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Crystallography in the Study of Protein-DNA Interactions

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Crystallographic Methods and Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 56))

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Abstract

Over the past few years, there has been a dramatic increase in the number of protein-DNA cocrystal structures solved at atomic resolution (Table 1; for reviews see [74–76]). This has allowed a detailed understanding of how specific proteins interact with DNA (e.g., prokaryotic repressors), but has not facilitated the formulation of a common protein-DNA recognition code, which although suggested earlier (54), now appears to be too simplistic (77). However, some general observations have emerged from these recent protein-DNA crystal structures, some of which are discussed below.

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References

  1. Jordan, S R and Pabo, C O (1988) Structure of the lambda complex at 2 5 Å resolution Details of the repressor-operator interactions. Science 242, 893–899

    CAS  Google Scholar 

  2. Jordan, S R, Whitcombe, T V., Berg, J M, Pabo, C O (1985) Systematic variation in DNA lengths yields highly ordered repressor-operator cocrystals. Science 230, 1383–1385

    CAS  Google Scholar 

  3. Beamer, L J and Pabo, C O (1992) Refined 18 Å structure of the λ repressor-operator complex. J Mol Biol 227, 177–196

    CAS  Google Scholar 

  4. Brennan, R G., Roderick, S L, Takeda, Y., and Matthews, B W. (1990) Protein-DNA conformational changes in the crystal structure of a λ cro-operator complex. Proc Natl Acad Sci USA 87, 8165–8169

    CAS  Google Scholar 

  5. Brennan, R G., Takeda, Y, Kim, J, Anderson, W F, and Matthews, B W (1986) Crystallisation of a complex of cro repressor with a 17 base-pair operator. J Mol Biol 188, 115–118

    CAS  Google Scholar 

  6. Aggarwal, A. K, Rodgers, D W, Drottar, M, Ptashne, M, and Harrison, S C (1988) Recognition of a DNA operator by the cro repressor of phage 434: a view at high resolution. Science 242, 899–907

    CAS  Google Scholar 

  7. Shimon, L. J W and Harrison, S. C (1993) The phage 434 OR2/R1-69 complex at 2 5 Å resolution. J Mol Biol 232, 826–838

    CAS  Google Scholar 

  8. Rodgers, D W and Harrison, S. C (1993) The complex between phage 434 repressor DNA-binding domain and operator site O(R)3— structural differences between consensus and non-consensus half-sites. Structure 1, 227–240

    CAS  Google Scholar 

  9. Anderson, J E, Ptashne, M, and Harrison, S C (1984) Co-crystals of the DNA-binding domain of phage 434 repressor and a synthetic 434 operator. Proc Natl Acad Sci USA 81, 1307,1308.

    CAS  Google Scholar 

  10. Anderson, J E, Ptashne, M, and Harrison, S C (1987) Structure of the repressor-operator complex of bacteriophage 434. Nature 326, 846–852

    CAS  Google Scholar 

  11. Wolberger, C and Harrison, S C (1987) Crystallisation and X-ray diffraction studies of a 434 cm-DNA complex. J Mol Biol 196, 951–954

    CAS  Google Scholar 

  12. Wolberger, C, Dong, Y-C, Ptashne, M., and Harrison, S C (1988) Structure of a phage 434 cro/DNA complex. Nature 335, 789–795

    CAS  Google Scholar 

  13. Mondragön, A. and Harrison, S. C (1991) The phage 434 cro/OR1 complex at 2 5 Å resolution. J Mol Biol 219, 321–334

    Google Scholar 

  14. Joachimiak, A, Marmorstein, R Q., Schevitz, R W, Mandecki, W., Fox, J L, and Sigler, P B. (1987) Crystals of the trp repressor-operator complex suitable for X-ray diffraction analysis. J Biol Chem 262, 4917–4921

    CAS  Google Scholar 

  15. Otwinowski, Z., Schevitz, R W., Zhang, R G., Lawson, C L Joachimiak, A, Marmorstein, R. Q., Luisi, B. F, and Sigler, P B. (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321–329

