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Volumn 52, Issue 32, 2013, Pages 5335-5344

Asymmetric DNA-search dynamics by symmetric dimeric proteins

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; COMPUTATIONAL TOOLS; DNA-BINDING PROTEIN; RESTRICTION ENDONUCLEASES; SALT CONCENTRATION; SEARCH EFFICIENCY; SLIDING MECHANISM;

EID: 84881640323     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400357m     Document Type: Article
Times cited : (25)

References (92)
  • 1
    • 33750078971 scopus 로고    scopus 로고
    • NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA
    • Iwahara, J., Zweckstetter, M., and Clore, G. M. (2006) NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA Proc. Natl. Acad. Sci. U. S. A. 103, 15062-15067
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 15062-15067
    • Iwahara, J.1    Zweckstetter, M.2    Clore, G.M.3
  • 3
    • 58149345492 scopus 로고    scopus 로고
    • Protein sliding along DNA: Dynamics and structural characterization
    • Givaty, O. and Levy, Y. (2009) Protein sliding along DNA: Dynamics and structural characterization J. Mol. Biol. 385, 1087-1097
    • (2009) J. Mol. Biol. , vol.385 , pp. 1087-1097
    • Givaty, O.1    Levy, Y.2
  • 4
    • 84856117713 scopus 로고    scopus 로고
    • Timing facilitated site transfer of an enzyme on DNA
    • Schonhoft, J. D. and Stivers, J. T. (2012) Timing facilitated site transfer of an enzyme on DNA Nat. Chem. Biol. 8, 205-210
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 205-210
    • Schonhoft, J.D.1    Stivers, J.T.2
  • 5
    • 49449088997 scopus 로고    scopus 로고
    • Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils
    • Porecha, R. H. and Stivers, J. T. (2008) Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils Proc. Natl. Acad. Sci. U. S. A. 105, 10791-10796
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 10791-10796
    • Porecha, R.H.1    Stivers, J.T.2
  • 6
    • 0019887628 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic-acids. 1. Models and theory
    • Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic-acids. 1. Models and theory Biochemistry 20, 6929-6948
    • (1981) Biochemistry , vol.20 , pp. 6929-6948
    • Berg, O.G.1    Winter, R.B.2    Von Hippel, P.H.3
  • 7
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel, P. H. and Berg, O. G. (1989) Facilitated target location in biological systems J. Biol. Chem. 264, 675-678
    • (1989) J. Biol. Chem. , vol.264 , pp. 675-678
    • Von Hippel, P.H.1    Berg, O.G.2
  • 8
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • Halford, S. E. and Marko, J. F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 9
    • 65549171477 scopus 로고    scopus 로고
    • An end to 40 years of mistakes in DNA-protein association kinetics?
    • Halford, S. E. (2009) An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 37, 343-348
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 343-348
    • Halford, S.E.1
  • 10
    • 79251584676 scopus 로고    scopus 로고
    • Physics of protein-DNA interactions: Mechanisms of facilitated target search
    • Kolomeisky, A. (2011) Physics of protein-DNA interactions: mechanisms of facilitated target search Phys. Chem. Chem. Phys. 13, 2088-2095
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 2088-2095
    • Kolomeisky, A.1
  • 11
    • 79957549084 scopus 로고    scopus 로고
    • Dancing on DNA: Kinetic aspects of search processes on DNA
    • Tafvizi, A., Mirny, L. A., and van Oijen, A. M. (2011) Dancing on DNA: kinetic aspects of search processes on DNA ChemPhysChem 12, 1481-1489
    • (2011) ChemPhysChem , vol.12 , pp. 1481-1489
    • Tafvizi, A.1    Mirny, L.A.2    Van Oijen, A.M.3
  • 12
    • 77949320402 scopus 로고    scopus 로고
    • Searching DNA via a "monkey bar" mechanism: The significance of disordered tails
    • Vuzman, D., Azia, A., and Levy, Y. (2010) Searching DNA via a "monkey bar" mechanism: the significance of disordered tails J. Mol. Biol. 396, 674-684
    • (2010) J. Mol. Biol. , vol.396 , pp. 674-684
    • Vuzman, D.1    Azia, A.2    Levy, Y.3
  • 14
    • 33646356250 scopus 로고    scopus 로고
    • Detecting transient intermediates in macromolecular binding by paramagnetic NMR
