메뉴 건너뛰기




Volumn 76, Issue 1 I, 1999, Pages 188-197

Unbinding of retinoic acid from its receptor studied by steered molecular dynamics

Author keywords

[No Author keywords available]

Indexed keywords

RETINOIC ACID; RETINOIC ACID RECEPTOR; TRANSCRIPTION FACTOR;

EID: 0032906662     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77188-2     Document Type: Article
Times cited : (155)

References (47)
  • 1
    • 0026698873 scopus 로고
    • Thyroid hormone alters the DNA binding properties of chicken thyroid hormone receptors α and β
    • Andersson, M. L., K. Nordström, S. Demczuck, M. Harbers, and B. Vennström. 1992. Thyroid hormone alters the DNA binding properties of chicken thyroid hormone receptors α and β. Nucleic Acids Res. 20:4803-4810.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 4803-4810
    • Andersson, M.L.1    Nordström, K.2    Demczuck, S.3    Harbers, M.4    Vennström, B.5
  • 2
    • 0030872242 scopus 로고    scopus 로고
    • Reconstructing potential energy functions from simulated force-induced unbinding processes
    • Balsera, M., S. Stepaniants, S. Izrailev, Y. Oono, and K. Schulten. 1997. Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys. J. 73:1281-1287.
    • (1997) Biophys. J. , vol.73 , pp. 1281-1287
    • Balsera, M.1    Stepaniants, S.2    Izrailev, S.3    Oono, Y.4    Schulten, K.5
  • 4
    • 0030941120 scopus 로고    scopus 로고
    • How hormone receptor-DNA binding affects nucleosomal DNA: The role of symmetry
    • Bishop, T. C., D. Kosztin, and K. Schutlen. 1997. How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry. Biophys. J. 72:2056-2067.
    • (1997) Biophys. J. , vol.72 , pp. 2056-2067
    • Bishop, T.C.1    Kosztin, D.2    Schutlen, K.3
  • 5
    • 0029012163 scopus 로고
    • Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-α
    • Bourguet, W., M. Ruff, P. Chambon, H. Gronemeyer, and D. Moras. 1995. Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-α. Nature. 375:377-382.
    • (1995) Nature , vol.375 , pp. 377-382
    • Bourguet, W.1    Ruff, M.2    Chambon, P.3    Gronemeyer, H.4    Moras, D.5
  • 8
    • 0003769049 scopus 로고
    • The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University
    • Brünger, A. T. 1992. X-PLOR, Version 3.1: A System for X-Ray Crystallography and NMR. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University.
    • (1992) X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR
    • Brünger, A.T.1
  • 10
    • 0024336324 scopus 로고
    • Protein encoded by v-erbA functions as a thyroid-hormone receptor antagonist
    • Damm, K., C. C. Thompson, and R. M. Evans. 1989. Protein encoded by v-erbA functions as a thyroid-hormone receptor antagonist. Nature. 339:593-597.
    • (1989) Nature , vol.339 , pp. 593-597
    • Damm, K.1    Thompson, C.C.2    Evans, R.M.3
  • 11
    • 0029814796 scopus 로고    scopus 로고
    • Ligand-induced conformational changes in the human retinoic acid receptor γ detected using monoclonal antibodies
    • Driscoll, J. E., C. L. Seachord, J. A. Lupisella, R. P. Darveau, and P. R. Reczek. 1996. Ligand-induced conformational changes in the human retinoic acid receptor γ detected using monoclonal antibodies. J. Biol. Chem. 271:22969-22975.
    • (1996) J. Biol. Chem. , vol.271 , pp. 22969-22975
    • Driscoll, J.E.1    Seachord, C.L.2    Lupisella, J.A.3    Darveau, R.P.4    Reczek, P.R.5
  • 12
    • 0031001349 scopus 로고    scopus 로고
    • Dynamic strength of molecular adhesion bonds
    • Evans, E., and K. Ritchie. 1997. Dynamic strength of molecular adhesion bonds. Biophys. J. 72:1541-1555.
    • (1997) Biophys. J. , vol.72 , pp. 1541-1555
    • Evans, E.1    Ritchie, K.2
  • 13
    • 0027498883 scopus 로고
    • On the mechanism of DNA binding by nuclear hormone receptors: A structural and functional perspective
    • Freedman, L. P., and B. F. Luisi. 1993. On the mechanism of DNA binding by nuclear hormone receptors: a structural and functional perspective. J. Cell. Biochem. 51:140-150.
    • (1993) J. Cell. Biochem. , vol.51 , pp. 140-150
    • Freedman, L.P.1    Luisi, B.F.2
  • 15
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmüller, H., B. Heymann, and P. Tavan. 1996. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271:997-999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 16
    • 0005754474 scopus 로고    scopus 로고
    • Simulation studies of protein-ligand interactions
    • Algorithms for Macromolecular Modelling. P Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel, and S. Reich, editors. Springer-Verlag, New York. In press
