메뉴 건너뛰기




Volumn 75, Issue 6, 1998, Pages 2712-2720

Visualization of trp repressor and its complexes with DNA by atomic force microscopy

Author keywords

[No Author keywords available]

Indexed keywords

DNA; REPRESSOR PROTEIN; TRYPTOPHAN;

EID: 0031795575     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77715-X     Document Type: Article
Times cited : (46)

References (51)
  • 1
    • 0031582053 scopus 로고    scopus 로고
    • Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites
    • Bareket-Samish, A., I. Cohen, and T. E. Haran. 1997. Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites. J. Mol. Biol. 267:103-117.
    • (1997) J. Mol. Biol. , vol.267 , pp. 103-117
    • Bareket-Samish, A.1    Cohen, I.2    Haran, T.E.3
  • 2
    • 0017822969 scopus 로고
    • Sequence analysis of operator constitutive mutants of the tryptophan operon of Escherichia Coli
    • Bennett, G. N., and C. Yanofsky. 1978. Sequence analysis of operator constitutive mutants of the tryptophan operon of Escherichia Coli. J. Mol. Biol. 121:179-192.
    • (1978) J. Mol. Biol. , vol.121 , pp. 179-192
    • Bennett, G.N.1    Yanofsky, C.2
  • 4
    • 0031881031 scopus 로고    scopus 로고
    • Analysis of various sequence-specific triplexes by electron and atomic force microscopies
    • Cherny, D. I., A. Fourcade, F. Svinarchuk, P. E. Nielsen, C. Malvy, and E. Detain. 1998. Analysis of various sequence-specific triplexes by electron and atomic force microscopies. Biophys. J. 74:1015-1023.
    • (1998) Biophys. J. , vol.74 , pp. 1015-1023
    • Cherny, D.I.1    Fourcade, A.2    Svinarchuk, F.3    Nielsen, P.E.4    Malvy, C.5    Detain, E.6
  • 5
    • 0027998091 scopus 로고
    • Functional selection and characterization of DNA binding sites for trp repressor of Escherichia coli
    • Czernik, P. J., D. S. Shin, and B. K. Hurlburt. 1994. Functional selection and characterization of DNA binding sites for trp repressor of Escherichia coli. J. Biol. Chem. 269:27869-27875.
    • (1994) J. Biol. Chem. , vol.269 , pp. 27869-27875
    • Czernik, P.J.1    Shin, D.S.2    Hurlburt, B.K.3
  • 6
    • 0038570200 scopus 로고
    • Comparative observations of biological specimens, especially DNA and filamentous actin molecules in atomic force, tunnelling and electron microscopy
    • Detain, E., A. Fourcade, J.-C. Poulin, A. Barbin, D. Coulaud, E. Le Cam, and E. Paris. 1992. Comparative observations of biological specimens, especially DNA and filamentous actin molecules in atomic force, tunnelling and electron microscopy. Microsc. Microanal. Microstruct. 3:457-470.
    • (1992) Microsc. Microanal. Microstruct. , vol.3 , pp. 457-470
    • Detain, E.1    Fourcade, A.2    Poulin, J.-C.3    Barbin, A.4    Coulaud, D.5    Le Cam, E.6    Paris, E.7
  • 7
    • 0030951962 scopus 로고    scopus 로고
    • High resolution imaging of native biological samples surfaces using scanning probe microscopy
    • Engel, A., C.-A. Schoenenberger, and D. J. Müller. 1997. High resolution imaging of native biological samples surfaces using scanning probe microscopy. Curr. Opin. Struct. Biol 7:279-284.
    • (1997) Curr. Opin. Struct. Biol , vol.7 , pp. 279-284
    • Engel, A.1    Schoenenberger, C.-A.2    Müller, D.J.3
  • 8
    • 0028631162 scopus 로고
    • DNA bending by Cro protein in specific and non-specific complexes: Implications for protein site recognition and specificity
    • Erie, D. A., G. Yang, H. C. Schultz, and C. Bustamante. 1994. DNA bending by Cro protein in specific and non-specific complexes: implications for protein site recognition and specificity. Science, 266: 1562-1566.
