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Volumn 33, Issue 13, 2005, Pages 4212-4222

Cooperative binding of DNA and CBFβ to the Runt domain of the CBFα studied via MD simulations

Author keywords

[No Author keywords available]

Indexed keywords

CORE BINDING FACTOR; CORE BINDING FACTOR BETA; DNA; TRANSCRIPTION FACTOR RUNX2; UNCLASSIFIED DRUG; AMINO ACID; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 2; TRANSCRIPTION FACTOR RUNX; TUMOR PROTEIN;

EID: 22844438435     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki724     Document Type: Article
Times cited : (21)

References (47)
  • 1
    • 0027220003 scopus 로고
    • PEBP2/PEA2 represents a family of transcription factors homologous to the products of the Drosophila runt gene and the human AML1 gene
    • Ogawa,E., Maruyama,M., Kagoshima,H., Inuzuka,M., Lu,J., Satake,M., Shigesada,K. and Ito,Y. (1993) PEBP2/PEA2 represents a family of transcription factors homologous to the products of the Drosophila runt gene and the human AML1 gene. Proc. Natl Acad. Sci. USA, 90, 6859-6863.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 6859-6863
    • Ogawa, E.1    Maruyama, M.2    Kagoshima, H.3    Inuzuka, M.4    Lu, J.5    Satake, M.6    Shigesada, K.7    Ito, Y.8
  • 2
    • 0030061554 scopus 로고    scopus 로고
    • AML1, the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis
    • Okuda,T., van Deursen,J., Hiebert,S.W., Grosveld,G. and Downing,J.R. (1996) AML1, the target of multiple chromosomal translocations in human leukemia, is essential for normal fetal liver hematopoiesis. Cell, 84, 321-330.
    • (1996) Cell , vol.84 , pp. 321-330
    • Okuda, T.1    van Deursen, J.2    Hiebert, S.W.3    Grosveld, G.4    Downing, J.R.5
  • 3
    • 0036186852 scopus 로고    scopus 로고
    • Mutations in the RUNX2 gene in patients with cleidocranial dysplasia
    • Otto,F., Kanegane,H. and Mundlos,S. (2002) Mutations in the RUNX2 gene in patients with cleidocranial dysplasia. Hum. Mutat., 19, 209-216.
    • (2002) Hum. Mutat. , vol.19 , pp. 209-216
    • Otto, F.1    Kanegane, H.2    Mundlos, S.3
  • 4
    • 0036527349 scopus 로고    scopus 로고
    • RUNX: A trilogy of cancer genes
    • Lund,A.H. and van Lohuizen,M. (2002) RUNX: A trilogy of cancer genes. Cancer Cell, 1, 213-215.
    • (2002) Cancer Cell , vol.1 , pp. 213-215
    • Lund, A.H.1    van Lohuizen, M.2
  • 5
    • 0034610754 scopus 로고    scopus 로고
    • Indispensable role of the transcription factor PEBP2/CBF in angiogenic activity of a murine endothelial cell MSS31
    • Namba,K., Abe,M., Saito,S., Satake,M., Ohmoto,T., Watanabe,T. and Sato,Y. (2000) Indispensable role of the transcription factor PEBP2/CBF in angiogenic activity of a murine endothelial cell MSS31. Oncogene, 19, 106-114.
    • (2000) Oncogene , vol.19 , pp. 106-114
    • Namba, K.1    Abe, M.2    Saito, S.3    Satake, M.4    Ohmoto, T.5    Watanabe, T.6    Sato, Y.7
  • 6
    • 0035393430 scopus 로고    scopus 로고
    • Runt-related gene 2 in endothelial cells: Inducible expression and specific regulation of cell migration and invasion
    • Sun,L., Vitolo,M. and Passaniti,A. (2001) Runt-related gene 2 in endothelial cells: Inducible expression and specific regulation of cell migration and invasion. Cancer Res., 61, 4994-5001.
    • (2001) Cancer Res. , vol.61 , pp. 4994-5001
    • Sun, L.1    Vitolo, M.2    Passaniti, A.3
  • 7
    • 0042346069 scopus 로고    scopus 로고
    • Hypermethylation of the RUNX3 gene promoter in testicular yolk sac tumor of infants
    • Kato,N., Tamura,G., Fukase,M., Shibuya,H. and Motoyama,T. (2003) Hypermethylation of the RUNX3 gene promoter in testicular yolk sac tumor of infants. Am. J. Pathol., 163, 387-391.