    • Hermans, J., G. Mann, L. Wang, and L. Zhang. 1998. Simulation studies of protein-ligand interactions. In Algorithms for Macromolecular Modelling. P Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, R. D. Skeel, and S. Reich, editors. Lecture Notes in Computational Science and Engineering. Springer-Verlag, New York. In press.
    • (1998) Lecture Notes in Computational Science and Engineering
    • Hermans, J.1    Mann, G.2    Wang, L.3    Zhang, L.4
  • 18
    • 0028258544 scopus 로고
    • Molecular dynamics study of bacteriorhodopsin and artificial pigments
    • Humphrey, W., I. Logunov, K. Schulten, and M. Sheves. 1994. Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry. 33:3668-3678.
    • (1994) Biochemistry , vol.33 , pp. 3668-3678
    • Humphrey, W.1    Logunov, I.2    Schulten, K.3    Sheves, M.4
  • 19
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
    • Isralewitz, B., S. Izrailev, and K. Schulten. 1997. Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophys. J. 73:2972-2979.
    • (1997) Biophys. J. , vol.73 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 20
    • 0030987036 scopus 로고    scopus 로고
    • Molecular dynamics study of unbinding of the avidin-biotin complex
    • Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J. 72:1568-1581.
    • (1997) Biophys. J. , vol.72 , pp. 1568-1581
    • Izrailev, S.1    Stepaniants, S.2    Balsera, M.3    Oono, Y.4    Schulten, K.5
  • 22
    • 17544384086 scopus 로고    scopus 로고
    • DNA recognition by normal and oncogenic thyroid hormone receptors - Unexpected diversity in half-site specificity controlled by non-zinc-finger determinants
    • Judelson, C., and M. L. Privalsky. 1996. DNA recognition by normal and oncogenic thyroid hormone receptors - unexpected diversity in half-site specificity controlled by non-zinc-finger determinants. J. Biol. Chem. 271:10800-10805.
    • (1996) J. Biol. Chem. , vol.271 , pp. 10800-10805
    • Judelson, C.1    Privalsky, M.L.2
  • 23
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A. 32:922-923.
    • (1976) Acta Crystallogr. A. , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 25
    • 0030805890 scopus 로고    scopus 로고
    • Binding of the estrogen receptor to DNA: The role of waters
    • Kosztin, D., T. C. Bishop, and K. Schulten. 1997. Binding of the estrogen receptor to DNA: the role of waters. Biophys. J. 73:557-570.
    • (1997) Biophys. J. , vol.73 , pp. 557-570
    • Kosztin, D.1    Bishop, T.C.2    Schulten, K.3
  • 26
    • 0022720813 scopus 로고
    • The chicken oestrogen receptor sequence: Homology with v-erbA and the human oestrogen and glucocorticoid receptors
    • Krust. A., S. Green, P. Argos, V. Kumar, P. Walter, J. Bornert, and P. Chambon. 1986. The chicken oestrogen receptor sequence: homology with v-erbA and the human oestrogen and glucocorticoid receptors. EMBO J. 5:891-897.
    • (1986) EMBO J. , vol.5 , pp. 891-897
    • Krust, A.1    Green, S.2    Argos, P.3    Kumar, V.4    Walter, P.5    Bornert, J.6    Chambon, P.7
  • 28
    • 0028890361 scopus 로고
    • Interaction of thyroid-hormone receptor with a conserved transcriptional mediator
    • Lee, J. W., F. Ryan, J. C. Swaffield, S. A. Johnston, and D. D. Moore. 1995. Interaction of thyroid-hormone receptor with a conserved transcriptional mediator. Nature. 374:91-94.
    • (1995) Nature , vol.374 , pp. 91-94
    • Lee, J.W.1    Ryan, F.2    Swaffield, J.C.3    Johnston, S.A.4    Moore, D.D.5
  • 29
    • 0030378980 scopus 로고    scopus 로고
    • SMD: Visual steering of molecular dynamics for protein design
    • Leech, J., J. Prins, and J. Hermans. 1996. SMD: visual steering of molecular dynamics for protein design. IEEE Comp. Sci. & Eng. 3:38-45.
    • (1996) IEEE Comp. Sci. & Eng. , vol.3 , pp. 38-45
    • Leech, J.1    Prins, J.2    Hermans, J.3
  • 30
    • 0031848099 scopus 로고    scopus 로고
    • Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
    • Lu, H., B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten. 1998. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75:662-671.
    • (1998) Biophys. J. , vol.75 , pp. 662-671
    • Lu, H.1    Isralewitz, B.2    Krammer, A.3    Vogel, V.4    Schulten, K.5
  • 31
    • 0007299919 scopus 로고    scopus 로고
    • Substrate access to cytochrome P450cam: A comparison of a thermal motion pathway analysis with molecular dynamics simulation data