    CAS  Google Scholar 

  16. Carey, J, Combatti, N, Lewis, D. A E., and Lawson, C L. (1993) Co-crystals of Escherichia coli trp repressor bound to an alternative operator DNA sequence. J Mol Biol 234, 496–498

    CAS  Google Scholar 

  17. Pace, H. C., Ponzy, L, and Lewis M. (1990) lac repressor. Crystallisation of intact tetramer and its complexes with inducer and operator DNA. Proc Natl Acad Sci USA 87, 1870–1873

    CAS  Google Scholar 

  18. Clark, K L., Halay, E. D, Lai, E., and Burley, S K (1993) Cocrystal structure of the HNF3/forkhead DNA-recognition motif resembles histone H5. Nature 364, 412–420.

    CAS  Google Scholar 

  19. Schultz, S C, Shields, G C., and Steitz, T. A. (1990) Crystallisation of Escherichia coli catabolite gene activator protein with its DNA binding site The use of modular DNA. J Mol Biol 213, 159–166

    CAS  Google Scholar 

  20. Schultz, S C, Shields, G C, and Steitz, T A (1991) Crystal structure of a CAP-DNA complex. The DNA is bent by 90°. Science 253, 1001–1007

    CAS  Google Scholar 

  21. Wolberger, C., Pabo, C O, Vershon, A. K., and Johnson, A. D. (1991) Crystallisation and preliminary X-ray diffraction studies of a MATα2 DNA complex. J Mol Biol 217, 11–13

    CAS  Google Scholar 

  22. Wolberger, C, Vershon, A. K, Liu, B, Johnson, A D, and Pabo, C O (1991) Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain DNA interactions. Cell 67, 517–528

    CAS  Google Scholar 

  23. Liu, B., Kissinger, C R., Pabo, C. O., Martin-Blanco, E., and Korberg, T. B. (1990) Crystallisation and preliminary diffraction studies of the engraved homeodomain-DNA complex. Biochim Biophys Res Commun 171, 257–259

    CAS  Google Scholar 

  24. Kissinger, C. R., Liu, B, Martin-Blanco, E., Korberg, T B., and Pabo, C O (1990) Crystal structure of engrailed homeodomain-DNA complex at 2 8 Å resolution. a framework for understanding homeodomain-DNA interactions. Cell 63, 579–590

    CAS  Google Scholar 

  25. Pavletich, N P and Pabo, C O. (1991) Zinc-finger-DNA recognition crystal structure of a Zif268-DNA complex at 2 1 Å. Science 252, 809–817

    CAS  Google Scholar 

  26. Marmorstein, R, Carey, M., Ptashne, M. Harrison, S. C (1992) DNA recognition by GAL4 Structure of a protein-DNA complex. Nature 356, 408–414

    CAS  Google Scholar 

  27. Fairall, L., Schwabe, J W. R., Chapman, L., Finch, J. T, and Rhodes, D (1993) The crystal structure of a two Zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature 366, 483–487.

    CAS  Google Scholar 

  28. Pavletlch, N P. and Pabo, C. O. (1993) Crystal structure of a five-finger GLI-DNA complex New perspectives on Zinc fingers. Science 261, 1701–1707

    Google Scholar 

  29. Luisi, B F, Xu, W. X, Otwinowskt, 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

    CAS  Google Scholar 

  30. Schwabe, J. W. R, Chapman, L., Finch, T., and Rhodes, D. (1993) The crystal structure of the estrogen receptor DNA-binding domain bound to DNA How receptors discriminate between their response elements. Cell 75, 567–578.

