메뉴 건너뛰기




Volumn 37, Issue 2, 1999, Pages 242-252

Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase

Author keywords

Catalytic mechanism; Conformational change; Domain movement; Molecular dynamics; Thymidine phosphorylase

Indexed keywords

THYMIDINE PHOSPHORYLASE;

EID: 0032719351     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991101)37:2<242::AID-PROT9>3.0.CO;2-5     Document Type: Article
Times cited : (25)

References (50)
  • 1
    • 0029961624 scopus 로고    scopus 로고
    • Mechanisms and therapeutic implications of angiogenesis
    • Bicknell R, Harris AL. Mechanisms and therapeutic implications of angiogenesis. Curr Opin Oncol 1996;8:60-65.
    • (1996) Curr Opin Oncol , vol.8 , pp. 60-65
    • Bicknell, R.1    Harris, A.L.2
  • 2
    • 0024563134 scopus 로고
    • Identification of the angiogenic activity and the cloning and expression of plateletderived endothelial cell growth factor
    • Ishikawa K, Miyazono U, Hellman H, et al. Identification of the angiogenic activity and the cloning and expression of plateletderived endothelial cell growth factor. Nature 1989;338:557-562.
    • (1989) Nature , vol.338 , pp. 557-562
    • Ishikawa, K.1    Miyazono, U.2    Hellman, H.3
  • 3
    • 0026690144 scopus 로고
    • Expression of platelet-derived endothelial cell growth factor in Escherichia coli and confirmation of its thymidine phosphorylase activity
    • Moghaddam A, Bicknell R. Expression of platelet-derived endothelial cell growth factor in Escherichia coli and confirmation of its thymidine phosphorylase activity. Biochemistry 1992;31:12141-12146.
    • (1992) Biochemistry , vol.31 , pp. 12141-12146
    • Moghaddam, A.1    Bicknell, R.2
  • 4
    • 0017395846 scopus 로고
    • Identification and comparative analysis of thymidine phosphorylase in the plasma of healthy subjects and cancer patients: Brief communication
    • Pauly J, Schuller M, Zelcer A, Kirss T, Gore S, Germain M. Identification and comparative analysis of thymidine phosphorylase in the plasma of healthy subjects and cancer patients: brief communication. J Natl Cancer Inst 1977;58:1587-1590.
    • (1977) J Natl Cancer Inst , vol.58 , pp. 1587-1590
    • Pauly, J.1    Schuller, M.2    Zelcer, A.3    Kirss, T.4    Gore, S.5    Germain, M.6
  • 5
    • 0025214992 scopus 로고
    • Purification and tissue distribution of human thymidine phosphorylase; high expression in lymphocytes, reticulocytes and tumors
    • Yoshimura A, Kuwazuru Y, Furukawa T, Yoshida H, Yamada K, Akiyama SS. Purification and tissue distribution of human thymidine phosphorylase; high expression in lymphocytes, reticulocytes and tumors. Biochim Biophys Acta 1990;1034:107-113.
    • (1990) Biochim Biophys Acta , vol.1034 , pp. 107-113
    • Yoshimura, A.1    Kuwazuru, Y.2    Furukawa, T.3    Yoshida, H.4    Yamada, K.5    Akiyama, S.S.6
  • 6
    • 0028809240 scopus 로고
    • Thymidine phosphorylase is angiogenic and promotes tumor growth
    • Moghaddam A, Zhang H-T, Fan T-PD, et al. Thymidine phosphorylase is angiogenic and promotes tumor growth. Proc Natl Acad Sci USA 1995;92:998-1002.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 998-1002
    • Moghaddam, A.1    Zhang, H.-T.2    T-Pd, F.3
  • 7
    • 0028961523 scopus 로고
    • Different angiogenic pathways characterize superficial and invasive bladder cancer
    • O'Brien T, Cranston T, Fuggle S, Bicknell R, Harris A. Different angiogenic pathways characterize superficial and invasive bladder cancer. Cancer Res 1995;55:510-513.
    • (1995) Cancer Res , vol.55 , pp. 510-513
    • O'Brien, T.1    Cranston, T.2    Fuggle, S.3    Bicknell, R.4    Harris, A.5
  • 8
    • 0029790296 scopus 로고    scopus 로고
    • Platelet-derived endothelial cell growth factor in human colon cancer angiogenesis: Role of infiltrating cells
    • Takahashi Y, Bucana C, Liu W, et al. Platelet-derived endothelial cell growth factor in human colon cancer angiogenesis: role of infiltrating cells. J Natl Cancer Inst 1996;88:1146-1151.
    • (1996) J Natl Cancer Inst , vol.88 , pp. 1146-1151
    • Takahashi, Y.1    Bucana, C.2    Liu, W.3
