메뉴 건너뛰기




Volumn 35, Issue 16, 2007, Pages 5275-5283

Correlation between binding rate constants and individual information of E. coli Fis binding sites

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CURVED DNA; FACTOR FOR INVERSION STIMULATION;

EID: 34548755108     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm471     Document Type: Article
Times cited : (30)

References (51)
  • 1
    • 0026323912 scopus 로고
    • Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA
    • Record,M.T. Jr, Ha,J.H. and Fisher,M.A. (1991) Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol., 208, 291-343.
    • (1991) Methods Enzymol , vol.208 , pp. 291-343
    • Record Jr, M.T.1    Ha, J.H.2    Fisher, M.A.3
  • 2
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • Schneider,T.D., Stormo,G.D., Gold,L. and Ehrenfeucht,A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431. http://www.ccrnp.ncifcrf.gov/~toms/paper/ schneiderl986/
    • (1986) J. Mol. Biol , vol.188 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 3
    • 0031583033 scopus 로고    scopus 로고
    • Information content of individual genetic sequences
    • Schneider,T.D. (1997) Information content of individual genetic sequences. J. Theor. Biol., 189, 427-441. http://www.ccrnp.ncifcrf.gov/~toms/paper/ri/
    • (1997) J. Theor. Biol , vol.189 , pp. 427-441
    • Schneider, T.D.1
  • 4
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon,C.E., (1948) A mathematical theory of communication. Bell System Tech. J., 27, 379-423, 623-656. http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html
    • (1948) Bell System Tech. J , vol.27
    • Shannon, C.E.1
  • 5
    • 0035850734 scopus 로고    scopus 로고
    • Anatomy of Escherichia coli ribosome binding sites
    • Shultzaberger,R.K., Bucheimer,R.E., Rudd,K.E. and Schneider,T.D. (2001) Anatomy of Escherichia coli ribosome binding sites. J. Mol. Biol., 313, 215-228. http://www.ccrnp.ncifcrf.gov/~toms/paper/ flexrbs/
    • (2001) J. Mol. Biol , vol.313 , pp. 215-228
    • Shultzaberger, R.K.1    Bucheimer, R.E.2    Rudd, K.E.3    Schneider, T.D.4
  • 6
    • 0031574384 scopus 로고    scopus 로고
    • Information analysis of Fis binding sites
    • Hengen,P.N., Bartram,S,L., Stewart,L.E. and Schneider,T.D. (1997) Information analysis of Fis binding sites. Nucleic Acids Res., 25, 4994-5002. http://www.ccrnp.ncifcrf.gov/~toms/paper/fisinfo/
    • (1997) Nucleic Acids Res , vol.25 , pp. 4994-5002
    • Hengen, P.N.1    Bartram, S.L.2    Stewart, L.E.3    Schneider, T.D.4
  • 7
    • 0031880376 scopus 로고    scopus 로고
    • Rogan,P.K., Faux,B.M. and Schneider,T.D. (1998) Information analysis of human splice site mutations. Hum. Mutat., 12, 153-171 Erratum in: Hum Mutat 1999;13(1):82. http://www.ccrnp.ncifcrf.gov/~toms/ paper/rfs/
    • Rogan,P.K., Faux,B.M. and Schneider,T.D. (1998) Information analysis of human splice site mutations. Hum. Mutat., 12, 153-171 Erratum in: Hum Mutat 1999;13(1):82. http://www.ccrnp.ncifcrf.gov/~toms/ paper/rfs/
  • 8
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins, statistical-mechanical theory and application to operators and promoters
    • Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins, statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
    • (1987) J. Mol. Biol , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 10
    • 0034615781 scopus 로고    scopus 로고
    • Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites
    • Roulet,E., Bucher,P., Schneider,R., Wingender,E., Dusserre,Y., Werner,T. and Mermod,N. (2000) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol., 297, 833-848.
    • (2000) J. Mol. Biol , vol.297 , pp. 833-848
    • Roulet, E.1    Bucher, P.2    Schneider, R.3    Wingender, E.4    Dusserre, Y.5    Werner, T.6    Mermod, N.7
  • 11
    • 0036396542 scopus 로고    scopus 로고
    • Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
    • Liu,X. and Clarke,N.D. (2002) Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol., 323 1-8.