    CAS  Google Scholar 

  31. Somers, W S and Phillips, S. E V. (1992) Crystal structure of the met repressor operator complex at 2 8 Å resolution reveals DNA recognition by B-strands. Nature 359, 387–393

    CAS  Google Scholar 

  32. 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

    CAS  Google Scholar 

  33. Kim, Y., Geiger, J. H, Hahn, S., and Sigler, P B (1993) Crystal structure of a yeast TBP/ TATA-box complex. Nature 365, 512–520

    CAS  Google Scholar 

  34. Kim, J, Nikolov, D B., and Burley, S K. (1993) Co-crystal structure of TBP recognising the minor groove of a TATA element. Nature 365, 520–527

    CAS  Google Scholar 

  35. Ferré-D’Amaré, A. R, Prendegast, G C., Ziff, E B., and Burley, S K (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38–45

    Google Scholar 

  36. Ellenberger, T E., Brandl, C J, Struhl, K, and Harrison, S C (1992) GCN4 Basic region leucine zipper binds DNA as a dimer of uninterrupted a-helices Crystal structure of the protein-DNA complex. Cell 71, 1223–1237

    CAS  Google Scholar 

  37. Ma, P C M, Rould, M A, Weintraub, H, and Pabo, C O (1994) Crystal-structure of MyoD bHLH domain-DNA complex—Perspectives on DNA recognition and implications for transcriptional activation. Cell 77, 451–459

    CAS  Google Scholar 

  38. Hegde, R S, Grossman, S. R, Laimins, L A., and Sigler, P B (1992) Structure of the bovine papillomavirus E2 DNA-binding domain bound to its target DNA. Nature 359, 505–512

    CAS  Google Scholar 

  39. Klemm, J D, Rould, M A., Aurora, R, Herr, W., and Pabo, C O. (1994) Crystalstructure of the Oct-1 Pou domain bound to an octamer site-DNA recognition with tethered DNA-binding modules. Cell 77, 21–32.

    CAS  Google Scholar 

  40. Jacob-Molina, A, Clark, A D, Jr, Willliams, R L, Nanni, R G, Clark, P, Ferris, A L, Hughes, S H., and Arnold, E. (1991) Crystals of a ternary complex of human immunodefficiency virus type 1 reverse transcriptase with a monoclonal antibody Fab fragment and double-stranded DNA diffract X-rays to 3 5 Å resolution. Proc Natl. Acad Sci USA 88, 10,895–10,899

    Google Scholar 

  41. Arnold, E, Jacob-Molina, A, Nanni, R G, Williams, R L, Lu, X, Ding, J, Clark, A D Jr, Zhang, A, Ferris, A L, Clark, P, Hizi, H, and Hughes, S H. (1992) Structure of HIV-1 reverse transcriptase/DNA complex at 7 Å resolution showing active site locations. Nature 357, 85–89.

    CAS  Google Scholar 

  42. Klimasauskus, S., Kumar, S, Roberts, R J., and Cheng, X (1994) Hhal methytransferase flips its target base out of the DNA helix. Cell 76, 357–369

    Google Scholar 

  43. Feng, J.-A, Simon, M., Mack, D P., Dervan, P. B., Johnson, R C., and Dickerson, R E (1993) Crystallisation and preliminary X-ray analysis of the DNA biding domain of the Hin recombinase with its DNA binding site. J Mol Biol 232, 982–986.

    CAS  Google Scholar 

  44. Lahm, A and Suck, D (1991) DNase λ-induced DNA conformation 2.0 Å of a DNase I octamer complex. J Mol Biol 221, 645–667

    Google Scholar 

  45. Suck, D, Lahm, A, and Oefner, C (1988) Structure refined to 2 0 Å of a nicked DNA octanucleotide complex with DNAse I. Nature 332, 464–468

    CAS  Google Scholar 

  46. Weston, S A, Lahm, A., and Suck, D (1992) X-ray structure of DNase l-d(GGTATACC)2 complex at 2.3 Å resolution. J Mol Biol 226, 1237–1256

    CAS  Google Scholar 

  47. Young, T-S., Modrich, P, Beth, A, Jay, E, and Kim, S-H (1981) Preliminary X-ray diffraction studies of EcoRI restriction endonuclease-DNA complex. J Mol Biol 145, 607–610