    • (2003) Am. J. Pathol. , vol.163 , pp. 387-391
    • Kato, N.1    Tamura, G.2    Fukase, M.3    Shibuya, H.4    Motoyama, T.5
  • 10
    • 0036383150 scopus 로고    scopus 로고
    • The Runx1 Runt domain at 1.25 Å resolution: A structural switch and specifically bound chloride ions modulate DNA binding
    • Backstrom,S., Wolf-Watz,M., Grundstrom,C., Hard,T., Grundstrom,T. and Sauer,U.H. (2002) The Runx1 Runt domain at 1.25 Å resolution: A structural switch and specifically bound chloride ions modulate DNA binding. J. Mol. Biol, 322, 259-272.
    • (2002) J. Mol. Biol. , vol.322 , pp. 259-272
    • Backstrom, S.1    Wolf-Watz, M.2    Grundstrom, C.3    Hard, T.4    Grundstrom, T.5    Sauer, U.H.6
  • 11
    • 14344284548 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein DNA complexes with involvement of AML1/Runx-1/CBFalpha Runt domain, CBFβ and the C/EBPβ bZip region
    • Tahirov,T.H., Inoue-Bungo,T., Sasaki,M., Shiina,M., Kimura,K., Sato,K., Kumasaka,T., Yamamoto,M., Kamiya,N. and Ogata,K. (2001) Crystallization and preliminary X-ray analyses of quaternary, ternary and binary protein DNA complexes with involvement of AML1/Runx-1/CBFalpha Runt domain, CBFβ and the C/EBPβ bZip region. Acta Crystallogr. D Biol. Crystallogr., 57, 850-853.
    • (2001) Acta Crystallogr. D. Biol. Crystallogr. , vol.57 , pp. 850-853
    • Tahirov, T.H.1    Inoue-Bungo, T.2    Sasaki, M.3    Shiina, M.4    Kimura, K.5    Sato, K.6    Kumasaka, T.7    Yamamoto, M.8    Kamiya, N.9    Ogata, K.10
  • 12
    • 0034660045 scopus 로고    scopus 로고
    • Structural basis for the heterodimeric interaction between the acute leukaemia-associated transcription factors AML1 and CBFβ
    • Warren,A.J., Bravo,J., Williams,R.L. and Rabbitts,T.H. (2000) Structural basis for the heterodimeric interaction between the acute leukaemia-associated transcription factors AML1 and CBFβ. EMBO J., 19, 3004-3015.
    • (2000) EMBO J. , vol.19 , pp. 3004-3015
    • Warren, A.J.1    Bravo, J.2    Williams, R.L.3    Rabbitts, T.H.4
  • 13
    • 0035066381 scopus 로고    scopus 로고
    • The Leukemia-associated AML1 (Runx1)-CBRβ complex functions as a DNA-induced molecular clamp
    • Bravo,J., Li,Z., Speck,N.A. and Warren,A.J. (2001) The Leukemia-associated AML1 (Runx1)-CBRβ complex functions as a DNA-induced molecular clamp. Nature Struct. Biol., 8, 371-377.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 371-377
    • Bravo, J.1    Li, Z.2    Speck, N.A.3    Warren, A.J.4
  • 14
    • 0036774088 scopus 로고    scopus 로고
    • DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the Runt domain and by DNA bending
    • Bartfeld,D., Shimon,L., Couture,G.C., Rabinovich,D., Frolow,F., Levanon,D., Groner,Y. and Shakked,Z. (2002) DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the Runt domain and by DNA bending. Structure, 10, 1395-1407.
    • (2002) Structure , vol.10 , pp. 1395-1407
    • Bartfeld, D.1    Shimon, L.2    Couture, G.C.3    Rabinovich, D.4    Frolow, F.5    Levanon, D.6    Groner, Y.7    Shakked, Z.8
  • 15
    • 0029860141 scopus 로고    scopus 로고
    • Biochemical and biophysical properties of the core-binding factor alpha2 (AML1) DNA-binding domain
    • Crute,B.E., Lewis,A.F., Wu,Z., Bushweller,J.H. and Speck,N.A. (1996) Biochemical and biophysical properties of the core-binding factor alpha2 (AML1) DNA-binding domain. J. Biol. Chem., 271, 26251-26260.
    • (1996) J. Biol. Chem. , vol.271 , pp. 26251-26260
    • Crute, B.E.1    Lewis, A.F.2    Wu, Z.3    Bushweller, J.H.4    Speck, N.A.5
  • 20
    • 4344649812 scopus 로고    scopus 로고
    • CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium
