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Volumn 37, Issue 2, 1999, Pages 157-165

Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods

Author keywords

Atomic charges; Density functional methods; Dihydrofolate; Electron density differences; Enzyme mechanism; Folate; NADPH; Quantum chemical methods; Reductase; Substrate polarization

Indexed keywords

DIHYDROFOLATE REDUCTASE;

EID: 0032693616     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0134(19991101)37:2<157::aid-prot2>3.0.co;2-j     Document Type: Article
Times cited : (26)

References (42)
  • 1
    • 0029198395 scopus 로고
    • Eukaryotic dihydrofolate reductase
    • Blakley RL. Eukaryotic dihydrofolate reductase. Adv Enzymol 1995;70:23-102.
    • (1995) Adv Enzymol , vol.70 , pp. 23-102
    • Blakley, R.L.1
  • 2
    • 0023847706 scopus 로고
    • Insights into enzyme function from studies on mutants of dihydrofolate reductase
    • Benkovic SJ, Fierke CA, Naylor AM. Insights into enzyme function from studies on mutants of dihydrofolate reductase. Science 1988;239:1105-1110.
    • (1988) Science , vol.239 , pp. 1105-1110
    • Benkovic, S.J.1    Fierke, C.A.2    Naylor, A.M.3
  • 3
    • 0027031391 scopus 로고
    • Exploring the molecular mechanism of dihydrofolate reductase
    • Brown KA, Kraut J. Exploring the molecular mechanism of dihydrofolate reductase. Faraday Discuss 1992;93:217-224.
    • (1992) Faraday Discuss , vol.93 , pp. 217-224
    • Brown, K.A.1    Kraut, J.2
  • 4
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallo-graphic evidence
    • Sawaya MR, Kraut J. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallo-graphic evidence. Biochemistry 1997;36:586-603.
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 5
    • 0028921374 scopus 로고
    • Detection of long-lived bound water molecules in complexes of human dihydrofolate reductase with methotrexate and NADPH
    • Meiering EM, Wagner G. Detection of long-lived bound water molecules in complexes of human dihydrofolate reductase with methotrexate and NADPH. J Mol Biol 1995;247:294-308.
    • (1995) J Mol Biol , vol.247 , pp. 294-308
    • Meiering, E.M.1    Wagner, G.2
  • 6
    • 0022408542 scopus 로고
    • Theoretical studies on the activation of the pterin cofactor in the catalytic mechanism of dihydrofolate reductase
    • Gready JE. Theoretical studies on the activation of the pterin cofactor in the catalytic mechanism of dihydrofolate reductase. Biochemistry 1985;24:4761-4766.
    • (1985) Biochemistry , vol.24 , pp. 4761-4766
    • Gready, J.E.1
  • 8
    • 84986524643 scopus 로고
    • Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydro-nicotinamide and folate and dihydrofolate analogue substrates of dihydrofolate reductase
    • Cummins PL, Gready JE. Mechanistic aspects of biological redox reactions involving NADH 2: a combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydro-nicotinamide and folate and dihydrofolate analogue substrates of dihydrofolate reductase. J Comput Chem 1990;11:791-804.
    • (1990) J Comput Chem , vol.11 , pp. 791-804
    • Cummins, P.L.1    Gready, J.E.2
  • 9
    • 37049082300 scopus 로고
    • Pterin 1H-3H tautomerism and its possible relevance to the binding of folate to dihydrofolate reductase
    • Schwalbe CH, Lowis DR, Richards WG. Pterin 1H-3H tautomerism and its possible relevance to the binding of folate to dihydrofolate reductase. J Chem Soc Chem Commun 1993;1199-1200.
    • (1993) J Chem Soc Chem Commun , pp. 1199-1200
    • Schwalbe, C.H.1    Lowis, D.R.2    Richards, W.G.3
  • 10
    • 0025912658 scopus 로고
    • The electrostatic potential of Escherichia coli dihydrofolate reductase
    • Bajorath J, Kitson DH, Kraut J, Hagler AT. The electrostatic potential of Escherichia coli dihydrofolate reductase. Proteins 1991;11:1-12.
    • (1991) Proteins , vol.11 , pp. 1-12
    • Bajorath, J.1    Kitson, D.H.2    Kraut, J.3    Hagler, A.T.4
  • 11
    • 0025972567 scopus 로고
    • Local density functional calculations on a protein system: Folate and Escherichia coli dihydrofolate reductase. Electron redistribution on binding of a substrate to an enzyme
    • Bajorath J, Kitson DH, Fitzgerald G, Andzelm J, Kraut J, Hagler AT. Local density functional calculations on a protein system: folate and Escherichia coli dihydrofolate reductase. Electron redistribution on binding of a substrate to an enzyme. Proteins 1991;9:217-224.
