Advertisement

NMR studies of protein-DNA recognition. The interaction of lac repressor headpiece with operator DNA

Chapter
  • 19 Downloads
Part of the Topics in Molecular and Structural Biology book series (TMSB)

Abstract

Repressors are proteins that regulate transcription by binding to DNA control regions (the so-called operators). The classic system for regulation of gene expression is the lac Operon of E. coli. Many ideas on negative control of transcription, and, indeed, the now familiar concept of an operon, were originally derived from a study of the E. coli lactose genes (Jacob and Monod, 1961). Lac repressor was also the first repressor that was isolated (Gilbert and Müller-Hill, 1966). Over the years, it has been the subject of numerous biochemical and genetic studies (for reviews see Bourgeois and Pfahl, 1976; Miller and Reznikoff, 1978; Miller, 1979; 1984). Initially, the lac repressor-lac operator system served as the principal model system for studies on specific DNA recognition by proteins. When it appeared that lac repressor refused to crystallize in a form suitable for X-ray crystallography, it lost its primacy and attention was turned to other proteins involved in gene regulation such as CAP and the phage λ repressors, cI and cro. The crystal structures of these proteins were solved in the early 1980s (McKay and Steitz, 1981; Pabo and Lewis, 1982; Anderson et al., 1981). This crystallographic work and its implications for protein-DNA recognition have been reviewed by Pabo and Sauer (1984). Later, the structure of the trp repressor was solved (Schevitz et al., 1985) and, at low resolution, that of a complex of 434 repressor and its cognate operator (Anderson et al., 1987).