    • Iwahara, J. and Clore, G. M. (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR Nature 440, 1227-1230
    • (2006) Nature , vol.440 , pp. 1227-1230
    • Iwahara, J.1    Clore, G.M.2
  • 15
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNA interaction: Facillated target location in sequence-dependent potential
    • Slutsky, M. and Mirny, L. A. (2004) Kinetics of protein-DNA interaction: facillated target location in sequence-dependent potential Biophys. J. 87, 4021-4035
    • (2004) Biophys. J. , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.A.2
  • 16
    • 27644460480 scopus 로고    scopus 로고
    • Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
    • Gowers, D. M., Wilson, G. G., and Halford, S. E. (2005) Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA Proc. Natl. Acad. Sci. U. S. A. 102, 15883-15888
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15883-15888
    • Gowers, D.M.1    Wilson, G.G.2    Halford, S.E.3
  • 17
    • 78650453629 scopus 로고    scopus 로고
    • DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail
    • Vuzman, D. and Levy, Y. (2010) DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail Proc. Natl. Acad. Sci. U. S. A. 107, 21004-21009
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 21004-21009
    • Vuzman, D.1    Levy, Y.2
  • 18
    • 82655179905 scopus 로고    scopus 로고
    • Intrinsically disordered regions as affinity tuners in protein-DNA interactions
    • Vuzman, D. and Levy, Y. (2012) Intrinsically disordered regions as affinity tuners in protein-DNA interactions Mol. BioSyst. 8, 45-57
    • (2012) Mol. BioSyst. , vol.8 , pp. 45-57
    • Vuzman, D.1    Levy, Y.2
  • 19
    • 77958168396 scopus 로고    scopus 로고
    • Facilitated DNA search by multidomain transcription factors: Cross talk via a flexible linker
    • Vuzman, D., Polonsky, M., and Levy, Y. (2010) Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker Biophys. J. 99, 1202-1211
    • (2010) Biophys. J. , vol.99 , pp. 1202-1211
    • Vuzman, D.1    Polonsky, M.2    Levy, Y.3
  • 20
    • 84856468942 scopus 로고    scopus 로고
    • Classes of fast and specific search mechanisms for proteins on DNA
    • Sheinman, M., Benichou, O., Kafri, Y., and Voituriez, R. (2012) Classes of fast and specific search mechanisms for proteins on DNA Rep. Prog. Phys. 75, 026601
    • (2012) Rep. Prog. Phys. , vol.75 , pp. 026601
    • Sheinman, M.1    Benichou, O.2    Kafri, Y.3    Voituriez, R.4
  • 22
    • 0026052405 scopus 로고
    • Diversity and specificity in transcriptional regulation: The benefits of heterotypic dimerization
    • Lamb, P. and McKnight, S. L. (1991) Diversity and specificity in transcriptional regulation: the benefits of heterotypic dimerization Trends Biochem. Sci. 16, 417-422
    • (1991) Trends Biochem. Sci. , vol.16 , pp. 417-422
    • Lamb, P.1    McKnight, S.L.2
  • 24
    • 0037154982 scopus 로고    scopus 로고
    • A unified theory of gene expression
    • Orphanides, G. and Reinberg, D. (2002) A unified theory of gene expression Cell 108, 439-451
    • (2002) Cell , vol.108 , pp. 439-451
    • Orphanides, G.1    Reinberg, D.2
  • 27
    • 0035830451 scopus 로고    scopus 로고
    • Kinetic studies of Fos center dot Jun center dot DNA complex formation: DNA binding prior to dimerization
    • Kohler, J. J. and Schepartz, A. (2001) Kinetic studies of Fos center dot Jun center dot DNA complex formation: DNA binding prior to dimerization Biochemistry 40, 130-142
    • (2001) Biochemistry , vol.40 , pp. 130-142
    • Kohler, J.J.1    Schepartz, A.2
  • 28
    • 84888277114 scopus 로고    scopus 로고
    • Dimeric transcription factors utilize a monomer binding pathway to achieve faster DNA binding kinetics and greater kinetic specificity
    • Kohler, J. J. and Schepartz, A. (1999) Dimeric transcription factors utilize a monomer binding pathway to achieve faster DNA binding kinetics and greater kinetic specificity Biophys. J. 76, A134-A134
    • (1999) Biophys. J. , vol.76
    • Kohler, J.J.1    Schepartz, A.2
  • 29
    • 0032978995 scopus 로고    scopus 로고
    • Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions
    • Rentzeperis, D., Jonsson, T., and Sauer, R. T. (1999) Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions Nat. Struct. Biol. 6, 569-573