  • 9
    • 0028957177 scopus 로고
    • Role of thymidine phosphorylase activity in the angiogenic effect of platelet-derived endothelial cell growth factor/thymidine phosphorylase
    • Miyadera K, Sumizawa T, Haraguchi M, et al. Role of thymidine phosphorylase activity in the angiogenic effect of platelet-derived endothelial cell growth factor/thymidine phosphorylase. Cancer Res 1995;55:1687-1690.
    • (1995) Cancer Res , vol.55 , pp. 1687-1690
    • Miyadera, K.1    Sumizawa, T.2    Haraguchi, M.3
  • 10
    • 0028851074 scopus 로고
    • Inhibition of 50′-deoxy-5-fluorouridine phosphorylase by acyclopyrimidinenucleosides in intestinal tissue homogenates
    • Hamada A, Fukushima S, Saneyoshi M, Kawaguchi T, Nakano M. Inhibition of 50′-deoxy-5-fluorouridine phosphorylase by acyclopyrimidinenucleosides in intestinal tissue homogenates. Biol Pharm Bull 1995;18:172-175.
    • (1995) Biol Pharm Bull , vol.18 , pp. 172-175
    • Hamada, A.1    Fukushima, S.2    Saneyoshi, M.3    Kawaguchi, T.4    Nakano, M.5
  • 11
    • 0025160874 scopus 로고
    • Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution
    • Walter M, Cook W, Cole L. Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution. J Biol Chem 1990;265:14016-14022.
    • (1990) J Biol Chem , vol.265 , pp. 14016-14022
    • Walter, M.1    Cook, W.2    Cole, L.3
  • 12
    • 0000453761 scopus 로고
    • Domain motions in proteins
    • Schulz GE. Domain motions in proteins. Curr Opin Struct Biol 1991;1:883-888.
    • (1991) Curr Opin Struct Biol , vol.1 , pp. 883-888
    • Schulz, G.E.1
  • 13
    • 0031030767 scopus 로고    scopus 로고
    • Synergistic effects of substrate induced conformational changes in phosphoglycerate kinase activation
    • Bernstein B, Michels P, Hol W. Synergistic effects of substrate induced conformational changes in phosphoglycerate kinase activation. Nature 1997;385:275-278.
    • (1997) Nature , vol.385 , pp. 275-278
    • Bernstein, B.1    Michels, P.2    Hol, W.3
  • 14
    • 0032516763 scopus 로고    scopus 로고
    • Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase
    • Pugmire M, Cook W, Jasanoff A, Walter M, Ealick S. Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase. J Mol Biol 1998;281:285-299.
    • (1998) J Mol Biol , vol.281 , pp. 285-299
    • Pugmire, M.1    Cook, W.2    Jasanoff, A.3    Walter, M.4    Ealick, S.5
  • 15
    • 2742524728 scopus 로고    scopus 로고
    • Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods
    • Burton N, Harrison M, Hart J, Hillier I, Sheppard D. Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods. Faraday Discuss 1998;110:463-475.
    • (1998) Faraday Discuss , vol.110 , pp. 463-475
    • Burton, N.1    Harrison, M.2    Hart, J.3    Hillier, I.4    Sheppard, D.5
  • 16
    • 0026341458 scopus 로고
    • Transitionstate analysis of nucleoside hydrolase from Crithidia fasciculata
    • Horenstein B, Parkin D, Estupinã́n B, Schramm V. Transitionstate analysis of nucleoside hydrolase from Crithidia fasciculata. Biochemistry 1991;30:10788-10795.
    • (1991) Biochemistry , vol.30 , pp. 10788-10795
    • Horenstein, B.1    Parkin, D.2    Estupinã́n, B.3    Schramm, V.4
  • 17
    • 0023129244 scopus 로고
    • Transition-state structures for the N-glycoside hydrolysis of AMP by acid and by AMP nucleosidase in the presence and absence of allosteric activator
    • Mentch F, Parkin D, Schramm V. Transition-state structures for the N-glycoside hydrolysis of AMP by acid and by AMP nucleosidase in the presence and absence of allosteric activator. Biochemistry 1987;26:921-930.
    • (1987) Biochemistry , vol.26 , pp. 921-930
    • Mentch, F.1    Parkin, D.2    Schramm, V.3
  • 19
    • 0028932756 scopus 로고
    • Pre-steady state transition state analysis of the hydrolytic reaction catalyzed by purine nucleoside phosphorylase
    • Kline P, Schramm V. Pre-steady state transition state analysis of the hydrolytic reaction catalyzed by purine nucleoside phosphorylase. Biochemistry 1995;34:1153-1162.
    • (1995) Biochemistry , vol.34 , pp. 1153-1162
    • Kline, P.1    Schramm, V.2
  • 20
    • 0027729453 scopus 로고