    • Yan,J., Liu,Y., Lukasik,S.M., Speck,N.A. and Bushweller,J.H. (2004) CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium. Nature Struct. Mol. Biol., 11, 901-906.
    • (2004) Nature Struct. Mol. Biol. , vol.11 , pp. 901-906
    • Yan, J.1    Liu, Y.2    Lukasik, S.M.3    Speck, N.A.4    Bushweller, J.H.5
  • 22
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Rat and Ras-RaIGDS complexes
    • Gohlke,H., Kiel,C. and Case,D.A. (2003) Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Rat and Ras-RaIGDS complexes. J. Mol. Biol., 330, 891-913.
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 23
    • 0037079572 scopus 로고    scopus 로고
    • Free-energy component analysis of 40 protein DNA complexes: A consensus view on the thermodynamics of binding at the molecular level
    • Jayaram,B., McConnell,K., Dixit,S.B., Das,A. and Beveridge,D.L. (2002) Free-energy component analysis of 40 protein DNA complexes: A consensus view on the thermodynamics of binding at the molecular level. J. Comput. Chem., 23, 1-14.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1-14
    • Jayaram, B.1    McConnell, K.2    Dixit, S.B.3    Das, A.4    Beveridge, D.L.5
  • 24
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman,P.A., Massova,I., Reyes,C., Kuhn,B., Huo,S.H., Chong,L., Lee,M., Lee,J., Duan,Y., Wang,W. et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res., 33, 889-897.
    • (2000) Acc. Chem. Res. , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.H.5    Chong, L.6    Lee, M.7    Lee, J.8    Duan, Y.9    Wang, W.10
  • 25
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still,W.C., Tempczyk,A., Hawley,R.C. and Hendrickson,T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112, 6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 27
    • 0034671749 scopus 로고    scopus 로고
    • Energetic and functional contribution of residues in the core binding factor β (CBFβ) subunit to heterodimerization with CBFalpha
    • Tang,Y.Y., Shi,J., Zhang,L., Davis,A., Bravo,J., Warren,A.J., Speck,N.A. and Bushweller,J.H. (2000) Energetic and functional contribution of residues in the core binding factor β (CBFβ) subunit to heterodimerization with CBFalpha. J. Biol. Chem., 275, 39579-39588.
    • (2000) J. Biol. Chem. , vol.275 , pp. 39579-39588
    • Tang, Y.Y.1    Shi, J.2    Zhang, L.3    Davis, A.4    Bravo, J.5    Warren, A.J.6    Speck, N.A.7    Bushweller, J.H.8
  • 30
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe,N. and MacKerell,A.D.Jr (2000) All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem., 21, 86-104.
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell Jr., A.D.2
  • 31
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution
    • MacKerell,A.D.Jr and Banavali,N. (2000) All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem., 21, 105-120.
    • (2000) J. Comput. Chem. , vol.21 , pp. 105-120
    • MacKerell Jr., A.D.1    Banavali, N.2
  • 32
    • 0000812183 scopus 로고
    • Theoretical studies of medium effects on conformational equilibria
    • Jorgensen,W.L. (1983) Theoretical studies of medium effects on conformational equilibria. J. Phys. Chem., 87, 5304-5312.
    • (1983) J. Phys. Chem. , vol.87 , pp. 5304-5312
    • Jorgensen, W.L.1
  • 33
    • 0031234042 scopus 로고    scopus 로고
    • An integral equation to describe the solvation of polar molecules in liquid water
    • Beglov,D. and Roux,B. (1997) An integral equation to describe the solvation of polar molecules in liquid water. J. Phys. Chem., 101, 7821-7826.
    • (1997) J. Phys. Chem. , vol.101 , pp. 7821-7826
    • Beglov, D.1    Roux, B.2
  • 34
    • 0015749250 scopus 로고
    • Refinement of the structure of b-dna and implications for the analysis of x-ray diffraction data from fibers of biopolymers
