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Volumn 32, Issue 13, 2004, Pages 4026-4032

Quantitative modeling of DNA-protein interactions: Effects of amino acid substitutions on binding specificity of the Mnt repressor

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DINUCLEOTIDE; DNA; EARLY GROWTH RESPONSE FACTOR; HISTIDINE; MNT REPRESSOR PROTEIN; REPRESSOR PROTEIN; THYMINE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; DNA BINDING PROTEIN; PHAGE REPRESSOR PROTEINS; VIRUS PROTEIN;

EID: 3242885203     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh729     Document Type: Article
Times cited : (17)

References (29)
  • 2
    • 0036220597 scopus 로고    scopus 로고
    • Mining genome databases to identify and understand new gene regulatory systems
    • Stormo,G.D. and Tan,K. (2002) Mining genome databases to identify and understand new gene regulatory systems. Curr. Opin. Microbiol., 5, 149-153.
    • (2002) Curr. Opin. Microbiol. , vol.5 , pp. 149-153
    • Stormo, G.D.1    Tan, K.2
  • 3
    • 0035232321 scopus 로고    scopus 로고
    • One-hybrid systems for detecting protein-DNA interactions
    • Alexander,M.K., Bourns,B.D. and Zakian,V.A. (2001) One-hybrid systems for detecting protein-DNA interactions. Methods Mol. Biol., 177, 241-59.
    • (2001) Methods Mol. Biol. , vol.177 , pp. 241-259
    • Alexander, M.K.1    Bourns, B.D.2    Zakian, V.A.3
  • 5
    • 0036022523 scopus 로고    scopus 로고
    • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
    • Roulet,E., Busso,S., Camargo,A.A., Simpson,A.J., Mermod,N. and Bucher,P. (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol., 20, 831-835.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 831-835
    • Roulet, E.1    Busso, S.2    Camargo, A.A.3    Simpson, A.J.4    Mermod, N.5    Bucher, P.6
  • 6
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk,M.L., Huang,X., Choo,Y., Church,G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl Acad. Sci. USA, 98, 7158-7163.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1    Huang, X.2    Choo, Y.3    Church, G.M.4
  • 7
    • 0036013781 scopus 로고    scopus 로고
    • Is there a code for protein-DNA recognition? Probab(ilistical)ly
    • Benos,P.V., Lapedes,A.S. and Stormo,G.D. (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays, 24, 466-475.
    • (2002) Bioessays , vol.24 , pp. 466-475
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 8
    • 0024294636 scopus 로고
    • Protein-DNA interaction. No code for recognition
    • Matthews,B.W. (1988) Protein-DNA interaction. No code for recognition. Nature, 335, 294-295.
    • (1988) Nature , vol.335 , pp. 294-295
    • Matthews, B.W.1
  • 9
    • 0031042082 scopus 로고    scopus 로고
    • Physical basis of a protein-DNA recognition code
    • Choo,Y. and Klug,A. (1997) Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol., 7, 117-125.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 117-125
    • Choo, Y.1    Klug, A.2
  • 10
    • 0033524954 scopus 로고    scopus 로고
    • Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
    • Wolfe,S.A., Greisman,H.A., Ramm,E.I. and Pabo,C.O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285, 1917-1934.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1917-1934
    • Wolfe, S.A.1    Greisman, H.A.2    Ramm, E.I.3    Pabo, C.O.4
  • 11
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • Mandel-Gutfreund,Y. and Margalit,H. (1998) Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Rev., 26, 2306-2312.
    • (1998) Nucleic Acids Rev. , vol.26 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 12
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • Benos,P.V., Lapedes,A.S. and Stormo.G.D. (2002) Probabilistic code for DNA recognition by proteins of the EGR family. J. Mol. Biol., 323, 701-727.
    • (2002) J. Mol. Biol. , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 14
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • Kono,H. and Sarai,A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 35, 114-131.
    • (1999) Proteins , vol.35 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 15
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 16
    • 0035875327 scopus 로고    scopus 로고
    • Non-independence of Mnt repressor-operator interaction determined by a new Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) assay
    • Man,T.-K. and Stormo,G.D. (2001) Non-independence of Mnt repressor-operator interaction determined by a new Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) assay. Nucleic Acids Res., 29, 2471-2478.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2471-2478
    • Man, T.-K.1    Stormo, G.D.2
  • 17
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk,M., Johnson,P.L. and Church,G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Rev., 30, 1255-1261.
    • (2002) Nucleic Acids Rev. , vol.30 , pp. 1255-1261
    • Bulyk, M.1    Johnson, P.L.2    Church, G.M.3
  • 18
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • Benos,P.V., Bulyk.M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 19
    • 0027211894 scopus 로고
    • Additivity of mutant effects assessed by binomial mutagenesis
    • Gregoret,L.M. and Sauer,R.T. (1993) Additivity of mutant effects assessed by binomial mutagenesis. Proc. Natl Acad. Sci. USA, 90, 4246-4250.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 4246-4250
    • Gregoret, L.M.1    Sauer, R.T.2
  • 20
    • 0028147466 scopus 로고
    • Major groove DNA recognition by β-sheets: The ribbon-helix-helix family of gene regulatory proteins
    • Raumann,B.E., Brown,B.M. and Sauer,R.T. (1994) Major groove DNA recognition by β-sheets: the ribbon-helix-helix family of gene regulatory proteins. Curr. Opin. Struct. Biol., 4, 36-43.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 36-43
    • Raumann, B.E.1    Brown, B.M.2    Sauer, R.T.3
  • 22
    • 0028843773 scopus 로고
    • Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor
    • Raumann,B.E., Knight,K.L. and Sauer,R.T. (1995) Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor. Nature Struct. Biol., 2, 1115-1122.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 1115-1122
    • Raumann, B.E.1    Knight, K.L.2    Sauer, R.T.3
  • 23
    • 0037115830 scopus 로고    scopus 로고
    • Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections
    • Silbaq,F.S. Ruttenberg,S.E. and Stormo,G.D. (2002) Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res., 30, 5539-5548.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 5539-5548
    • Silbaq, F.S.1    Ruttenberg, S.E.2    Stormo, G.D.3
  • 24
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 26
    • 0032032780 scopus 로고    scopus 로고
    • Specificity, energy and information in DNA-protein interactions
    • Stormo,G.D. and Fields,D.S. (1998) Specificity, energy and information in DNA-protein interactions. Trends Biochem. Sci., 23, 109-113.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 109-113
    • Stormo, G.D.1    Fields, D.S.2
  • 27
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
    • Gutell,R.R., Power,A., Hertz,G.Z., Putz,E.J. and Stormo,G.D. (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-57.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 5785-6757
    • Gutell, R.R.1    Power, A.2    Hertz, G.Z.3    Putz, E.J.4    Stormo, G.D.5
  • 28
    • 0031473030 scopus 로고    scopus 로고
    • Displaying the information contents of structural RNA alignments: The structure logos
    • Gorodkin,J., Heyer,L.J., Brunak,S. and Stormo,G.D. (1997) Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., 13, 583-586.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 583-586
    • Gorodkin, J.1    Heyer, L.J.2    Brunak, S.3    Stormo, G.D.4
  • 29
    • 0028177303 scopus 로고
    • DNA recognition by beta-sheets in the Arc repressor-operator crystal structure
    • Raumann,B.E., Rould,M.A., Pabo,C.O. and Sauer,R.T. (1994) DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature, 367, 754-757.
    • (1994) Nature , vol.367 , pp. 754-757
    • Raumann, B.E.1    Rould, M.A.2    Pabo, C.O.3    Sauer, R.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.