    CAS  Google Scholar 

  48. Grable, J, Frederick, C. A, Samudzi, C., Jen-Jacobsen, L., Lesser, D., Greene, P, Boyer, H W, Itakura, K, and Rosenberg, J. M (1984) E coli restriction endonuclease EcoRI + DNA. J Biomol Struct Dynam. 1, 1149–1160

    CAS  Google Scholar 

  49. McClarin, J. A., Frederick, C. A., Wang, B.-C, Greene, P., Boyer, H. W, Grable, J, and Rosenberg, J M. (1986) Structure of the DNA EcoRI endonuclease recognition complex at 3 Å resolution. Science 234, 1526–1541

    CAS  Google Scholar 

  50. Kim, Y., Grable, J. C., Love, R., Greene, P. J., and Rosenberg, J M. (1990) Refinement of EcoRI endonuclease crystal structure. a revised protein chain tracing. Science 249, 1307–1309.

    CAS  Google Scholar 

  51. Freemont, P S., Friedman, J. M, Beese, L., Sanderson, M R, and Steitz, T A. (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci USA 85, 8924–8928.

    CAS  Google Scholar 

  52. Chandrasegaran, S, Smith, H. O, Amzel, M. L., and Ysern, X (1986) Preliminary X-Ray diffraction analysis of Hhall endonuclease-DNA cocrystals. Proteins Struct Funct Genetics 1, 263–266

    CAS  Google Scholar 

  53. Winkler, F. K., D’Arcy, A., Blocker, H, Frank, R, and van Boom, J H. (1991) Crystallisation of complexes of EcoRV endonuclease with cognate and non-cognate DNA fragments. J Mol Biol 217, 235–238.

    CAS  Google Scholar 

  54. Winkler, F K, Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S, Heathman, S P., Bryan, R. K., Martin, P D., Petratos, K., and Wilson, K. S (1993) The crystal structure of EcoRV endonuclease with cognate and non-cognate DNA fragments. EMBO J 12, 1781–1795

    CAS  Google Scholar 

  55. Ghosh, G., Vanduyne, G., Ghosh, S., and Sigler, P. B. (1995) Structure of NF-kappa-B P50 homodimer bound to a Kappa-B site. Nature 373, 303–310.

    CAS  Google Scholar 

  56. Muller, C W., Rey, F. A., Sodeoka, M., Verdine, G. L., and Harrison, S. C (1995) Structure of the NF-kappa-B P50 homodimer bound to DNA. Nature 373, 311–317

    CAS  Google Scholar 

  57. Glover, J N M and Harrison, S. C. (1995) Crystal-structure of the heterodimeric BZIP transcription factor C-Fos-C-Jun bound to DNA. Nature 373, 257–261

    CAS  Google Scholar 

  58. Xu, W. G, Rould, M. A, Jun, S., Desplan, C., and Pabo, C O. (1995) Crystal-structure of a paired domain-DNA complex at 2.5-Angstrom resolution reveals structural basis for Pax developmental mutations. Cell 80, 639–650

    CAS  Google Scholar 

  59. Cho, Y. J, Gorina, S., Jeffrey, P. D., and Pavletich, N. P. (1994) Crystal-structure of a P53 tumor-suppressor DNA complex-Understanding tumorigenic mutations. Science 265, 346–355

    CAS  Google Scholar 

  60. Yang, W. and Steitz, T. A (1995) Crystal-structure of the site-specific recombinase gamma-delta resolvase complexed with a 34 bp cleavage site. Cell 82, 193–207

    CAS  Google Scholar 

  61. Reinisch, K. M., Chen, L., Verdine, G. L, and Lipscomb, W. N (1994) Crystallisation and preliminary crystallographic analysis of a DNA (cytosine-5)-methyltransferase from Haemophilus-aegyptius bound covalently to DNA. J Mol Biol 238, 626–629.

    CAS  Google Scholar 

  62. Reinisch, K M., Chen, L, Verdine, G L., and Lipscomb, W N (1995) The crystal-structure of HaeIII methyltransferase covalently complexed to DNA—an extrahelical cytosine and rearranged base-pairing. Cell 82, 143–153.