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 569-573
    • Rentzeperis, D.1    Jonsson, T.2    Sauer, R.T.3
  • 30
    • 68049120378 scopus 로고    scopus 로고
    • Arc-repressor dimerization on DNA: Folding rate enhancement by colocalization
    • Marcovitz, A. and Levy, Y. (2009) Arc-repressor dimerization on DNA: Folding rate enhancement by colocalization Biophys. J. 96, 4212-4220
    • (2009) Biophys. J. , vol.96 , pp. 4212-4220
    • Marcovitz, A.1    Levy, Y.2
  • 31
    • 0036146923 scopus 로고    scopus 로고
    • Immigration control of DNA in bacteria: Self versus non-self
    • Murray, N. E. (2002) Immigration control of DNA in bacteria: self versus non-self Microbiology 148, 3-20
    • (2002) Microbiology , vol.148 , pp. 3-20
    • Murray, N.E.1
  • 32
    • 0018380779 scopus 로고
    • Promotion and limitation of genetic exchange
    • Arber, W. (1979) Promotion and limitation of genetic exchange Experientia 35, 287-293
    • (1979) Experientia , vol.35 , pp. 287-293
    • Arber, W.1
  • 33
    • 0029885422 scopus 로고    scopus 로고
    • Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites
    • JenJacobson, L., Engler, L. E., Lesser, D. R., Kurpiewski, M. R., Yee, C., and McVerry, B. (1996) Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites EMBO J. 15, 2870-2882
    • (1996) EMBO J. , vol.15 , pp. 2870-2882
    • Jenjacobson, L.1    Engler, L.E.2    Lesser, D.R.3    Kurpiewski, M.R.4    Yee, C.5    McVerry, B.6
  • 34
    • 0015692158 scopus 로고
    • Suggested nomenclature for bacterial host modification and restriction systems and their enzymes
    • Smith, H. O. and Nathans, D. (1973) Suggested nomenclature for bacterial host modification and restriction systems and their enzymes J. Mol. Biol. 81, 419-423
    • (1973) J. Mol. Biol. , vol.81 , pp. 419-423
    • Smith, H.O.1    Nathans, D.2
  • 36
    • 0028932881 scopus 로고
    • Structure and function of restriction endonucleases
    • Aggarwal, A. K. (1995) Structure and function of restriction endonucleases Curr. Opin. Struct. Biol. 5, 11-19
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 11-19
    • Aggarwal, A.K.1
  • 37
    • 77953255142 scopus 로고    scopus 로고
    • The type IIB restriction endonucleases
    • Marshall, J. J. and Halford, S. E. (2010) The type IIB restriction endonucleases Biochem. Soc. Trans. 38, 410-416
    • (2010) Biochem. Soc. Trans. , vol.38 , pp. 410-416
    • Marshall, J.J.1    Halford, S.E.2
  • 38
    • 0036440653 scopus 로고    scopus 로고
    • Type II restriction endonucleases
    • Perona, J. J. (2002) Type II restriction endonucleases Methods 28, 353-364
    • (2002) Methods , vol.28 , pp. 353-364
    • Perona, J.J.1
  • 39
    • 0030911133 scopus 로고    scopus 로고
    • Recognition and cleavage of DNA by type-II restriction endonucleases
    • Pingoud, A. and Jeltsch, A. (1997) Recognition and cleavage of DNA by type-II restriction endonucleases Eur. J. Biochem. 246, 1-22
    • (1997) Eur. J. Biochem. , vol.246 , pp. 1-22
    • Pingoud, A.1    Jeltsch, A.2
  • 40
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • Pingoud, A. and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases Nucleic Acids Res. 29, 3705-3727
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 41
    • 17044403057 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structure and mechanism
    • Pingoud, A., Fuxreiter, M., Pingoud, V., and Wende, W. (2005) Type II restriction endonucleases: structure and mechanism Cell. Mol. Life Sci. 62, 685-707
    • (2005) Cell. Mol. Life Sci. , vol.62 , pp. 685-707
    • Pingoud, A.1    Fuxreiter, M.2    Pingoud, V.3    Wende, W.4
  • 42
    • 0032493296 scopus 로고    scopus 로고
    • Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases
    • Kovall, R. A. and Matthews, B. W. (1998) Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases Proc. Natl. Acad. Sci. U. S. A. 95, 7893-7897
    • (1998) Proc. Natl. Acad. Sci. U. S. A. , vol.95 , pp. 7893-7897
    • Kovall, R.A.1    Matthews, B.W.2
  • 43
    • 0020160863 scopus 로고
    • Involvement of outside DNA-sequences in the major kinetic path by which ecori endonuclease locates and leaves its recognition sequence