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Anderson, J. E., Ptashne, M. and Harrison, S. C. (1987). Nature (London), 326, 846–849CrossRefGoogle Scholar
  2. Anderson, W., Ohlendorf, D., Takeda, Y. and Matthews, B. (1981). Nature (London), 290, 754–758CrossRefGoogle Scholar
  3. Arndt, K. T., Boschelli, F., Lu, P. and Miller, J. H. (1981). Biochemistry, 20, 6109–6118CrossRefGoogle Scholar
  4. Barkley, M. D. and Bourgeois, S. (1978). In The Operon, 2nd edn, Miller, J. H. and Reznikoff, W. S. (eds), Cold Spring Harbor Press, New York, 177–220Google Scholar
  5. Beyreuther, K., Adler, K., Geisler, N. and Klemm, A. (1973). Proc. Natl Acad. Sci. USA, 70, 3576–3580CrossRefGoogle Scholar
  6. Billeter, M., Havel, T. F. and Kuntz, I. D. (1987). J. Comp. Chem., 8, 132–141CrossRefGoogle Scholar
  7. Blumenthal, L. M. (1970). Theory and Applications of Distance Geometry, Chelsea, New YorkGoogle Scholar
  8. Boelens, R., Scheek, R. M., Dijkstra, K. and Kaptein, R. (1985). J. Magn. Reson., 62, 378–386Google Scholar
  9. Boelens, R., Scheek, R. M., van Boom, J. H. and Kaptein, R. (1987a). J. Mol. Biol., 193, 213–216CrossRefGoogle Scholar
  10. Boelens, R., Scheek, R. M., Lamerichs, R. M. J. N., de Vlieg, J., van Boom, J. H. and Kaptein, R. (1987b). In DNA-Ligand Interactions, Guschlbauer, W. and Saenger, W. (eds), Plenum, New York, 191–215CrossRefGoogle Scholar
  11. Boelens, R., Lamerichs, R. M. J. N., Rullmann, J. A. C., van Boom, J. H. and Kaptein, R. (1988). Prot. Seq. Data Anal., 1, 487–498Google Scholar
  12. Bourgeois, S. and Pfahl, M. (1976). Adv. Protein Chem., 30, 1–99CrossRefGoogle Scholar
  13. Braun, W. and Go, N. (1985). J. Mol. Biol., 186, 611–626CrossRefGoogle Scholar
  14. Buck, F., Rüterjans, H. and Beyreuther, K. (1978). FEBS Lett., 96, 335–338CrossRefGoogle Scholar
  15. Buck, F., Rüterjans, H., Kaptein, R. and Beyreuther, K. (1980). Proc. Natl Acad. Sci. USA, 77, 5145–5148CrossRefGoogle Scholar
  16. Buck, F., Hahn, K. D., Zemann, W., Rüterjans, H., Sadler, J. R., Beyreuther, K., Kaptein, R., Scheek, R. M. and Hull, W. E. (1983). Eur. J. Biochem., 132, 321–327CrossRefGoogle Scholar
  17. Caruthers, M. H. (1980). Acc. Chem. Res., 13, 155–160CrossRefGoogle Scholar
  18. Clore, G. M., Gronenborn, A. M., Brünger, A. T. and Karplus, M. (1985). J.Mol. Biol., 186, 435–455CrossRefGoogle Scholar
  19. Culard, F., Schnarr, M. and Maurizot, J. C. (1982). EMBO J., 1, 1405–1409Google Scholar
  20. De Vlieg, J., Boelens, R., Scheek, R. M., Kaptein, R. and van Gunsteren, W. F. (1986). Israel J. Chem., 27, 181–188CrossRefGoogle Scholar
  21. Ebright, R. H., Cossart, P., Gicquel-Sanzey, B. and Beckwith, J. (1984). Nature (London), 311, 232–235CrossRefGoogle Scholar
  22. Ebright, R. H. (1985). J. Biomolec. Struct. Dyn., 3, 281–297CrossRefGoogle Scholar
  23. Ernst, R. R., Bodenhausen, G. and Wokaun, A. (1987). Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Clarendon Press, OxfordGoogle Scholar
  24. Geisler, N. and Weber, K. (1977). Biochemistry, 16, 938–943CrossRefGoogle Scholar
  25. Gilbert, W., Gralla, J., Majors, J. and Maxam, A. (1976). In Protein-Ligand Interactions, Sund, H. and Blauer, G. (eds), de Gruyter, Berlin, 193–210Google Scholar
  26. Gilbert, W. and Maxam, A. (1973). Proc. Natl Acad. Sci. USA, 70, 3581–3584CrossRefGoogle Scholar