    • (2002) J. Mol. Biol , vol.323 , pp. 1-8
    • Liu, X.1    Clarke, N.D.2
  • 13
    • 0025970050 scopus 로고
    • Theory of molecular machines. II. Energy dissipation from molecular machines
    • Schneider,T.D. (1991) Theory of molecular machines. II. Energy dissipation from molecular machines. J. Theor. Biol., 148, 125-137. http://www.ccrnp.ncifcrf.gov/~toms/paper/edmin/
    • (1991) J. Theor. Biol , vol.148 , pp. 125-137
    • Schneider, T.D.1
  • 14
    • 0023645192 scopus 로고
    • Kinetic studies on Cro repressor-operator DNA interaction
    • Kim,J.G., Takeda, Y., Matthews,B.W. and Anderson, W.F. (1987) Kinetic studies on Cro repressor-operator DNA interaction. J. Mol. Biol., 196, 149-158.
    • (1987) J. Mol. Biol , vol.196 , pp. 149-158
    • Kim, J.G.1    Takeda, Y.2    Matthews, B.W.3    Anderson, W.F.4
  • 15
    • 0038206541 scopus 로고    scopus 로고
    • Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR
    • Schaufler,L.E. and Klevit,R.E. (2003) Mechanism of DNA binding by the ADR1 zinc finger transcription factor as determined by SPR. J. Mol. Biol., 329, 931-939.
    • (2003) J. Mol. Biol , vol.329 , pp. 931-939
    • Schaufler, L.E.1    Klevit, R.E.2
  • 17
    • 0028269682 scopus 로고
    • Real-time DNA binding measurements of the ETS1 recombinant oncoproteins reveal significant kinetic differences between the p42 and p51 isoforms
    • Fisher,R.J., Fivash,M.; Casas-Finet,J., Erickson,J.W., Kondoh,A., Bladen,S.V., Fisher,C., Watson,D.K. and Papas,T. (1994) Real-time DNA binding measurements of the ETS1 recombinant oncoproteins reveal significant kinetic differences between the p42 and p51 isoforms. Protein Sci., 3, 257-266.
    • (1994) Protein Sci , vol.3 , pp. 257-266
    • Fisher, R.J.1    Fivash, M.2    Casas-Finet, J.3    Erickson, J.W.4    Kondoh, A.5    Bladen, S.V.6    Fisher, C.7    Watson, D.K.8    Papas, T.9
  • 19
    • 33845931650 scopus 로고    scopus 로고
    • Survey of the year 2005 commercial optical biosensor literature
    • Rich,R.L. and Myszka,D.G. (2006) Survey of the year 2005 commercial optical biosensor literature. J. Mol. Recognit., 19, 478-534.
    • (2006) J. Mol. Recognit , vol.19 , pp. 478-534
    • Rich, R.L.1    Myszka, D.G.2
  • 20
    • 0035082155 scopus 로고    scopus 로고
    • DNA supercoiling and transcription in Escherichia coli: The FIS connection
    • Travers,A., Schneider,R. and Muskhelishvili,G. (2001) DNA supercoiling and transcription in Escherichia coli: The FIS connection. Biochimie, 83, 213-217.
    • (2001) Biochimie , vol.83 , pp. 213-217
    • Travers, A.1    Schneider, R.2    Muskhelishvili, G.3
  • 23
    • 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. http://www.ccrnp.ncifcrf.gov/~toms/paper/logopaper/
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 24
    • 0029806673 scopus 로고    scopus 로고
    • Reading of DNA sequence logos: Prediction of major groove binding by information theory
    • Schneider,T.D. (1996) Reading of DNA sequence logos: Prediction of major groove binding by information theory. Methods Enzymol., 274, 445-455. http://www.ocrnp.ncifcrf.gov/~toms/paper/oxyr/
    • (1996) Methods Enzymol , vol.274 , pp. 445-455
    • Schneider, T.D.1
  • 25
    • 33847390219 scopus 로고    scopus 로고
    • Computational analysis of nucleic acid information defines binding sites,
    • United States Patent 5867402
    • Schneider,T.D. and Rogan,P.K. (1999) Computational analysis of nucleic acid information defines binding sites, United States Patent 5867402.
    • (1999)
    • Schneider, T.D.1    Rogan, P.K.2
  • 26
    • 0020480251 scopus 로고
    • Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli
    • Stormo,G.D., Schneider,T.D., Gold,L. and Ehrenfeucht,A. (1982) Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res., 10, 2997-3011.
    • (1982) Nucleic Acids Res , vol.10 , pp. 2997-3011
    • Stormo, G.D.1    Schneider, T.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 28
    • 0028587703 scopus 로고
    • Promoter strength prediction based on occurrence frequencies of consensus patterns
    • Weller,K. and Recknagel,R.D. (1994) Promoter strength prediction based on occurrence frequencies of consensus patterns. J. Theor. Biol., 171, 355-359.