    • (1994) Science , vol.266 , pp. 1562-1566
    • Erie, D.A.1    Yang, G.2    Schultz, H.C.3    Bustamante, C.4
  • 9
    • 0026569112 scopus 로고
    • Role of protein-protein interactions in the regulation of transcription by trp repressor investigated by fluorescence spectroscopy
    • Fernando, T., and C. A. Royer. 1992. Role of protein-protein interactions in the regulation of transcription by trp repressor investigated by fluorescence spectroscopy. Biochemistry. 31:3429-3441.
    • (1992) Biochemistry , vol.31 , pp. 3429-3441
    • Fernando, T.1    Royer, C.A.2
  • 10
    • 0027984749 scopus 로고
    • Probing chromatin with the scanning force microscope
    • Fritzsche, W., A. Schaper, and T. M. Jovin. 1994. Probing chromatin with the scanning force microscope. Chromosoma. 103:231-236.
    • (1994) Chromosoma , vol.103 , pp. 231-236
    • Fritzsche, W.1    Schaper, A.2    Jovin, T.M.3
  • 11
    • 0031425683 scopus 로고    scopus 로고
    • Application of atomic force microscopy to visualization of DNA, chromatin, and chromosomes
    • Fritzsche, W., L. Takac, and E. Henderson. 1997. Application of atomic force microscopy to visualization of DNA, chromatin, and chromosomes. Crit. Rev. Eukaryotic Gene Expression. 7:231-240.
    • (1997) Crit. Rev. Eukaryotic Gene Expression , vol.7 , pp. 231-240
    • Fritzsche, W.1    Takac, L.2    Henderson, E.3
  • 12
    • 0011023559 scopus 로고
    • Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor
    • Gunsalus, R. P., and C. Yanofsky. 1980. Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc. Natl. Acad. Sci. USA. 77:7117-7121.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 7117-7121
    • Gunsalus, R.P.1    Yanofsky, C.2
  • 13
    • 0028559915 scopus 로고
    • Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope
    • Guthold, M., M. Bezanilla, D. A. Erie, B. Jenkins, H. G. Hansma, and C. Bustamante. 1994. Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope. Proc. Natl. Acad. Sci. USA. 91:12927-12931.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12927-12931
    • Guthold, M.1    Bezanilla, M.2    Erie, D.A.3    Jenkins, B.4    Hansma, H.G.5    Bustamante, C.6
  • 14
    • 0028364295 scopus 로고
    • Biomolecular imaging with the atomic force microscope
    • Hansma, H. G., and J. H. Hoh. 1994. Biomolecular imaging with the atomic force microscope. Annu. Rev. Biophys. Biomol. Struct. 23: 115-139.
    • (1994) Annu. Rev. Biophys. Biomol. Struct. , vol.23 , pp. 115-139
    • Hansma, H.G.1    Hoh, J.H.2
  • 17
    • 0031917850 scopus 로고    scopus 로고
    • Statistical and structural analysis of trp binding sites: Comparison of natural and in vitro selected sequences
    • Haran, T. E. 1998. Statistical and structural analysis of trp binding sites: comparison of natural and in vitro selected sequences. J. Biomol. Struct. Dyn. 15:689-701.
    • (1998) J. Biomol. Struct. Dyn. , vol.15 , pp. 689-701
    • Haran, T.E.1
  • 18
    • 0026652596 scopus 로고
    • The DNA target of the trp repressor
    • Haran, T. E., A. Joachimiak, and P. B. Sigler. 1992. The DNA target of the trp repressor. EMBO J. 11:3021-3030.
    • (1992) EMBO J. , vol.11 , pp. 3021-3030
    • Haran, T.E.1    Joachimiak, A.2    Sigler, P.B.3
  • 19
    • 0025957686 scopus 로고
    • Cloning, nucleotide sequence, and characterization of mtr, the structural gene for a tryptophan-specific permease of Escherichia coli. K-12
    • Heatwole, V. M., and R. L. Sommerville. 1991. Cloning, nucleotide sequence, and characterization of mtr, the structural gene for a tryptophan-specific permease of Escherichia coli. K-12. J. Bacteriol. 173: 108-115.
