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Volumn 54, Issue 2, 2004, Pages 237-246

Free Energies of Binding of Polychlorinated Biphenyls to the Estrogen Receptor from a Single Simulation

Author keywords

Binding modes; Molecular dynamics simulation; Single step perturbation; Soft core interaction

Indexed keywords

17 HYDROXYLATED POLYCHLORINATED BIPHENYL; ESTROGEN RECEPTOR; POLYCHLORINATED BIPHENYL; UNCLASSIFIED DRUG;

EID: 0346458810     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10558     Document Type: Article
Times cited : (79)

References (43)
  • 1
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu HY, Mark AE, van Gunsteren WF. Estimating the relative free energy of different molecular states with respect to a single reference state. J Phys Chem 1996;100:9485-9494.
    • (1996) J Phys Chem , vol.100 , pp. 9485-9494
    • Liu, H.Y.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 5
    • 0031831117 scopus 로고    scopus 로고
    • Detection of weak estrogenic flavonoids using a recombinant yeast strain and a modified MCF7 cell proliferation assay
    • Breinholt V, Larsen JC. Detection of weak estrogenic flavonoids using a recombinant yeast strain and a modified MCF7 cell proliferation assay. Chem Res Toxicol 1998;11:622-629.
    • (1998) Chem Res Toxicol , vol.11 , pp. 622-629
    • Breinholt, V.1    Larsen, J.C.2
  • 8
  • 12
    • 0033976103 scopus 로고    scopus 로고
    • Differential binding affinities of PCBs, HO-PCBs, and aroclors with recombinant human, rainbow trout (Onchorhynkiss mykiss), and green anole (Anolis carolinensis) estrogen receptors, using a semi-high throughput competitive binding assay
    • Matthews J, Zacharewski T. Differential binding affinities of PCBs, HO-PCBs, and aroclors with recombinant human, rainbow trout (Onchorhynkiss mykiss), and green anole (Anolis carolinensis) estrogen receptors, using a semi-high throughput competitive binding assay. Toxicol Sci 2000;53:326-339.
    • (2000) Toxicol Sci , vol.53 , pp. 326-339
    • Matthews, J.1    Zacharewski, T.2
  • 14
    • 0023839436 scopus 로고
    • Estrogen receptor-binding activity of polychlorinated hydroxybiphenyls-conformationally restricted structural probes
    • Korach KS, Sarver P, Chae K, McLachlan JA, McKinney JD. Estrogen receptor-binding activity of polychlorinated hydroxybiphenyls-conformationally restricted structural probes. Mol Pharmacol 1988;33:120-126.
    • (1988) Mol Pharmacol , vol.33 , pp. 120-126
    • Korach, K.S.1    Sarver, P.2    Chae, K.3    McLachlan, J.A.4    McKinney, J.D.5
  • 18
    • 0032446607 scopus 로고    scopus 로고
    • The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
    • Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998;95:927-937.
    • (1998) Cell , vol.95 , pp. 927-937
    • Shiau, A.K.1    Barstad, D.2    Loria, P.M.3    Cheng, L.4    Kushner, P.J.5    Agard, D.A.6    Greene, G.L.7
  • 19
    • 0031059270 scopus 로고    scopus 로고
    • The estradiol pharmacophore: Ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site
    • Anstead GM, Carlson KE, Katzenellenbogen JA. The estradiol pharmacophore: ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site. Steroids 1997;62:268-303.
    • (1997) Steroids , vol.62 , pp. 268-303
    • Anstead, G.M.1    Carlson, K.E.2    Katzenellenbogen, J.A.3
  • 20
    • 0024578173 scopus 로고
    • Free-energy via molecular simulation-applications to chemical and biomolecular systems
    • Beveridge DL, DiCapua FM. Free-energy via molecular simulation-applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 1989;18:431-492.
    • (1989) Annu Rev Biophys Biophys Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 21
    • 0001577491 scopus 로고    scopus 로고
    • Free energy perturbation (FEP)
    • von Ragné Schleyer, ed. New York: John Wiley & Sons
    • Mark AE. Free energy perturbation (FEP). In: von Ragné Schleyer, ed. Encyclopedia of Computational Chemistry. New York: John Wiley & Sons; 1998. p 1070-1083
    • (1998) Encyclopedia of Computational Chemistry , pp. 1070-1083
    • Mark, A.E.1
  • 22
    • 7044239742 scopus 로고
    • Free-energy calculations-applications to chemical and biochemical phenomena
    • Kollman P. Free-energy calculations-applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 23
    • 0001272783 scopus 로고    scopus 로고
    • Estimating relative free energies from a single ensemble: Hydration free energies
    • Schäfer H, van Gunsteren WF, Alark AE. Estimating relative free energies from a single ensemble: hydration free energies. J Comput Chem 1999;20:1604-1617.
    • (1999) J Comput Chem , vol.20 , pp. 1604-1617
    • Schäfer, H.1    Van Gunsteren, W.F.2    Alark, A.E.3
  • 24
    • 0029435083 scopus 로고
    • Rapid non-empirical approaches for estimating relative binding free energies
    • Mark AE, Xu YW, Liu HY, van Gunsteren WF. Rapid non-empirical approaches for estimating relative binding free energies. Acta Biochim Pol 1995;42:525-535.