  27. Gilbert, W. and Müller-Hill, B. (1966). Proc. Natl Acad. Sci. USA, 56, 1891–1898CrossRefGoogle Scholar
  28. Hare, D. R., Wemmer, D. E., Chou, S. H., Drobny, G. H. and Reid, B. R. (1983). J. Mol. Biol., 171, 319–336CrossRefGoogle Scholar
  29. Havel, T. F., Crippen, G. M. and Kuntz, I. D. (1979). Biopolymers 18, 73–81CrossRefGoogle Scholar
  30. Havel, T. F., Kuntz, I. D. and Crippen, G. M. (1983). Bull. Math. Biol., 45, 665–720CrossRefGoogle Scholar
  31. Havel, T. F. and Wüthrich, K. (1985). J. Mol. Biol., 182 281–294CrossRefGoogle Scholar
  32. Hochschild, A., Douhan, J. and Ptashne, M. (1986). Cell, 47, 807–816CrossRefGoogle Scholar
  33. Hochschild, A. and Ptashne, M. (1986). Cell, 44, 925–933CrossRefGoogle Scholar
  34. Jacob, F. and Monod, J. (1961). J. Mol. Biol., 3, 318–353CrossRefGoogle Scholar
  35. Jarema, M. C., Lu, P. and Miller, J. H. (1981). Proc. Natl Acad. Sci. USA, 78, 2707–2711CrossRefGoogle Scholar
  36. Jeener, J., Meier, B. H., Backmann, P. and Ernst, R. R. (1979). J. Chem. Phys., 71, 4546–4553CrossRefGoogle Scholar
  37. Kania, J. and Brown, D. T. (1976). Proc. Natl Acad. Sci. USA, 73, 3529–3533CrossRefGoogle Scholar
  38. Kaptein, R. (1982). In Biological Magnetic Resonance, Berliner, L. J. and Reuben, J. (eds), Plenum, New York, Vol. 4, 145–191CrossRefGoogle Scholar
  39. Kaptein, R., Boelens, R., Scheek, R. M. and van Gunsteren, W. F. (1988). Biochemistry, 27, 5389–5395CrossRefGoogle Scholar
  40. Kaptein, R., Scheek, R. M., Zuiderweg, E. R. P., Boelens, R., Klappe, K. J. M., van Boom, J. H., Rüterjans, H. and Beyreuther, K. (1983). In Structure and Dynamics: Nucleic Acids and Proteins, Clementi, E. and Sarma, R. H. (eds), Adenine Press, New York, 209–225Google Scholar
  41. Kaptein, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. and van Gunsteren, W. F. (1985). J. Mol. Biol., 182, 179–182CrossRefGoogle Scholar
  42. Karplus, M. (1959). J. Chem. Phys., 30, 11–15CrossRefGoogle Scholar
  43. Lehming, N., Sartorius, J., Niemöller, M., Genenger, G., von Wilcken-Bergmann, B. and Müller-Hill, B. (1987). EMBO J., 6, 3145–3153Google Scholar
  44. Lu, P., Cheung, S. and Arndt, K. (1983). J. Biomol. Struct. Dyn., 1, 509–521CrossRefGoogle Scholar
  45. McCammon, J. A. and Harvey, S. C. (1987). Dynamics of Proteins and Nucleic Acids, Cambridge University Press, CambridgeCrossRefGoogle Scholar
  46. McKay, D. and Steitz, T. (1981). Nature, 290, 744–749CrossRefGoogle Scholar
  47. Matthews, B. W., Ohlendorf, D. H., Anderson, W. F. and Takeda, Y. (1982). Proc. Natl Acad. Sci. USA, 79, 1428–1452CrossRefGoogle Scholar
  48. Miller, J. H. (1979). J. Mol. Biol., 131, 249–258CrossRefGoogle Scholar
  49. Miller, J. H. (1984). J. Mol. Biol., 180, 205–212CrossRefGoogle Scholar
  50. Miller, J. H. and Reznikoff, W. (1978). The Operon, 2nd edn, Cold Spring Harbor Press, New YorkGoogle Scholar
  51. Nick, H., Arndt, H., Boschelli, F., Jarema, M. C., Lillis, M., Sadler, J., Caruthers, M. and Lu, P. (1982). Proc. Natl Acad. Sci. USA, 79, 218–222CrossRefGoogle Scholar
  52. Ogata, R. T. and Gilbert, W. (1979). J. Mol. Biol., 132, 709–728CrossRefGoogle Scholar
  53. Ohlendorf, D. H., Anderson, W. F., Fischer, R. G., Takeda, Y. and Matthews, B. (1982). Nature (London), 298, 718–723CrossRefGoogle Scholar
  54. Pabo, C. and Lewis, M. (1982). Nature (London), 298, 443–447CrossRefGoogle Scholar