    • (1991) J. Bacteriol. , vol.173 , pp. 108-115
    • Heatwole, V.M.1    Sommerville, R.L.2
  • 22
    • 0023389847 scopus 로고
    • E. coli tryptophan repressor binds multiple sites within the aroH and trp operators
    • Kumamoto, A., W. Miller, and R. P. Gunsalus. 1987. E. coli tryptophan repressor binds multiple sites within the aroH and trp operators. Genes Dev. 1:556-564.
    • (1987) Genes Dev. , vol.1 , pp. 556-564
    • Kumamoto, A.1    Miller, W.2    Gunsalus, R.P.3
  • 23
    • 0027372621 scopus 로고
    • Tandem binding in crystals of a trp repressor/operator half-site complex
    • Lawson, C. L., and J. Carey. 1993. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature (Lond.). 366:178-182.
    • (1993) Nature (Lond.) , vol.366 , pp. 178-182
    • Lawson, C.L.1    Carey, J.2
  • 24
    • 0028113847 scopus 로고
    • Observation of binding and polymerization of fur repressor onto operator-containing DNA with electron and atomic force microscopes
    • Le Cam, E., D. Frechon, M. Barray, A. Fourcade, and E. Delain. 1994. Observation of binding and polymerization of Fur repressor onto operator-containing DNA with electron and atomic force microscopes. Proc. Natl. Acad. Sci. USA. 91:11816-11820.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11816-11820
    • Le Cam, E.1    Frechon, D.2    Barray, M.3    Fourcade, A.4    Delain, E.5
  • 25
    • 0027214299 scopus 로고
    • Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding
    • Le Tilly, V., and C. A. Royer. 1993. Fluorescence anisotropy assays implicate protein-protein interactions in regulating trp repressor DNA binding. Biochemistry. 32:7753-7758.
    • (1993) Biochemistry , vol.32 , pp. 7753-7758
    • Le Tilly, V.1    Royer, C.A.2
  • 26
    • 0027370156 scopus 로고
    • Dependence of trp repressor-operator affinity, stoichiometry, and apparent cooperativity on DNA sequence and size
    • Liu, Y.-C., and K. S. Matthews. 1993. Dependence of trp repressor-operator affinity, stoichiometry, and apparent cooperativity on DNA sequence and size. J. Biol. Chem. 268:23239-23249.
    • (1993) J. Biol. Chem. , vol.268 , pp. 23239-23249
    • Liu, Y.-C.1    Matthews, K.S.2
  • 28
    • 0031017249 scopus 로고    scopus 로고
    • Visualization of supercoiled DNA with atomic force microscopy in situ
    • Lyubchenko, Y. L., and L. S. Shlyakhtenko. 1997. Visualization of supercoiled DNA with atomic force microscopy in situ. Proc. Natl. Acad. Sci. USA. 94:496-501.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 496-501
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2
  • 29
    • 0030797236 scopus 로고    scopus 로고
    • Atomic force microscopic demonstration of DNA looping br GalR and HU
    • Lyubchenko, Y. L., L. S. Shlyakhtenko, T. Aki, and S. Adhya. 1997. Atomic force microscopic demonstration of DNA looping br GalR and HU. Nucleic Acids Res. 25:873-876.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 873-876
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2    Aki, T.3    Adhya, S.4
  • 31
    • 0028127919 scopus 로고
    • Structures of large T antigen at the origin of SV40 DNA replication by atomic force microscopy
    • Mastrangelo, I. A., M. Bezanilla, P. K. Hansma, P. V. C. Hough, and H. G. Hansma. 1994. Structures of large T antigen at the origin of SV40 DNA replication by atomic force microscopy. Biophys. J. 68:293-298.