    • Jack, W. E., Terry, B. J., and Modrich, P. (1982) Involvement of outside DNA-sequences in the major kinetic path by which ecori endonuclease locates and leaves its recognition sequence Proc. Natl. Acad. Sci. U. S. A. 79, 4010-4014
    • (1982) Proc. Natl. Acad. Sci. U. S. A. , vol.79 , pp. 4010-4014
    • Jack, W.E.1    Terry, B.J.2    Modrich, P.3
  • 44
    • 0028782732 scopus 로고
    • Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA
    • Jeltsch, A., Alves, J., Wolfes, H., Maass, G., and Pingoud, A. (1994) Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA Biochemistry 33, 10215-10219
    • (1994) Biochemistry , vol.33 , pp. 10215-10219
    • Jeltsch, A.1    Alves, J.2    Wolfes, H.3    Maass, G.4    Pingoud, A.5
  • 45
    • 0023034951 scopus 로고
    • Differences in the kinetic-properties of bamhi endonuclease and methylase with linear DNA substrates
    • Nardone, G., George, J., and Chirikjian, J. G. (1986) Differences in the kinetic-properties of bamhi endonuclease and methylase with linear DNA substrates J. Biol. Chem. 261, 2128-2133
    • (1986) J. Biol. Chem. , vol.261 , pp. 2128-2133
    • Nardone, G.1    George, J.2    Chirikjian, J.G.3
  • 46
    • 0029790522 scopus 로고    scopus 로고
    • Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme
    • Jeltsch, A., Wenz, C., Stahl, F., and Pingoud, A. (1996) Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme EMBO J. 15, 5104-5111
    • (1996) EMBO J. , vol.15 , pp. 5104-5111
    • Jeltsch, A.1    Wenz, C.2    Stahl, F.3    Pingoud, A.4
  • 47
    • 0032562139 scopus 로고    scopus 로고
    • Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA
    • Jeltsch, A. and Pingoud, A. (1998) Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA Biochemistry 37, 2160-2169
    • (1998) Biochemistry , vol.37 , pp. 2160-2169
    • Jeltsch, A.1    Pingoud, A.2
  • 51
    • 81055141525 scopus 로고    scopus 로고
    • Frustration in protein-DNA binding influences conformational switching and target search kinetics
    • Marcovitz, A. and Levy, Y. (2011) Frustration in protein-DNA binding influences conformational switching and target search kinetics Proc. Natl. Acad. Sci. U. S. A. 108, 17957-17962
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 17957-17962
    • Marcovitz, A.1    Levy, Y.2
  • 52
    • 79953695332 scopus 로고    scopus 로고
    • Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains
    • Khazanov, N. and Levy, Y. (2011) Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains J. Mol. Biol. 408, 335-355
    • (2011) J. Mol. Biol. , vol.408 , pp. 335-355
    • Khazanov, N.1    Levy, Y.2
  • 53
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi, C., Nymeyer, H., and Onuchic, J. N. (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298, 937-953
    • (2000) J. Mol. Biol. , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 54
    • 63449129633 scopus 로고    scopus 로고
    • Insights from coarse-grained go models for protein folding and dynamics
    • Hills, R. D. and Brooks, C. L. (2009) Insights from coarse-grained go models for protein folding and dynamics Int. J. Mol. Sci. 10, 889-905
    • (2009) Int. J. Mol. Sci. , vol.10 , pp. 889-905
    • Hills, R.D.1    Brooks, C.L.2
  • 55
    • 0027216519 scopus 로고
    • The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures
    • Paull, T. T., Haykinson, M. J., and Johnson, R. C. (1993) The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures Genes Dev. 7, 1521-1534
    • (1993) Genes Dev. , vol.7 , pp. 1521-1534
    • Paull, T.T.1    Haykinson, M.J.2    Johnson, R.C.3
  • 56
    • 0035281548 scopus 로고    scopus 로고
    • HMG1 and 2, and related 'architectural' DNA-binding proteins
    • Thomas, J. O. and Travers, A. A. (2001) HMG1 and 2, and related 'architectural' DNA-binding proteins Trends Biochem. Sci. 26, 167-174
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 167-174
    • Thomas, J.O.1    Travers, A.A.2
  • 57
    • 84881652478 scopus 로고    scopus 로고
    • Sliding dynamics along DNA: A molecular perspective
    • in, Vol. pp, Royal Society of Chemistry, London. - 262
    • Marcovitz, A. and Levy, Y. (2012) Sliding dynamics along DNA: a molecular perspective, in Innovations in Biomolecular Modeling and Simulation, Vol. 24, pp 237-262, Royal Society of Chemistry, London.