    • (1995) Acta Biochim Pol , vol.42 , pp. 525-535
    • Mark, A.E.1    Xu, Y.W.2    Liu, H.Y.3    Van Gunsteren, W.F.4
  • 25
  • 26
    • 0035892155 scopus 로고    scopus 로고
    • One-step perturbation methods for solvation free energies of polar solutes
    • Pitera JW, van Gunsteren WF. One-step perturbation methods for solvation free energies of polar solutes. J Phys Chem B 2001;105: 11264-11274.
    • (2001) J Phys Chem B , vol.105 , pp. 11264-11274
    • Pitera, J.W.1    Van Gunsteren, W.F.2
  • 27
    • 0000249851 scopus 로고
    • Avoiding singularities and numerical instabilities in free-energy calculations based on molecular simulations
    • Beutler TC, Mark AE, Van Schaik RC, Gerber PR, van Gunsteren WF. Avoiding singularities and numerical instabilities in free-energy calculations based on molecular simulations. Chem Phys Lett 1994;222:529-539.
    • (1994) Chem Phys Lett , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 28
    • 0037187412 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: Insight into structure-based ligand design
    • Huo SH, Wang JM, Cieplak P, Kollman PA, Kuntz ID. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J Med Chem 2002;45:1412-1419.
    • (2002) J Med Chem , vol.45 , pp. 1412-1419
    • Huo, S.H.1    Wang, J.M.2    Cieplak, P.3    Kollman, P.A.4    Kuntz, I.D.5
  • 29
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • Wang JM, Morin P, Wang W, Kollman PA. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 2001;123: 5221-5230.
    • (2001) J Am Chem Soc , vol.123 , pp. 5221-5230
    • Wang, J.M.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 30
    • 0028155689 scopus 로고
    • New method for predicting binding-affinity in computer-aided drug Design
    • Aqvist J, Medina C, Samuelsson JE. New method for predicting binding-affinity in computer-aided drug Design. Protein Eng 1994;7:385-391.
    • (1994) Protein Eng , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 32
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson T, Marelius J, Aqvist J. Ligand binding affinity prediction by linear interaction energy methods. J Comput-Aided Mol Des 1998;12:27-35.
    • (1998) J Comput-Aided Mol Des , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 36
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman BE, editor. Dordrecht, The Netherlands: Reidel
    • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman BE, editor. Intermolecular forces. Dordrecht, The Netherlands: Reidel; 1981. p 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 38
    • 33646940952 scopus 로고
    • Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J Comput Phys 1977;23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 39
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular-dynamics simulations
    • Tironi IG, Sperb R, Smith PE, van Gunsteren WF. A generalized reaction field method for molecular-dynamics simulations. J Chem Phys 1995;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
  • 40
    • 2242491482 scopus 로고
    • Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K
    • Smith PE, van Gunsteren WF. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J Chem Phys 1994;100:3169-3174.
    • (1994) J Chem Phys , vol.100 , pp. 3169-3174
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 41
    • 0029852782 scopus 로고    scopus 로고
    • Quantitative structure-activity relationships for polychlorinated hydroxybiphenyl estrogen receptor binding affinity: An assessment of conformer flexibility
    • Bradbury SP, Mekenyan OG, Ankley GT. Quantitative structure-activity relationships for polychlorinated hydroxybiphenyl estrogen receptor binding affinity: an assessment of conformer flexibility. Environ Toxicol Chem 1996;15:1945-1954.
    • (1996) Environ Toxicol Chem , vol.15 , pp. 1945-1954
    • Bradbury, S.P.1    Mekenyan, O.G.2    Ankley, G.T.3
  • 42
    • 0034599656 scopus 로고    scopus 로고
    • Use of a combined human liver microsome-estrogen receptor binding assay to assess potential estrogen modulating activity of PCB metabolites
    • Vakharia DD, Gierthy JF. Use of a combined human liver microsome-estrogen receptor binding assay to assess potential estrogen modulating activity of PCB metabolites. Toxicol Lett 2000;114:55-65.
    • (2000) Toxicol Lett , vol.114 , pp. 55-65
    • Vakharia, D.D.1    Gierthy, J.F.2
  • 43
    • 0031172739 scopus 로고    scopus 로고
    • Hydroxylated polychlorinated biphenyl metabolites are anti-estrogenic in a stably transfected human breast adenocarcinoma (MCF7) cell line
    • Kramer VJ, Helferich WG, Bergman A, Klasson Wehler E, Giesy JP. Hydroxylated polychlorinated biphenyl metabolites are anti-estrogenic in a stably transfected human breast adenocarcinoma (MCF7) cell line. Toxicol Appl Pharmacol 1997;144:363-376.
    • (1997) Toxicol Appl Pharmacol , vol.144 , pp. 363-376
    • Kramer, V.J.1    Helferich, W.G.2    Bergman, A.3    Klasson Wehler, E.4    Giesy, J.P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.