    • Purine nucleoside phosphorylase. Catalytic mechanism and transition-state analysis of the arsenolysis reaction
    • Kline P, Schramm V. Purine nucleoside phosphorylase. Catalytic mechanism and transition-state analysis of the arsenolysis reaction. Biochemistry 1993;32:13212-13219.
    • (1993) Biochemistry , vol.32 , pp. 13212-13219
    • Kline, P.1    Schramm, V.2
  • 21
    • 0030817010 scopus 로고    scopus 로고
    • Purine nucleoside phosphorylase: 1. Structure-function studies
    • Erion M, Takabayashi, K., Smith, H. Purine nucleoside phosphorylase: 1. Structure-function studies. Biochemistry 1997;36:11725-11734.
    • (1997) Biochemistry , vol.36 , pp. 11725-11734
    • Erion, M.1    Takabayashi, K.2    Smith, H.3
  • 23
    • 0025021597 scopus 로고
    • Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 Å resolution
    • Ealick S, Rule S, Carter D, et al. Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 Å resolution. J Biol Chem 1990;265:1812-1820.
    • (1990) J Biol Chem , vol.265 , pp. 1812-1820
    • Ealick, S.1    Rule, S.2    Carter, D.3
  • 24
    • 0032485918 scopus 로고    scopus 로고
    • Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
    • Dagano M, Almo S, Sacchettini J, Schramm V. Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor. Biochemistry 1998;37:6277-6285.
    • (1998) Biochemistry , vol.37 , pp. 6277-6285
    • Dagano, M.1    Almo, S.2    Sacchettini, J.3    Schramm, V.4
  • 25
    • 0028247284 scopus 로고
    • Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity
    • Mushegian A, Koonin E. Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity. Protein Sci 1994;3:1081-1088.
    • (1994) Protein Sci , vol.3 , pp. 1081-1088
    • Mushegian, A.1    Koonin, E.2
  • 27
    • 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
  • 29
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • York DM, Darden TA, Pedersen LG. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J Chem Phys 1993;99:8345-8348.
    • (1993) J Chem Phys , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 32
    • 3342922190 scopus 로고
    • Density functional Gaussian-type-orbital approach to molecular geometries, vibrations, and reaction energies
    • Andzelm J, Wimmer E. Density functional Gaussian-type-orbital approach to molecular geometries, vibrations, and reaction energies. J Chem Phys 1992;96:1280-1303.
    • (1992) J Chem Phys , vol.96 , pp. 1280-1303
    • Andzelm, J.1    Wimmer, E.2
  • 33
    • 0000216001 scopus 로고
    • Accurate spin-dependent electron liquid correlation energies for local spin density calculation: A critical analysis
    • Vosko S, Wilk L, Nusair M. Accurate spin-dependent electron liquid correlation energies for local spin density calculation: a critical analysis. Can J Phys 1980;58:1200-1210.
    • (1980) Can J Phys , vol.58 , pp. 1200-1210
    • Vosko, S.1    Wilk, L.2    Nusair, M.3
  • 34
    • 0001470765 scopus 로고
    • Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation
    • Godbout N, Salahub D, Andzelm J, Wimmer E. Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation. Can J Chem 1992;70:560-571.
    • (1992) Can J Chem , vol.70 , pp. 560-571
    • Godbout, N.1    Salahub, D.2    Andzelm, J.3    Wimmer, E.4
  • 35
    • 36449000295 scopus 로고
    • Molecular gradients and hessians implemented in density functional theory
    • Komornicki A, Fitzgerald G. Molecular gradients and hessians implemented in density functional theory. J Chem Phys 1993;98: 1398-1421.
    • (1993) J Chem Phys , vol.98 , pp. 1398-1421
    • Komornicki, A.1    Fitzgerald, G.2
  • 36
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford P. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-857.
    • (1985) J Med Chem , vol.28 , pp. 849-857
    • Goodford, P.1
  • 37
    • 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
  • 39
    • 0028956684 scopus 로고
    • Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations
    • Paulsen MD, Ornstein RL. Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations. Proteins 1995;21:237-243.
    • (1995) Proteins , vol.21 , pp. 237-243