    • (2012) Innovations in Biomolecular Modeling and Simulation , vol.24 , pp. 237
    • Marcovitz, A.1    Levy, Y.2
  • 60
    • 0032530311 scopus 로고    scopus 로고
    • Crystal structure of restriction endonuclease Bg/I bound to its interrupted DNA recognition sequence
    • Newman, M., Lunnen, K., Wilson, G., Greci, J., Schildkraut, I., and Phillips, S. E. V. (1998) Crystal structure of restriction endonuclease Bg/I bound to its interrupted DNA recognition sequence EMBO J. 17, 5466-5476
    • (1998) EMBO J. , vol.17 , pp. 5466-5476
    • Newman, M.1    Lunnen, K.2    Wilson, G.3    Greci, J.4    Schildkraut, I.5    Phillips, S.E.V.6
  • 61
    • 0033634983 scopus 로고    scopus 로고
    • Structure of BamHI bound to nonspecific DNA: A model for DNA sliding
    • Viadiu, H. and Aggarwal, A. K. (2000) Structure of BamHI bound to nonspecific DNA: A model for DNA sliding Mol. Cell 5, 889-895
    • (2000) Mol. Cell , vol.5 , pp. 889-895
    • Viadiu, H.1    Aggarwal, A.K.2
  • 62
    • 0032485391 scopus 로고    scopus 로고
    • Structure of the DNA binding domains from NFAT, Fos and Jun bound specifically to DNA
    • Chen, L., Glover, J. N. M., Hogan, P. G., Rao, A., and Harrison, S. C. (1998) Structure of the DNA binding domains from NFAT, Fos and Jun bound specifically to DNA Nature 392, 42-48
    • (1998) Nature , vol.392 , pp. 42-48
    • Chen, L.1    Glover, J.N.M.2    Hogan, P.G.3    Rao, A.4    Harrison, S.C.5
  • 63
    • 37849019258 scopus 로고    scopus 로고
    • Crystal structure of E47 neuroD1/Beta2 bHLH domain DNA complex: Heterodimer selectivity and DNA recognition
    • Longo, A., Guanga, G. P., and Rose, R. B. (2008) Crystal structure of E47 neuroD1/Beta2 bHLH domain DNA complex: Heterodimer selectivity and DNA recognition Biochemistry 47, 218-229
    • (2008) Biochemistry , vol.47 , pp. 218-229
    • Longo, A.1    Guanga, G.P.2    Rose, R.B.3
  • 64
    • 0028215362 scopus 로고
    • Crystal-structure of Myod Bhlh domain-DNA complex - Perspectives on DNA recognition and implications for transcriptional activation
    • Ma, P. C. M., Rould, M. A., Weintraub, H., and Pabot, C. O. (1994) Crystal-structure of Myod Bhlh domain-DNA complex-perspectives on DNA recognition and implications for transcriptional activation Cell 77, 451-459
    • (1994) Cell , vol.77 , pp. 451-459
    • Ma, P.C.M.1    Rould, M.A.2    Weintraub, H.3    Pabot, C.O.4
  • 65
    • 0037462459 scopus 로고    scopus 로고
    • X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors
    • Nair, S. K. and Burley, S. K. (2003) X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors Cell 112, 193-205
    • (2003) Cell , vol.112 , pp. 193-205
    • Nair, S.K.1    Burley, S.K.2
  • 66
    • 0031569798 scopus 로고    scopus 로고
    • The crystal structure of an intact human Max-DNA complex: New insights into mechanisms of transcriptional control
    • Brownlie, P., Ceska, T. A., Lamers, M., Romier, C., Stier, G., Teo, H., and Suck, D. (1997) The crystal structure of an intact human Max-DNA complex: New insights into mechanisms of transcriptional control Structure 5, 509-520
    • (1997) Structure , vol.5 , pp. 509-520
    • Brownlie, P.1    Ceska, T.A.2    Lamers, M.3    Romier, C.4    Stier, G.5    Teo, H.6    Suck, D.7
  • 68
    • 0025780755 scopus 로고
    • Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
    • Luisi, B. F., Xu, W. X., Otwinowski, Z., Freedman, L. P., Yamamoto, K. R., and Sigler, P. B. (1991) Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA Nature 352, 497-505
    • (1991) Nature , vol.352 , pp. 497-505
    • Luisi, B.F.1    Xu, W.X.2    Otwinowski, Z.3    Freedman, L.P.4    Yamamoto, K.R.5    Sigler, P.B.6
  • 69
    • 0024284650 scopus 로고