    • Lüdemann, S. K., O. Carugo, and R. C. Wade. 1997. Substrate access to cytochrome P450cam: a comparison of a thermal motion pathway analysis with molecular dynamics simulation data. J. Mol. Model. 3:369-374.
    • (1997) J. Mol. Model. , vol.3 , pp. 369-374
    • Lüdemann, S.K.1    Carugo, O.2    Wade, R.C.3
  • 34
    • 0031880829 scopus 로고    scopus 로고
    • Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations
    • Marrink, S.-J., O. Berger, P. Tieleman, and F. Jähnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys. J. 74:931-943.
    • (1998) Biophys. J. , vol.74 , pp. 931-943
    • Marrink, S.-J.1    Berger, O.2    Tieleman, P.3    Jähnig, F.4
  • 36
    • 0343889438 scopus 로고
    • Molecular Simulations Inc., Burlington, Massachusetts
    • MSI. 1994. Quanta 4.0. Molecular Simulations Inc., Burlington, Massachusetts.
    • (1994) Quanta 4.0
  • 38
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., K. A. Sharp, and B. Honig. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct., Fund., Genet. 11:281-296.
    • (1991) Proteins: Struct., Fund., Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 39
    • 0032488839 scopus 로고    scopus 로고
    • Serine 232 and methionine 272 define the ligand binding pocket in retinoic acid receptor subtypes
    • J. E. S. Jr.
    • Ostrowski, J., T. Roalsvig, L. Hammer, A. Marinier, J. E. S. Jr., K. L. Yu, and P. R. Reczek. 1998. Serine 232 and methionine 272 define the ligand binding pocket in retinoic acid receptor subtypes. J. Biol. Chem. 273: 3490-3495.
    • (1998) J. Biol. Chem. , vol.273 , pp. 3490-3495
    • Ostrowski, J.1    Roalsvig, T.2    Hammer, L.3    Marinier, A.4    Yu, K.L.5    Reczek, P.R.6
  • 40
    • 0029643780 scopus 로고
    • Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid
    • Renaud, J. P., N. Rochel, M. Ruff, V. Vivat, P. Chambon, H. Gronemeyer, and D. Moras. 1995. Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid. Nature. 378:681-689.
    • (1995) Nature , vol.378 , pp. 681-689
    • Renaud, J.P.1    Rochel, N.2    Ruff, M.3    Vivat, V.4    Chambon, P.5    Gronemeyer, H.6    Moras, D.7
  • 41
    • 0001068789 scopus 로고    scopus 로고
    • Extraction of lipids from phospholipid membranes by steered molecular dynamics
    • Stepaniants, S., S. Izrailev, and K. Schulten. 1997. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J. Mol Model. 3:473-475.
    • (1997) J. Mol Model. , vol.3 , pp. 473-475
    • Stepaniants, S.1    Izrailev, S.2    Schulten, K.3
  • 42
    • 0032568527 scopus 로고    scopus 로고
    • Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains
    • Tanenbaum, D. M., Y. Wang, S. P. Williams, and P. B. Sigler. 1998. Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Proc. Natl. Acad Sci. USA. 95:5998-6003.
    • (1998) Proc. Natl. Acad Sci. USA , vol.95 , pp. 5998-6003
    • Tanenbaum, D.M.1    Wang, Y.2    Williams, S.P.3    Sigler, P.B.4
  • 43
    • 0029824793 scopus 로고    scopus 로고
    • Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins
    • van Aalten, D. M. F., B. L. de Groot, H. Berendsen, and J. B. C. Findlay. 1996. Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins. Biochem. J. 319:543-550.
    • (1996) Biochem. J. , vol.319 , pp. 543-550
    • Van Aalten, D.M.F.1    De Groot, B.L.2    Berendsen, H.3    Findlay, J.B.C.4
  • 44
    • 0032079794 scopus 로고    scopus 로고
    • The yeast ADA complex mediates the ligand-dependent activation function AF-2 of retinoid X and estrogen receptors
    • Vombaur, E., M. Harbers, S. J. Um, A. Benecke, P. Chambon, and R. Losson. 1998. The yeast ADA complex mediates the ligand-dependent activation function AF-2 of retinoid X and estrogen receptors. Genes Dev. 12:1278-1289.
    • (1998) Genes Dev. , vol.12 , pp. 1278-1289
    • Vombaur, E.1    Harbers, M.2    Um, S.J.3    Benecke, A.4    Chambon, P.5    Losson, R.6
  • 46
    • 0032575057 scopus 로고    scopus 로고
    • Atomic structure of progesterone complexed with its receptor
    • Williams, S. P., and P. B. Sigler. 1998. Atomic structure of progesterone complexed with its receptor. Nature. 393:392-396.
    • (1998) Nature , vol.393 , pp. 392-396
    • Williams, S.P.1    Sigler, P.B.2
  • 47
    • 0344534333 scopus 로고    scopus 로고
    • Investigating a back door mechanism of actin phosphate release by steered molecular dynamics
    • in press
    • Wriggers, W., and K. Schulten. 1998. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins Struct. Funct. Genet, (in press).
    • (1998) Proteins Struct. Funct. Genet
    • Wriggers, W.1    Schulten, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.