    • (1991) Proteins , vol.9 , pp. 217-224
    • Bajorath, J.1    Kitson, D.H.2    Fitzgerald, G.3    Andzelm, J.4    Kraut, J.5    Hagler, A.T.6
  • 13
    • 0026095360 scopus 로고
    • Theoretical studies on the dihydrofolate reductase mechanism: Electronic polarization of bound substrates
    • Bajorath J, Kraut J, Li Z, Kitson DH, Hagler AT. Theoretical studies on the dihydrofolate reductase mechanism: electronic polarization of bound substrates. Proc Natl Acad Sci USA 1991;88: 6423-6426.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 6423-6426
    • Bajorath, J.1    Kraut, J.2    Li, Z.3    Kitson, D.H.4    Hagler, A.T.5
  • 14
    • 0030944408 scopus 로고    scopus 로고
    • Electrostatic characterization of enzyme complexes: Evaluation of the mechanism of catalysis of dihydrofolate reductase
    • Cannon WR, Garrison BJ, Benkovic SJ. Electrostatic characterization of enzyme complexes: evaluation of the mechanism of catalysis of dihydrofolate reductase. J Am Chem Soc 1997;119:2386-2395.
    • (1997) J Am Chem Soc , vol.119 , pp. 2386-2395
    • Cannon, W.R.1    Garrison, B.J.2    Benkovic, S.J.3
  • 15
    • 0030875357 scopus 로고    scopus 로고
    • Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate
    • Cannon WR, Garrison BJ, Benkovic SJ. Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate. J Mol Biol 1997;271:656-668.
    • (1997) J Mol Biol , vol.271 , pp. 656-668
    • Cannon, W.R.1    Garrison, B.J.2    Benkovic, S.J.3
  • 16
    • 0031557394 scopus 로고    scopus 로고
    • Domain motions in dihydrofolate reductase: A molecular dynamics study
    • Verma CS, Caves LSD, Hubbard RE, Roberts GCK. Domain motions in dihydrofolate reductase: a molecular dynamics study. J Mol Biol 1997;266:776-796.
    • (1997) J Mol Biol , vol.266 , pp. 776-796
    • Verma, C.S.1    Caves, L.S.D.2    Hubbard, R.E.3    Roberts, G.C.K.4
  • 17
    • 0001704148 scopus 로고    scopus 로고
    • A molecular dynamics and free energy perturbation (MD/FEP) study of the hydride-ion transfer step in dihydrofolate reductase using a combined quantum and molecular mechanical (QM/MM) model
    • Cummins PL, Gready JE. A molecular dynamics and free energy perturbation (MD/FEP) study of the hydride-ion transfer step in dihydrofolate reductase using a combined quantum and molecular mechanical (QM/MM) model. J Comput Chem 1998;19:977-988.
    • (1998) J Comput Chem , vol.19 , pp. 977-988
    • Cummins, P.L.1    Gready, J.E.2
  • 18
    • 0024341092 scopus 로고
    • Enzymic properties of a new mechanism-based substrate for dihydrofolate reductase
    • Thibault V, Koen M, Gready JE. Enzymic properties of a new mechanism-based substrate for dihydrofolate reductase. Biochemistry 1989;28:6042-6049.
    • (1989) Biochemistry , vol.28 , pp. 6042-6049
    • Thibault, V.1    Koen, M.2    Gready, J.E.3
  • 19
    • 0028179399 scopus 로고
    • Ionization state and pKa of pterin-analogue ligands bound to dihydrofolate reductase
    • Jeong S-S, Gready JE. Ionization state and pKa of pterin-analogue ligands bound to dihydrofolate reductase. Eur J Biochem 1994;221:1055-1062.
    • (1994) Eur J Biochem , vol.221 , pp. 1055-1062
    • Jeong, S.-S.1    Gready, J.E.2
  • 21
    • 0000049872 scopus 로고    scopus 로고
    • Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations
    • Eurenius KP, Chatfield DC, Brooks BL, Hodoscek M. Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations. Int J Quant Chem 1996;60: 1189-1200.
    • (1996) Int J Quant Chem , vol.60 , pp. 1189-1200
    • Eurenius, Kp.1    Chatfield, D.C.2    Brooks, B.L.3    Hodoscek, M.4
  • 22
    • 1842410903 scopus 로고    scopus 로고
    • A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics
    • Peräkylä M, Kollman PA. A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics. J Am Chem Soc 1997;119:1189-1196.
    • (1997) J Am Chem Soc , vol.119 , pp. 1189-1196
    • Peräkylä, M.1    Kollman, P.A.2
  • 24
    • 85050534684 scopus 로고    scopus 로고
    • An introduction to density functional theory
    • Lipkowitz KB, Boyd DB, editors. New York: VCH
    • Bartolotti LJ, Flurchick K. An introduction to density functional theory. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol. 7. New York: VCH; 1996. p 187-216.
    • (1996) Reviews in Computational Chemistry , vol.7 , pp. 187-216
    • Bartolotti, L.J.1    Flurchick, K.2
  • 25
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic-behavior