    • Recognition of a DNA operator by the repressor of Phage-434 - A view at high-resolution
    • Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M., and Harrison, S. C. (1988) Recognition of a DNA operator by the repressor of Phage-434-a view at high-resolution Science 242, 899-907
    • (1988) Science , vol.242 , pp. 899-907
    • Aggarwal, A.K.1    Rodgers, D.W.2    Drottar, M.3    Ptashne, M.4    Harrison, S.C.5
  • 70
    • 0026656038 scopus 로고
    • Crystal-structure at 1.7-Angstrom of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target
    • Hegde, R. S., Grossman, S. R., Laimins, L. A., and Sigler, P. B. (1992) Crystal-structure at 1.7-Angstrom of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target Nature 359, 505-512
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.S.1    Grossman, S.R.2    Laimins, L.A.3    Sigler, P.B.4
  • 71
    • 0033534152 scopus 로고    scopus 로고
    • Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus
    • Veeraraghavan, S., Mello, C. C., Androphy, E. J., and Baleja, J. D. (1999) Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus Biochemistry 38, 16115-16124
    • (1999) Biochemistry , vol.38 , pp. 16115-16124
    • Veeraraghavan, S.1    Mello, C.C.2    Androphy, E.J.3    Baleja, J.D.4
  • 72
    • 0034877122 scopus 로고    scopus 로고
    • Hopping, jumping and looping by restriction enzymes
    • Halford, S. E. (2001) Hopping, jumping and looping by restriction enzymes Biochem. Soc. Trans. 29, 363-373
    • (2001) Biochem. Soc. Trans. , vol.29 , pp. 363-373
    • Halford, S.E.1
  • 73
    • 0034387984 scopus 로고    scopus 로고
    • One- and three-dimensional pathways for proteins to reach specific DNA sites
    • Stanford, N. P., Szczelkun, M. D., Marko, J. F., and Halford, S. E. (2000) One- and three-dimensional pathways for proteins to reach specific DNA sites EMBO J. 19, 6546-6557
    • (2000) EMBO J. , vol.19 , pp. 6546-6557
    • Stanford, N.P.1    Szczelkun, M.D.2    Marko, J.F.3    Halford, S.E.4
  • 74
    • 4644265622 scopus 로고    scopus 로고
    • Obsatcle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding
    • Kampmann, M. (2004) Obsatcle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding J. Biol. Chem. 279, 38715-38720
    • (2004) J. Biol. Chem. , vol.279 , pp. 38715-38720
    • Kampmann, M.1
  • 75
    • 0032935393 scopus 로고    scopus 로고
    • Transition from monomeric to homodimeric DNA binding by nuclear receptors: Identification of RevErbA alpha determinants required for ROR alpha homodimer complex formation
    • Moraitis, A. N. and Giguere, V. (1999) Transition from monomeric to homodimeric DNA binding by nuclear receptors: Identification of RevErbA alpha determinants required for ROR alpha homodimer complex formation Mol. Endocrinol. 13, 431-439
    • (1999) Mol. Endocrinol. , vol.13 , pp. 431-439
    • Moraitis, A.N.1    Giguere, V.2
  • 76
    • 10844296697 scopus 로고    scopus 로고
    • Engineering the loop region of a homeodomain-leucine zipper protein promotes efficient binding to a monomeric DNA binding site
    • Tron, A. E., Welchen, E., and Gonzalez, D. H. (2004) Engineering the loop region of a homeodomain-leucine zipper protein promotes efficient binding to a monomeric DNA binding site Biochemistry 43, 15845-15851
    • (2004) Biochemistry , vol.43 , pp. 15845-15851
    • Tron, A.E.1    Welchen, E.2    Gonzalez, D.H.3
  • 77
    • 1642494891 scopus 로고    scopus 로고
    • Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site
    • Cranz, S., Berger, C., Baici, A., Jelesarov, I., and Bosshard, H. R. (2004) Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site Biochemistry 43, 718-727
    • (2004) Biochemistry , vol.43 , pp. 718-727
    • Cranz, S.1    Berger, C.2    Baici, A.3    Jelesarov, I.4    Bosshard, H.R.5