  55. Pabo, C. and Sauer, R. (1984). Ann. Rev. Biochem., 53, 293–321CrossRefGoogle Scholar
  56. Ribeiro, A. A., Wemmer, D., Bray, R. P., Wade-Jardetzky, N. G. and Jardetzky, O. (1981). Biochemistry, 20, 818–823CrossRefGoogle Scholar
  57. Sadler, J. R., Sasmor, H. and Betz, J. L. (1983). Proc. Natl Acad. Sci. USA, 80, 6785–6789CrossRefGoogle Scholar
  58. Sauer, R. T., Yocum, R. R., Doolittle, R. F., Lewis, M. and Pabo, C. O. (1982). Nature (London), 298, 447–451CrossRefGoogle Scholar
  59. Scheek, R. M., Russo, N., Boelens, R. and Kaptein, R. (1983a). J. Am. Chem. Soc., 105, 2914–2916CrossRefGoogle Scholar
  60. Scheek, R. M., Zuiderweg, E. R. P., Klappe, K. J. M., van Boom, J. H., Kaptein, R., Rüterjans, H. and Beyreuther, K. (1983b). Biochemistry, 22, 228–235CrossRefGoogle Scholar
  61. Scheek, R. M., Boelens, R., Russo, N., van Boom, J. H. and Kaptein, R. (1984). Biochemistry, 23, 1371–1376CrossRefGoogle Scholar
  62. Scheek, R. M., Boelens, R., Russo, N. and Kaptein, R. (1985). In Structure and Motion: Membranes, Nucleic Acids and Proteins, Clementi, E., Corongiu, G., Sarma, M. H. and Sarma, R. H. (eds), Adenine Press, Guilderland, 485–495Google Scholar
  63. Scheek, R. M. and Kaptein, R. (1989). In NMR in Enzymology, Oppenheimer, N. J. and James, T. L. (eds), Academic Press, New York, in the pressGoogle Scholar
  64. Schevitz, R. G., Otwinowski, Z., Joachimiak, A., Lawson, C. L. and Sigler, P. B. (1985). Nature (London), 317, 782–786CrossRefGoogle Scholar
  65. Simons, A., Tils, D., von Wilcken-Bergmann, B. and Müller-Hill, B. (1984). Proc. Natl Acad. Sci. USA, 81, 1624–1628CrossRefGoogle Scholar
  66. Steitz, T. A., Ohlendorf, D. H., McKay, D. B., Anderson, W. F. and Matthews, B. W. (1982). Proc. Natl Acad. Sci. USA, 79, 3097–3100CrossRefGoogle Scholar
  67. Van Gunsteren, W. F., Kaptein, R. and Zuiderweg, E. R. P. (1983). In Nucleic Acid Conformation and Dynamics, Olson, W. K. (ed.), Report of Nato/CECAM Workshop, Orsay, 79–92Google Scholar
  68. Wagner, G., Braun, W., Havel, T. F., Schaumann, T., Go, N. and Wüthrich, K. (1987). J. Mol. Biol., 196, 611–639CrossRefGoogle Scholar
  69. Weber, I. T., McKay, D. B. M. and Steitz, T. A. (1982). Nucl. Acids. Res., 10, 5085–5102CrossRefGoogle Scholar
  70. Wharton, P. P. and Ptashne, M. (1985). Nature, 316, 601–605CrossRefGoogle Scholar
  71. Wharton, P. P. and Ptashne, M. (1987). Nature (London), 326, 888–891CrossRefGoogle Scholar
  72. Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids, Wiley, New YorkGoogle Scholar
  73. Zuiderweg, E. R. P., Scheek, R. M., Veeneman, G., Kaptein, R., Rüterjans, H. and Beyreuther, K. (1981). Nucl. Acids. Res., 9, 6553–6569CrossRefGoogle Scholar
  74. Zuiderweg, E. R. P., Kaptein, R. and Wüthrich, K. (1983a). Eur. J. Biochem., 137, 279–292CrossRefGoogle Scholar
  75. Zuiderweg, E. R. P., Kaptein, R. and Wüthrich, K. (1983b). Proc. Natl Acad. Sci. USA, 80, 5837–5841CrossRefGoogle Scholar
  76. Zuiderweg, E. R. P., Scheek, R. M. and Kaptein, R. (1985a). Biopolymers, 24, 2257–2277CrossRefGoogle Scholar
  77. Zuiderweg, E. R. P., Scheek, R. M., Boelens, R., van Gunsteren, W. F. and Kaptein, R. (1985b). Biochimie, 67, 707–715CrossRefGoogle Scholar

Copyright information

© The Contributors 1989

Authors and Affiliations

There are no affiliations available

Personalised recommendations