxalase II from rat erythrocytes. Biochemistry 27: 8818-8822.
    • (1988) Biochemistry , vol.27 , pp. 8818-8822
    • Guha, M.K.1    Vander Jagt, D.L.2    Creighton, D.J.3
  • 24
    • 0030027452 scopus 로고    scopus 로고
    • Molecular cloning, heterologous expression, and characterization of human glyoxalase II
    • Ridderstrom M, Saccucci F, Hellman U, Bergman T, Principato G, et al. (1996) Molecular cloning, heterologous expression, and characterization of human glyoxalase II. J Biol Chem 271: 319-323.
    • (1996) J Biol Chem , vol.271 , pp. 319-323
    • Ridderstrom, M.1    Saccucci, F.2    Hellman, U.3    Bergman, T.4    Principato, G.5
  • 25
    • 0033486132 scopus 로고    scopus 로고
    • Heterologous expression, purification, and kinetic comparison of the cytoplasmic and mitochondrial glyoxalase II enzymes, Glo2p and Glo4p, from Saccharomyces cerevisiae
    • Bito A, Haider M, Briza P, Strasser P, Breitenbach M, (1999) Heterologous expression, purification, and kinetic comparison of the cytoplasmic and mitochondrial glyoxalase II enzymes, Glo2p and Glo4p, from Saccharomyces cerevisiae. Protein Expr Purif 17: 456-464.
    • (1999) Protein Expr Purif , vol.17 , pp. 456-464
    • Bito, A.1    Haider, M.2    Briza, P.3    Strasser, P.4    Breitenbach, M.5
  • 26
    • 0033150867 scopus 로고    scopus 로고
    • Glyoxalase II in Saccharomyces cerevisiae: in situ kinetics using the 5,5′-dithiobis(2-nitrobenzoic acid) assay
    • Martins AM, Cordeiro C, Freire AP, (1999) Glyoxalase II in Saccharomyces cerevisiae: in situ kinetics using the 5,5′-dithiobis(2-nitrobenzoic acid) assay. Arch Biochem Biophys 366: 15-20.
    • (1999) Arch Biochem Biophys , vol.366 , pp. 15-20
    • Martins, A.M.1    Cordeiro, C.2    Freire, A.P.3
  • 27
    • 0034828640 scopus 로고    scopus 로고
    • In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae
    • Martins AM, Mendes P, Cordeiro C, Freire AP, (2001) In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. Eur J Biochem 268: 3930-3936.
    • (2001) Eur J Biochem , vol.268 , pp. 3930-3936
    • Martins, A.M.1    Mendes, P.2    Cordeiro, C.3    Freire, A.P.4
  • 29
    • 24644494767 scopus 로고    scopus 로고
    • Protein glycation in Saccharomyces cerevisiae. Argpyrimidine formation and methylglyoxal catabolism
    • Gomes RA, Sousa Silva M, Vicente Miranda H, Ferreira AE, Cordeiro CA, et al. (2005) Protein glycation in Saccharomyces cerevisiae. Argpyrimidine formation and methylglyoxal catabolism. FEBS J 272: 4521-4531.
    • (2005) FEBS J , vol.272 , pp. 4521-4531
    • Gomes, R.A.1    Sousa Silva, M.2    Vicente Miranda, H.3    Ferreira, A.E.4    Cordeiro, C.A.5
  • 30
    • 18944383472 scopus 로고    scopus 로고
    • Quantitative assessment of the glyoxalase pathway in Leishmania infantum as a therapeutic target by modelling and computer simulation
    • Sousa Silva M, Ferreira AEN, Tomás AM, Cordeiro C, Ponces Freire A, (2005) Quantitative assessment of the glyoxalase pathway in Leishmania infantum as a therapeutic target by modelling and computer simulation. FEBS Journal 272: 2388-2398.
    • (2005) FEBS Journal , vol.272 , pp. 2388-2398
    • Sousa Silva, M.1    Ferreira, A.E.N.2    Tomás, A.M.3    Cordeiro, C.4    Ponces Freire, A.5
  • 31
    • 0015791806 scopus 로고
    • The steady-state kinetics of glyoxalase I from porcine erythrocytes. Evidence for a random-pathway mechanism involving one- and two-substrate branches
    • Mannervik B, Gorna-Hall B, Bartfai T, (1973) The steady-state kinetics of glyoxalase I from porcine erythrocytes. Evidence for a random-pathway mechanism involving one- and two-substrate branches. Eur J Biochem 37: 270-281.
    • (1973) Eur J Biochem , vol.37 , pp. 270-281
    • Mannervik, B.1    Gorna-Hall, B.2    Bartfai, T.3
  • 32
    • 0015939408 scopus 로고
    • Discrimination between steady-state kinetic models of the Mechanism of action of yeast glyoxalase I
    • Bartfai T, Ekwall K, Mannervik B, (1973) Discrimination between steady-state kinetic models of the Mechanism of action of yeast glyoxalase I. Biochemistry 12: 387-391.
    • (1973) Biochemistry , vol.12 , pp. 387-391
    • Bartfai, T.1    Ekwall, K.2    Mannervik, B.3
  • 33
    • 0025298551 scopus 로고
    • The glyoxalase system: new developments towards functional characterization of a metabolic pathway fundamental to biological life
    • Thornalley PJ, (1990) The glyoxalase system: new developments towards functional characterization of a metabolic pathway fundamental to biological life. Biochem J 269: 1-11.
    • (1990) Biochem J , vol.269 , pp. 1-11
    • Thornalley, P.J.1
  • 34
    • 0018710893 scopus 로고
    • Comparison of glyoxalase I purified from yeast (Saccharomyces cerevisiae) with the enzyme from mammalian sources
    • Marmstal E, Aronsson AC, Mannervik B, (1979) Comparison of glyoxalase I purified from yeast (Saccharomyces cerevisiae) with the enzyme from mammalian sources. Biochem J 183: 23-30.