    CAS  Google Scholar 

  63. Ellenberger, T., Fass, D., Arnaud, M, and Harrison, S. C. (1994) Crystal-structure of transcription factor E47-E-box recognition by a basic region helix-loop-helix dimer. Genes & Development 8, 970–980.

    CAS  Google Scholar 

  64. Feé-D’Amar, A. R, Pognonec, P., Roeder, R. G., and Burley, S. K (1994) Structure and function of the B/HLH/Z domain of USF. EMBO J 13, 180–189.

    Google Scholar 

  65. Marmorstein, R and Harrison, S. C (1994) Crystal-structure of a PPR1-DNA complex DNA recognition by proteins containing a Zn(2)Cys(6) binuclear cluster. Genes & Development 8, 2504–2512

    CAS  Google Scholar 

  66. Strzelecka, T, Newman, M, Dorner, L. F., and Knott, R, Schildkraut, I, and Aggarwal, A K. (1994) Crystallisation and preliminary X-ray analysis of restriction endonuclease BamHI-DNA complex. J Mol Biol 239, 430–432

    CAS  Google Scholar 

  67. Newman, M, Strzelecka, T, Dorner, L F, Schildkraut, I., and Aggarwal, A K (1995) Structure of BamHI endonuclease bound to DNA—Partial folding and unfolding on DNA-binding. Science 269, 656–663

    CAS  Google Scholar 

  68. Balendnan, K., Bonventre, J, Knott, R, Jack, W, Benner, J, Schildkraut, I, and Anderson, J E (1994) Expression, purification, and Crystallisation of restriction endonuclease PvuII with DNA containing its recognition site. Proteins-Structure Function and Genetics 19, 77–79

    Google Scholar 

  69. Cheng, X D, Balendiran, K, Schildkraut, I, and Anderson, J E (1995) Crystal-structure of the PvuII restriction-endonuclease. Gene 157, 139–140

    CAS  Google Scholar 

  70. Li, T., Stark, M, Johnson, A D, and Wolberger, C (1995) Crystallisation and preliminary X-ray diffraction studies of an Al/Alpha-2/DNA ternary complex. Proteins-Structure Function and Genetics 21, 161–164

    Google Scholar 

  71. Hirsch, J A and Aggarwal, A K (1995) Purification, crystallisation; and preliminary X-ray diffraction analysis of even-skipped homeodomain complexed to DNA. Proteins-Structure Function and Genetics 21, 268–271

    CAS  Google Scholar 

  72. Vassylyev, D. G, Kashiwagi, T., Mikami, Y., Ariyoshi, M, Iwai, S, Ohtsuka, E, and Morikawa, K. (1995) Crystal-structure of T4 endonuclease-V in complex with a DNA substrate. Protein Engineering 8, 64

    Google Scholar 

  73. Nikolov, D B, Chen, H, Halay, E D, Usheva, A A., Hisatake, K, Lee, D K., Roeder, R G, and Burley, S K (1995) Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377, 119–128

    CAS  Google Scholar 

  74. Brennan, R. G. and Matthews, B. W (1989) Structural basis of DNA-protein recognition. TIBS 14, 286–290

    CAS  Google Scholar 

  75. Freemont, P. S, Lane, A L, and Sanderson, M R. (1991) Structural aspects of protein-DNA recognition. Biochem J 278, 1–23

    CAS  Google Scholar 

  76. Wolberger, C. (1993) Transcrtption factor structure and DNA binding. Curr Opinion in Struct Biol 3, 3–10

    CAS  Google Scholar 

  77. Matthews, B W (1988) No code for recognition. Nature 335, 294,295

    CAS  Google Scholar 

  78. Richmond, T J., Finch, J. T, Rushton, B, Rhodes, D, and Klug, A. (1984) Structure of the nucleosome core particle at 7 Å resolution. Nature 311, 532–537