    • (1994) J. Theor. Biol , vol.171 , pp. 355-359
    • Weller, K.1    Recknagel, R.D.2
  • 29
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for cooperatively binding factors
    • Guha Thakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • Guha Thakurta, D.1    Stormo, G.D.2
  • 30
    • 0034661690 scopus 로고    scopus 로고
    • Evolution of biological information
    • Schneider,T.D. (2000) Evolution of biological information. Nucleic Acids Res., 28, 2794-2799. http://www.ccrnp.ncifcrf.gov/~toms/ paper/ev/
    • (2000) Nucleic Acids Res , vol.28 , pp. 2794-2799
    • Schneider, T.D.1
  • 31
    • 0030658850 scopus 로고    scopus 로고
    • Schneider,T.D. (1997) Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res., 25, 4408-4415. Erratum: NAR 1998, 26(4):1135. http://www.ccrnp.ncifcrf.gov/~toms/paper/walker/
    • Schneider,T.D. (1997) Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res., 25, 4408-4415. Erratum: NAR 1998, 26(4):1135. http://www.ccrnp.ncifcrf.gov/~toms/paper/walker/
  • 32
    • 0024411476 scopus 로고
    • DNA-binding properties of the Hin recombinase
    • Glasgow,A.C., Bruist,M.F. and Simon,M.I. (1989) DNA-binding properties of the Hin recombinase. J. Biol. Chem., 264, 10072-10082.
    • (1989) J. Biol. Chem , vol.264 , pp. 10072-10082
    • Glasgow, A.C.1    Bruist, M.F.2    Simon, M.I.3
  • 33
    • 0027570442 scopus 로고    scopus 로고
    • Finkel,S.E. and Johnson,R-C. (1992) The Fis protein: It's not just for DNA inversion anymore (erratum). Mol. Microbiol., 6, 1023.
    • Finkel,S.E. and Johnson,R-C. (1992) The Fis protein: It's not just for DNA inversion anymore (erratum). Mol. Microbiol., 6, 1023.
  • 34
    • 0029932864 scopus 로고    scopus 로고
    • Identification of new Fis binding sites by DNA scission with Fis-1, 10-phenanthroline-copper(I) chimeras
    • Pan,C.Q., Johnson,R.C. and Sigman,D.S. (1996) Identification of new Fis binding sites by DNA scission with Fis-1, 10-phenanthroline-copper(I) chimeras. Biochemistry, 35, 4326-4333.
    • (1996) Biochemistry , vol.35 , pp. 4326-4333
    • Pan, C.Q.1    Johnson, R.C.2    Sigman, D.S.3
  • 35
    • 0029938543 scopus 로고    scopus 로고
    • The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis
    • Green,J., Anjum,M.F. and Guest,J.R. (1996) The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis. Mol. Microbiol., 19 1043-1055.
    • (1996) Mol. Microbiol , vol.19 , pp. 1043-1055
    • Green, J.1    Anjum, M.F.2    Guest, J.R.3
  • 36
    • 0026739435 scopus 로고
    • The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site
    • Slany,R.K. and Kersten,H. (1992) The promoter of the tgt/sec operon in Escherichia coli is preceded by an upstream activation sequence that contains a high affinity FIS binding site. Nucleic Acids Res., 20, 4193-4198.
    • (1992) Nucleic Acids Res , vol.20 , pp. 4193-4198
    • Slany, R.K.1    Kersten, H.2
  • 37
    • 0026620949 scopus 로고
    • Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli
    • Ball,C.A., Osuna,R., Ferguson,K.C. and Johnson,R.C. (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol., 174, 8043-8056.
    • (1992) J. Bacteriol , vol.174 , pp. 8043-8056
    • Ball, C.A.1    Osuna, R.2    Ferguson, K.C.3    Johnson, R.C.4
  • 38
    • 0025140817 scopus 로고
    • FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli
    • Bosch,L., Nilsson,L., Vijgenboom,E. and Verbeek,H. (1990) FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli. Biochim. Biophys. Acta, 1050, 293-301.
    • (1990) Biochim. Biophys. Acta , vol.1050 , pp. 293-301
    • Bosch, L.1    Nilsson, L.2    Vijgenboom, E.3    Verbeek, H.4
  • 39
    • 0035581124 scopus 로고    scopus 로고
    • Lyakhov,I.G., Hengen,P.N., Rubens,D. and Schneider.T.D. (2001) The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping. Nucleic Acids Res., 29, 4892-4900. http://www.ccrnp.ncifcrf.gov/~toms/paper/ repan3/
    • Lyakhov,I.G., Hengen,P.N., Rubens,D. and Schneider.T.D. (2001) The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping. Nucleic Acids Res., 29, 4892-4900. http://www.ccrnp.ncifcrf.gov/~toms/paper/ repan3/
  • 40
    • 0037035547 scopus 로고    scopus 로고
    • Subunit exchange and the role of dimer flexibility in DNA binding by the Fis protein
    • Merickel,S.K., Sanders,E.R., Vazquez-Ibar,J.L. and Johnson,R.C. (2002) Subunit exchange and the role of dimer flexibility in DNA binding by the Fis protein. Biochemistry, 41, 5788-5798.