    • (1979) Biochem J , vol.183 , pp. 23-30
    • Marmstal, E.1    Aronsson, A.C.2    Mannervik, B.3
  • 35
    • 0021112323 scopus 로고
    • Reversal of the reaction catalyzed by glyoxalase I. Calculation of the equilibrium constant for the enzymatic reaction
    • Sellin S, Mannervik B, (1983) Reversal of the reaction catalyzed by glyoxalase I. Calculation of the equilibrium constant for the enzymatic reaction. J Biol Chem 258: 8872-8875.
    • (1983) J Biol Chem , vol.258 , pp. 8872-8875
    • Sellin, S.1    Mannervik, B.2
  • 37
    • 0001739947 scopus 로고
    • The mechanism of action of glyoxalase
    • Racker E, (1951) The mechanism of action of glyoxalase. J Biol Chem 190: 685-696.
    • (1951) J Biol Chem , vol.190 , pp. 685-696
    • Racker, E.1
  • 40
    • 0018189176 scopus 로고
    • A convenient quantitative synthesis of methylglyoxal for glyoxalase I assays
    • Kellum MW, Oray B, Norton SJ, (1978) A convenient quantitative synthesis of methylglyoxal for glyoxalase I assays. Anal Biochem 85: 586-590.
    • (1978) Anal Biochem , vol.85 , pp. 586-590
    • Kellum, M.W.1    Oray, B.2    Norton, S.J.3
  • 41
    • 0042163579 scopus 로고    scopus 로고
    • An introduction to differential evolution
    • In: Corne D, Dorigo M, Glover F, editors, London, McGraw-Hill
    • Price KV, (1999) An introduction to differential evolution. In: Corne D, Dorigo M, Glover F, editors. New Ideas in Optimization London McGraw-Hill pp. 79-108.
    • (1999) New Ideas in Optimization , pp. 79-108
    • Price, K.V.1
  • 42
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: a comparison of global optimization methods
    • Moles CG, Mendes P, Banga JR, (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13: 2467-2474.
    • (2003) Genome Res , vol.13 , pp. 2467-2474
    • Moles, C.G.1    Mendes, P.2    Banga, J.R.3
  • 44
    • 33751423943 scopus 로고    scopus 로고
    • Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
    • Rodriguez-Fernandez M, Egea JA, Banga JR, (2006) Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics 7: 483.
    • (2006) BMC Bioinformatics , vol.7 , pp. 483
    • Rodriguez-Fernandez, M.1    Egea, J.A.2    Banga, J.R.3
  • 45
    • 33646364037 scopus 로고    scopus 로고
    • Identification of metabolic system parameters using global optimization methods
    • Polisetty PK, Voit EO, Gatzke EP, (2006) Identification of metabolic system parameters using global optimization methods. Theor Biol Med Model 3: 4.
    • (2006) Theor Biol Med Model , vol.3 , pp. 4
    • Polisetty, P.K.1    Voit, E.O.2    Gatzke, E.P.3
  • 46
    • 0142000477 scopus 로고    scopus 로고
    • Differential evolution - A simple and efficient heuristic for global optimization over continuous spaces
    • Storn R, Price K, (1997) Differential evolution- A simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization 11: 341-359.
    • (1997) Journal of Global Optimization , vol.11 , pp. 341-359
    • Storn, R.1    Price, K.2
  • 47
    • 0000238336 scopus 로고
    • A Simplex-Method for Function Minimization
    • Nelder JA, Mead R, (1965) A Simplex-Method for Function Minimization. Computer Journal 7: 308-313.
    • (1965) Computer Journal , vol.7 , pp. 308-313
    • Nelder, J.A.1    Mead, R.2
  • 49
    • 33746251985 scopus 로고    scopus 로고
    • Evolutionary Multiobjective Optimization: Theoretical Advances and Applications
    • In: Wu X, Jain L, editors, London, Springer-Verlag
    • Abraham A, Jain L, Goldberg R, (2005) Evolutionary Multiobjective Optimization: Theoretical Advances and Applications; In: Wu X, Jain L, editors. London Springer-Verlag.
    • (2005)
    • Abraham, A.1    Jain, L.2    Goldberg, R.3
  • 51
    • 53349128672 scopus 로고    scopus 로고
    • An efficient non-dominated sorting method for evolutionary algorithms
    • Fang HB, Wang Q, Tu YC, Horstemeyer ME, (2008) An efficient non-dominated sorting method for evolutionary algorithms. Evolutionary Computation 16: 355-384.
    • (2008) Evolutionary Computation , vol.16 , pp. 355-384
    • Fang, H.B.1    Wang, Q.2    Tu, Y.C.3    Horstemeyer, M.E.4
  • 53
    • 0001811061 scopus 로고
    • ODEPACK, a Systematized Collection of ODE Solvers
    • In: Stepleman RSea, editors, Amsterdam, North-Holland
    • Hindmarsh AC, (1983) ODEPACK, a Systematized Collection of ODE Solvers. In: Stepleman RSea, editors. Scientific Computing Amsterdam North-Holland pp. 55-64.
    • (1983) Scientific Computing , pp. 55-64
    • Hindmarsh, A.C.1
  • 54
    • 0000536084 scopus 로고
    • Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations
    • Hindmarsh AC, Petzold LR, (1983) Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations. SIAM J Sci Stat Comput 4: 136-148.
    • (1983) SIAM J Sci Stat Comput , vol.4 , pp. 136-148
    • Hindmarsh, A.C.1    Petzold, L.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.