  • 78
    • 0031030809 scopus 로고    scopus 로고
    • Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA
    • Metallo, S. J. and Schepartz, A. (1997) Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA Nat. Struct. Biol. 4, 115-117
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 115-117
    • Metallo, S.J.1    Schepartz, A.2
  • 79
    • 0032549490 scopus 로고    scopus 로고
    • Diffusion-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor
    • Berger, C., Piubelli, L., Haditsch, U., and Bosshard, H. R. (1998) Diffusion-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor FEBS Lett. 425, 14-18
    • (1998) FEBS Lett. , vol.425 , pp. 14-18
    • Berger, C.1    Piubelli, L.2    Haditsch, U.3    Bosshard, H.R.4
  • 80
    • 0032516861 scopus 로고    scopus 로고
    • CAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA
    • Wu, X. L., Spiro, C., Owen, W. G., and McMurray, C. T. (1998) cAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA J. Biol. Chem. 273, 20820-20827
    • (1998) J. Biol. Chem. , vol.273 , pp. 20820-20827
    • Wu, X.L.1    Spiro, C.2    Owen, W.G.3    McMurray, C.T.4
  • 82
    • 0036412071 scopus 로고    scopus 로고
    • Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding
    • Selvaraj, S., Kono, H., and Sarai, A. (2002) Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding J. Mol. Biol. 322, 907-915
    • (2002) J. Mol. Biol. , vol.322 , pp. 907-915
    • Selvaraj, S.1    Kono, H.2    Sarai, A.3
  • 83
    • 84861324339 scopus 로고    scopus 로고
    • Extent of structural asymmetry in homodimeric proteins: Prevalence and relevance
    • Swapna, L. S., Srikeerthana, K., and Srinivasan, N. (2012) Extent of structural asymmetry in homodimeric proteins: prevalence and relevance PLoS One 7, e36688
    • (2012) PLoS One , vol.7 , pp. 36688
    • Swapna, L.S.1    Srikeerthana, K.2    Srinivasan, N.3
  • 85
    • 0029952910 scopus 로고    scopus 로고
    • Symmetry and the energy landscapes of biomolecules
    • Wolynes, P. G. (1996) Symmetry and the energy landscapes of biomolecules Proc. Natl. Acad. Sci. U. S. A. 93, 14249-14255
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 14249-14255
    • Wolynes, P.G.1
  • 86
    • 0029949156 scopus 로고    scopus 로고
    • Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
    • Blundell, T. L. and Srinivasan, N. (1996) Symmetry, stability, and dynamics of multidomain and multicomponent protein systems Proc. Natl. Acad. Sci. U. S. A. 93, 14243-14248
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 14243-14248
    • Blundell, T.L.1    Srinivasan, N.2
  • 87
    • 29344461522 scopus 로고    scopus 로고
    • Breaking symmetry in protein dimers: Designs and functions
    • Brown, J. H. (2006) Breaking symmetry in protein dimers: designs and functions Protein Sci. 15, 1-13
    • (2006) Protein Sci. , vol.15 , pp. 1-13
    • Brown, J.H.1
  • 88
    • 0032899753 scopus 로고    scopus 로고
    • Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein
    • King, D. A., Zhang, L., Guarente, L., and Marmorstein, R. (1999) Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein Nat. Struct. Biol. 6, 64-71
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 64-71
    • King, D.A.1    Zhang, L.2    Guarente, L.3    Marmorstein, R.4
  • 92
    • 84865714640 scopus 로고    scopus 로고
    • P53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains
    • Terakawa, T., Kenzaki, H., and Takada, S. (2012) p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains J. Am. Chem. Soc. 134, 14555-14562
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 14555
    • Terakawa, T.1    Kenzaki, H.2    Takada, S.3


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