    • (2002) Biochemistry , vol.41 , pp. 5788-5798
    • Merickel, S.K.1    Sanders, E.R.2    Vazquez-Ibar, J.L.3    Johnson, R.C.4
  • 41
    • 0032701484 scopus 로고    scopus 로고
    • Improving biosensor analysis
    • Myszka,D.G. (1999) Improving biosensor analysis. J. Mol. Recognit. 12, 279-284.
    • (1999) J. Mol. Recognit , vol.12 , pp. 279-284
    • Myszka, D.G.1
  • 42
    • 0031958764 scopus 로고    scopus 로고
    • CLAMP: A biosensor kinetic data analysis program
    • Myszka,D.G. and Morton,T.A. (1998) CLAMP: A biosensor kinetic data analysis program. Trends Biochem. Sci., 23, 149-150.
    • (1998) Trends Biochem. Sci , vol.23 , pp. 149-150
    • Myszka, D.G.1    Morton, T.A.2
  • 43
    • 0842309823 scopus 로고    scopus 로고
    • Sodium boric acid: A Tris-free, cooler conductive medium for DNA electrophoresis
    • Brody,J.R. and Kern,S.E. (2004) Sodium boric acid: A Tris-free, cooler conductive medium for DNA electrophoresis. Biotechniques, 36 214-216.
    • (2004) Biotechniques , vol.36 , pp. 214-216
    • Brody, J.R.1    Kern, S.E.2
  • 44
    • 0025939520 scopus 로고
    • The molecular structure. of wild-type and a mutant Fis protein: Relationship between mutational changes and recombinational enhancer function or DNA binding
    • Yuan,H.S., Finkel,S.E., Feng,J.-A., Kaczor-Grzeskowiak,M., Johnson,R.C. and Dickerson,R.E. (1991) The molecular structure. of wild-type and a mutant Fis protein: Relationship between mutational changes and recombinational enhancer function or DNA binding. Proc. Natl Acad. Sci. USA, 88, 9558-9562.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 9558-9562
    • Yuan, H.S.1    Finkel, S.E.2    Feng, J.-A.3    Kaczor-Grzeskowiak, M.4    Johnson, R.C.5    Dickerson, R.E.6
  • 45
    • 0032535149 scopus 로고    scopus 로고
    • Equilibrium analysis of high affinity interactions using BIACORE
    • Myszka,D.G., Jonsen,M.D. and Graves,B.J. (1998) Equilibrium analysis of high affinity interactions using BIACORE. Anal. Biochem., 265 326-330.
    • (1998) Anal. Biochem , vol.265 , pp. 326-330
    • Myszka, D.G.1    Jonsen, M.D.2    Graves, B.J.3
  • 46
    • 0032702275 scopus 로고    scopus 로고
    • Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology
    • Karlsson,R. (1999) Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIAcore technology. J. Mol. Recognit., 12, 285-292.
    • (1999) J. Mol. Recognit , vol.12 , pp. 285-292
    • Karlsson, R.1
  • 47
    • 0023947427 scopus 로고
    • Selection of DNA binding sites by regulatory proteins
    • Berg,O.G. and vonHippel,P.H. (1988) Selection of DNA binding sites by regulatory proteins. Trends Biochem. Sci., 13, 207-211.
    • (1988) Trends Biochem. Sci , vol.13 , pp. 207-211
    • Berg, O.G.1    vonHippel, P.H.2
  • 49
    • 0036529540 scopus 로고    scopus 로고
    • Structural analysis of conserved base pairs in protein-DNA complexes
    • Mirny,L.A. and Gelfand,M.S. (2002) Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res., 30, 1704-1711.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1704-1711
    • Mirny, L.A.1    Gelfand, M.S.2
  • 50
    • 84911837213 scopus 로고
    • Communication in the presence of noise
    • Shannon,C.E. (1949) Communication in the presence of noise. Proc. IRE 37, 10-21.
    • (1949) Proc. IRE , vol.37 , pp. 10-21
    • Shannon, C.E.1
  • 51
    • 19244372639 scopus 로고    scopus 로고
    • Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts
    • Pan,C.Q., Finkel,S.E., Cramton,S.E., Feng,J.A., Sigman,D.S. and Johnson,R.C. (1996) Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts. J. Mol. Biol., 264, 675-695.
    • (1996) J. Mol. Biol , vol.264 , pp. 675-695
    • Pan, C.Q.1    Finkel, S.E.2    Cramton, S.E.3    Feng, J.A.4    Sigman, D.S.5    Johnson, R.C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.