    • (1994) Biophys. J. , vol.68 , pp. 293-298
    • Mastrangelo, I.A.1    Bezanilla, M.2    Hansma, P.K.3    Hough, P.V.C.4    Hansma, H.G.5
  • 32
    • 0029127492 scopus 로고
    • High-resolution atomic-force microscopy of DNA: The pitch of the double helix
    • Mou, J., D. M. Czajkowsky, Y. Zhang, and Z. Shao. 1995. High-resolution atomic-force microscopy of DNA: the pitch of the double helix. FEBS Lett. 371:279-282.
    • (1995) FEBS Lett. , vol.371 , pp. 279-282
    • Mou, J.1    Czajkowsky, D.M.2    Zhang, Y.3    Shao, Z.4
  • 34
    • 0023056195 scopus 로고
    • High-level production and rapid purification of the Escherichia coli trp repressor
    • Paluh, J. H., and C. Yanofsky. 1986. High-level production and rapid purification of the Escherichia coli trp repressor. Nucleic Acids Res. 14:7851-7860.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 7851-7860
    • Paluh, J.H.1    Yanofsky, C.2
  • 35
    • 0031592940 scopus 로고    scopus 로고
    • Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides
    • Reedstrom, R. J., M. P. Brown, A. Grillo, D. Roen, and C. A. Royer. 1997. Affinity and specificity of trp repressor-DNA interactions studied with fluorescent oligonucleotides. J. Mol. Biol. 273:572-585.
    • (1997) J. Mol. Biol. , vol.273 , pp. 572-585
    • Reedstrom, R.J.1    Brown, M.P.2    Grillo, A.3    Roen, D.4    Royer, C.A.5
  • 36
    • 0030598345 scopus 로고    scopus 로고
    • Characterization of charge change super-repressor mutants of trp repressor: Effects on oligomerization, conformation, ligation and stability
    • Reedstrom, R. J., K. S. Martin, S. Vangala, S. Mahoney, E. W. Wilker, and C. A. Royer. 1996. Characterization of charge change super-repressor mutants of trp repressor: effects on oligomerization, conformation, ligation and stability. J. Mol. Biol. 264:32-45.
    • (1996) J. Mol. Biol. , vol.264 , pp. 32-45
    • Reedstrom, R.J.1    Martin, K.S.2    Vangala, S.3    Mahoney, S.4    Wilker, E.W.5    Royer, C.A.6
  • 37
    • 0028882449 scopus 로고
    • Evidence for coupling of folding and function in trp repressor: Physical characterization of the superrepressor mutant AV77
    • Reedstrom, R. J., and C. A. Royer. 1995. Evidence for coupling of folding and function in trp repressor: physical characterization of the superrepressor mutant AV77. J. Mol. Biol. 253:741-750.
    • (1995) J. Mol. Biol. , vol.253 , pp. 741-750
    • Reedstrom, R.J.1    Royer, C.A.2
  • 39
    • 0030596081 scopus 로고    scopus 로고
    • Scanning force microscopy of DNA deposited onto mica: Equilibrium versus kinetic trapping studied by statistical polymer chain analysis
    • Rivetti, C., M. Guthold, and C. Bustamante. 1996. Scanning force microscopy of DNA deposited onto mica: equilibrium versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol. 264:919-932.
    • (1996) J. Mol. Biol. , vol.264 , pp. 919-932
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 40
    • 0345451829 scopus 로고
    • Interaction of the operator of the tryptophan operon with repressor
    • Rose, J. K., and C. Yanofsky. 1974. Interaction of the operator of the tryptophan operon with repressor. Proc. Natl. Acad. Sci. USA. 71: 3134-3138.
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 3134-3138
    • Rose, J.K.1    Yanofsky, C.2
  • 41
    • 0027992756 scopus 로고
    • The scanning force microscopy of DNA in air and in n-propanol using new spreading agents
    • Schaper, A., J. P. P. Starink, and T. M. Jovin. 1994. The scanning force microscopy of DNA in air and in n-propanol using new spreading agents. FEBS Lett. 355:91-95.