    • Becke AD. Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys Rev A 1988;38:3098-3100.
    • (1988) Phys Rev A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 26
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation energy formula into a functional of the electron density
    • Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation energy formula into a functional of the electron density. Phys Rev B 1988;37:785-789.
    • (1988) Phys Rev B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 27
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 1993;98:5648-5652.
    • (1993) J Chem Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 28
    • 33645898818 scopus 로고
    • Accurate and simple analytic representation of the electron gas correlation energy
    • Perdew JP, Wang Y. Accurate and simple analytic representation of the electron gas correlation energy. Phys Rev B 1992;45:13244-13249.
    • (1992) Phys Rev B , vol.45 , pp. 13244-13249
    • Perdew, J.P.1    Wang, Y.2
  • 30
    • 0000216001 scopus 로고
    • Accurate spin-dependent electron liquid correlation energies for local spin density calculations: A critical analysis
    • Vosko SH, Wilk L, Nusair M. Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can J Phys 1980;58:1200-1211.
    • (1980) Can J Phys , vol.58 , pp. 1200-1211
    • Vosko, S.H.1    Wilk, L.2    Nusair, M.3
  • 32
    • 0029011701 scopus 로고
    • A second generation force-field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell WD, Cieplak P, Bayly CI, et al. A second generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
    • (1995) J Am Chem Soc , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3
  • 33
    • 11644266970 scopus 로고
    • Electron population analysis on LCAO-MO molecular wave functions. I
    • Mulliken RS. Electron population analysis on LCAO-MO molecular wave functions. I. J Chem Phys 1955;23:1833-1840.
    • (1955) J Chem Phys , vol.23 , pp. 1833-1840
    • Mulliken, R.S.1
  • 34
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler BH, Merz Jr, KM, Kollman PA. Atomic charges derived from semiempirical methods. J Comput Chem 1990;11:431-439.
    • (1990) J Comput Chem , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz K.M., Jr.2    Kollman, P.A.3
  • 35
    • 85047695237 scopus 로고    scopus 로고
    • Medium ring compounds and their anions: A systematic density functional theory study
    • Rienstra-Kiracofe JC, Graham DE, Schaefer III HF. Medium ring compounds and their anions: a systematic density functional theory study. Mol Phys 1998;94:767-787.
    • (1998) Mol Phys , vol.94 , pp. 767-787
    • Rienstra-Kiracofe, J.C.1    Graham, D.E.2    Schaefer H.F. III3
  • 36
    • 0002198868 scopus 로고    scopus 로고
    • Predicting electron affinities with density functional theory: Some positive results for negative ions
    • Tschumper GS, Schaefer III, HF. Predicting electron affinities with density functional theory: some positive results for negative ions. J Chem Phys 1997;107:2529-2541.
    • (1997) J Chem Phys , vol.107 , pp. 2529-2541
    • Tschumper, G.S.1    Schaefer H.F. III2
  • 37
    • 22244474611 scopus 로고    scopus 로고
    • Assessment of Gaussian-2 and density functional theories for the computation of ionization potentials and electron affinities
    • Curtiss LA, Redfern PC, Raghavachari K, Pople JA. Assessment of Gaussian-2 and density functional theories for the computation of ionization potentials and electron affinities. J Chem Phys 1998;109:42-55.
    • (1998) J Chem Phys , vol.109 , pp. 42-55
    • Curtiss, L.A.1    Redfern, P.C.2    Raghavachari, K.3    Pople, J.A.4
  • 38
    • 0002867675 scopus 로고    scopus 로고
    • Application of density functional theory to calculation of in-crystal anionic polarizability
    • Domene C, Fowler PW, Jemmer P, Madden P. Application of density functional theory to calculation of in-crystal anionic polarizability. Chem Phys Lett 1999;299:51-56.
    • (1999) Chem Phys Lett , vol.299 , pp. 51-56
    • Domene, C.1    Fowler, P.W.2    Jemmer, P.3    Madden, P.4
  • 39
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
    • (1997) Methods Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 40
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991;24:946-950.
    • (1991) J Appl Cryst , vol.24 , pp. 946-950
    • Kraulis, P.J.1


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