    • Arnott,S. and Hukins,D.W.L. (1973) Refinement of the structure of b-dna and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J. Mol. Biol., 81, 93-105.
    • (1973) J. Mol. Biol. , vol.81 , pp. 93-105
    • Arnott, S.1    Hukins, D.W.L.2
  • 35
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation - The langevin piston method
    • Feller,S.E., Zhang,Y.H., Pastor,R.W. and Brooks,B.R. (1995) Constant-pressure molecular-dynamics simulation - the langevin piston method. J. Chem. Phys., 103, 4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 36
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 37
    • 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,D.M., Darden,T.A. and Pedersen,L.G. (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. J. Chem. Phys., 99, 8345-8348.
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 38
    • 84986534166 scopus 로고
    • New spherical-cutoff methods for long-range forces in macromolecular simulation
    • Steinbach,P.J. and Brooks,B.R. (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem., 15, 667-683.
    • (1994) J. Comput. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2
  • 40
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D photorealistic molecular graphics
    • Merritt,E.A. and Bacon,D.J. (1997) Raster3D photorealistic molecular graphics. Methods Enzymol., 277, 505-524.
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 41
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee,B. and Richards,F.M. (1971) The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 43
    • 0026869597 scopus 로고
    • Langevin dynamics of peptides - The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide
    • Loncharich,R.J., Brooks,B.R. and Pastor,R.W. (1992) Langevin dynamics of peptides - the frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers, 32, 523-535.
    • (1992) Biopolymers , vol.32 , pp. 523-535
    • Loncharich, R.J.1    Brooks, B.R.2    Pastor, R.W.3
  • 44
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • MacKerell,A.D.Jr (2004) Empirical force fields for biological macromolecules: Overview and issues. J. Comput. Chem., 25, 1584-1604.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1584-1604
    • MacKerell Jr., A.D.1
  • 45
    • 0034687674 scopus 로고    scopus 로고
    • DNA tightens the dimeric DNA-binding domain of human papillomavirus E2 protein without changes in volume
    • Lima,L.M.T.R., Foguel,D. and Silva,J.L. (2000) DNA tightens the dimeric DNA-binding domain of human papillomavirus E2 protein without changes in volume. Proc. Natl Acad. Sci. USA, 97, 14289-14294.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 14289-14294
    • Lima, L.M.T.R.1    Foguel, D.2    Silva, J.L.3
  • 46
    • 0033569711 scopus 로고    scopus 로고
    • The Ig fold of the core binding factor alpha Runt domain is a member of a family of structurally and functionally related Ig-fold DNA-binding domains
    • Berardi,M.J., Sun,C., Zehr,M., Abildgaard,F., Peng,J., Speck,N.A. and Bushweller,J.H. (1999) The Ig fold of the core binding factor alpha Runt domain is a member of a family of structurally and functionally related Ig-fold DNA-binding domains. Struct. Fold. Des., 7, 1247-1256.
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1247-1256
    • Berardi, M.J.1    Sun, C.2    Zehr, M.3    Abildgaard, F.4    Peng, J.5    Speck, N.A.6    Bushweller, J.H.7
  • 47
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • Ma,B., Elkayam,T., Wolfson,H. and Nussinov,R. (2003) Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA, 100, 5772-5777.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4


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