    • (1994) FEBS Lett. , vol.355 , pp. 91-95
    • Schaper, A.1    Starink, J.P.P.2    Jovin, T.M.3
  • 43
    • 0005418557 scopus 로고    scopus 로고
    • Effects of elastic and inelastic interactions on phase contrast images in tapping-mode scanning force microscopy
    • Tamayo, J., and R. Garcia. 1997. Effects of elastic and inelastic interactions on phase contrast images in tapping-mode scanning force microscopy. Appl. Phys. Lett. 16:2394-2396.
    • (1997) Appl. Phys. Lett. , vol.16 , pp. 2394-2396
    • Tamayo, J.1    Garcia, R.2
  • 44
    • 0026897003 scopus 로고
    • Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope
    • Vesenka, J., M. Guthold, C. L. Tang, D. Keller, E. Delain, and C. Bustamante. 1992. Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy 42: 1243-1249.
    • (1992) Ultramicroscopy , vol.42 , pp. 1243-1249
    • Vesenka, J.1    Guthold, M.2    Tang, C.L.3    Keller, D.4    Delain, E.5    Bustamante, C.6
  • 45
    • 0028831314 scopus 로고
    • Determination of heat-shock transcription factor 2 stoichiometry at looped DNA complexes using scanning force microscopy
    • Wyman, C., E. Grotkopp, C. Bustamante, and H. C. M. Nelson. 1995. Determination of heat-shock transcription factor 2 stoichiometry at looped DNA complexes using scanning force microscopy. EMBO J. 14:117-123.
    • (1995) EMBO J. , vol.14 , pp. 117-123
    • Wyman, C.1    Grotkopp, E.2    Bustamante, C.3    Nelson, H.C.M.4
  • 46
    • 0030894489 scopus 로고    scopus 로고
    • Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein
    • Wyman, C., I. Rombel, A. K. North, C. Bustamante, and S. Kustu. 1997. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science. 275:1658-1661.
    • (1997) Science , vol.275 , pp. 1658-1661
    • Wyman, C.1    Rombel, I.2    North, A.K.3    Bustamante, C.4    Kustu, S.5
  • 48
    • 0029106435 scopus 로고
    • Recent advances in biological atomic force microscopy
    • Yang, J., and Z. Shao. 1995. Recent advances in biological atomic force microscopy. Micron. 26:35-49.
    • (1995) Micron. , vol.26 , pp. 35-49
    • Yang, J.1    Shao, Z.2
  • 49
    • 0026559478 scopus 로고
    • Atomic force microscopy of DNA molecules
    • Yang, J., K. Takeyasu, and Z. Shao. 1992. Atomic force microscopy of DNA molecules. FEBS Lett. 301:173-176.
    • (1992) FEBS Lett. , vol.301 , pp. 173-176
    • Yang, J.1    Takeyasu, K.2    Shao, Z.3
  • 50
    • 0023256884 scopus 로고
    • The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity
    • Zhang, R. G., A. Joachimiak, C. L. Lawson, R. W. Schewitz, Z. Otwinowski, and P. B. Sigler. 1987. The crystal structure of trp aporepressor at 1.8 Å shows how binding tryptophan enhances DNA affinity. Nature (Lond.). 327:591-597.
    • (1987) Nature (Lond.). , vol.327 , pp. 591-597
    • Zhang, R.G.1    Joachimiak, A.2    Lawson, C.L.3    Schewitz, R.W.4    Otwinowski, Z.5    Sigler, P.B.6
  • 51
    • 0019382235 scopus 로고
    • Structure and regulation of aroH, the structural gene for the tryptophanrepressible 3-deoxy-D-arabino-heptulosonic acid-7-phosphate synthetase of Escherichia coli
    • Zurawski, G., R. P. Gunsalus, K. D. Brown, and C. Yanofsky. 1981. Structure and regulation of aroH, the structural gene for the tryptophanrepressible 3-deoxy-D-arabino-heptulosonic acid-7-phosphate synthetase of Escherichia coli. J. Mol. Biol. 145:47-73.
    • (1981) J. Mol. Biol. , vol.145 , pp. 47-73
    • Zurawski, G.1    Gunsalus, R.P.2    Brown, K.D.3    Yanofsky, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.