    • Paulsen, M.D.1    Ornstein, R.L.2
  • 40
    • 0029162947 scopus 로고
    • Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes
    • Smith LJ, Mark AE, Dobson CM, van Gunsteren WF. Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes. Biochemistry 1995;34:10918-10931.
    • (1995) Biochemistry , vol.34 , pp. 10918-10931
    • Smith, L.J.1    Mark, A.E.2    Dobson, C.M.3    Van Gunsteren, W.F.4
  • 41
    • 0029156702 scopus 로고
    • Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: Flexibility, possible hinges, and levers of the conformational transition
    • Díaz JF, Wroblowski B, Engelborghs Y. Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: flexibility, possible hinges, and levers of the conformational transition. Biochemistry 1995;34:12038-12047.
    • (1995) Biochemistry , vol.34 , pp. 12038-12047
    • Díaz, J.F.1    Wroblowski, B.2    Engelborghs, Y.3
  • 42
    • 0026755515 scopus 로고
    • Cutoff size does strongly influence molecular dynamics results on solvated polypeptides
    • Schreiber H, Steinhauser O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 1992;31:5856-5860.
    • (1992) Biochemistry , vol.31 , pp. 5856-5860
    • Schreiber, H.1    Steinhauser, O.2
  • 43
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
    • Mathiowetz AM, Jain A, Karasawa N, Goddard W III. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 1994;20:227-247.
    • (1994) Proteins , vol.20 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard W. III4
  • 44
    • 0029886930 scopus 로고    scopus 로고
    • Study of global motions in proteins by weighted masses molecular dynamics: Adenylate kinase as a test case
    • Elamrani S, Berry MB, Phillips GN Jr, McCammon JA. Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins 1996;25:79-88.
    • (1996) Proteins , vol.25 , pp. 79-88
    • Elamrani, S.1    Berry, M.B.2    Phillips G.N., Jr.3    McCammon, J.A.4
  • 45
    • 0030939896 scopus 로고    scopus 로고
    • A new method for modeling large-scale rearrangements of protein domains
    • Maiorov V, Abagyan R. A new method for modeling large-scale rearrangements of protein domains. Proteins 1997;27:410-424.
    • (1997) Proteins , vol.27 , pp. 410-424
    • Maiorov, V.1    Abagyan, R.2
  • 46
    • 0032031362 scopus 로고    scopus 로고
    • A general method of domain closure if applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme
    • Chandra NR, Muirhead H, Holbrook JJ, Bernstein BE, Hol WGJ, Sessions RB. A general method of domain closure if applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. Proteins 1998;30: 372-380.
    • (1998) Proteins , vol.30 , pp. 372-380
    • Chandra, N.R.1    Muirhead, H.2    Holbrook, J.J.3    Bernstein, B.E.4    Hol, W.G.J.5    Sessions, R.B.6
  • 47
    • 0015244537 scopus 로고
    • Thymidine phosphorylase from Escherichia coli. Properties and kinetics
    • Schartz M. Thymidine phosphorylase from Escherichia coli. Properties and kinetics. Eur J Biochem 1971;21:191-198.
    • (1971) Eur J Biochem , vol.21 , pp. 191-198
    • Schartz, M.1
  • 48
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • Becke A. 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.1
  • 49
    • 5944261746 scopus 로고
    • Density-functional approximation for the correlation energy of the inhomogeneous electron gas
    • Perdew J. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 1986;33: 8822-8824.
    • (1986) Phys Rev B , vol.33 , pp. 8822-8824
    • Perdew, J.1
  • 50
    • 2842520383 scopus 로고
    • Potential energy surfaces of the gas-phase SN2 reactions X-+ CH3X = XCH3 + X-(X = F, Cl, Br, I): A comparative study by density functional theory and ab initio methods
    • Deng L, Branchadell V, Ziegler T. Potential energy surfaces of the gas-phase SN2 reactions X-+ CH3X = XCH3 + X-(X = F, Cl, Br, I): a comparative study by density functional theory and ab initio methods. J Am Chem Soc 1994;116:10645-10656.
    • (1994) J Am Chem Soc , vol.116 , pp. 10645-10656
    • Deng, L.1    Branchadell, V.2    Ziegler, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.