    CAS  Google Scholar 

  79. Burlingame, R. W., Love, W. E, Wang, B. C, Hamlin, R, Xuong, N H., and Moudroianakis, E N. (1985) Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3 3 Å. Science 228, 546–553

    CAS  Google Scholar 

  80. Richmond, T J, Rechsteiner, T, and Luger, K (1993) Studies of nucleosome structure. Cold Spring Harbor Symposia On Quantitative Biology 58, 265–272

    CAS  Google Scholar 

  81. McPherson, A (1982) The Preparation and Analysis of Protein Crystals Wiley, New York

    Google Scholar 

  82. McPherson, A (1985) Crystallisation of macromolecules. Methods Enzymol 114, 112–120

    CAS  Google Scholar 

  83. Walker, J. M. (ed.) (1984) Methods in Molecular Biology, vol 1 Proteins, Humana, Clifton, NJ

    Google Scholar 

  84. Scopes, R. K. (1987) protein Purtification Princitples and Practice Springer-Verlag, New York.

    Google Scholar 

  85. Ausubel, F. M., Brent R, Kingston, R. E, Moore, D D, Seidman, J G, Smith, J. A, and Struhl, K (eds) (1989) Current Protocols in Molecular Biology, vol. 2 DNA-protein Interactions, Chapter 12, Harvard University Press, Cambridge, MA.

    Google Scholar 

  86. Kadonaga, J. T and Tjian, R. (1986) Affinity purification of sequence-specific DNA binding proteins. Proc Natl. Acad. Set USA 83, 5889–5893.

    CAS  Google Scholar 

  87. Joyce, C M. and Grindley, N D F. (1983) Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of E coli. Proc Natl Acad Sci USA 80, 1830–1834

    CAS  Google Scholar 

  88. Wray, W., Boulikas, T., Wray, V. P., and Hancock, R. (1981) Silver staining of proteins in polyacrylamide gels. Anal Biochem 118, 197–203

    CAS  Google Scholar 

  89. Caruthers, M. H. (1985) Gene syntheses. DNA chemistry and its uses. Science 230, 281–285.

    CAS  Google Scholar 

  90. Applied Biosystems, Model 380/381 User Bulletin (1987) The evaluation and purification of synthetic oligonucleotides

    Google Scholar 

  91. Becker, C R., Efcavitch, J. W., Heiner, C R., and Kaiser, N F (1985) Use of a reverse phase column for the HPLC purificatton of synthetic oligonucleotides. J Chromatogr 326, 293–299

    CAS  Google Scholar 

  92. Ausubel, F M., Brent, R., Kingston, R E., Moore, D D, Seidman, J G, Smith, J A, and Struhl, K (eds) (1989) Current Protocols in Molecular Biology, vol 1 Harvard University Press, Cambridge, MA

    Google Scholar 

  93. Fasman, G D (ed) (1975) Handbook of Biochemistry and Molecular Biology, vol 1 Nucleic Acids, 589, 3rd ed, CRC, Boca Raton, FL

    Google Scholar 

  94. Felsenfeld, G. and Sandeen, G (1962) The dispersion of the hyperchromic effect in thermally induced transitions of nucleic acids. J Mol Biol 5, 587–610

    CAS  Google Scholar 

  95. Aggarwal, A K (1990) Crystallisation of DNA binding proteins with oligodeoxy-nucleotides. Methods (a companion to Methods in Enzymol) 1, 83–90

    CAS  Google Scholar 

  96. Dock-Bregeon, A C and Moras, D (1992) Crystallisation of nucleic acids and cocrystallisation of proteins and nucleic acids, in Crystallisation of Nucleic Acids and Proteins (Ducruix, A. and Giegé, C, R., eds.), IRL Press at Oxford University Press, Oxford, UK, pp 145–174

    Google Scholar 

  97. Carter, C. W., Baldwin, E. T., and Frick, L (1988) Statistical design of expertments for protein crystal growth and the use of a pre-crystallisation assay. J Crystal Growth 90, 60–73

    CAS  Google Scholar 

  98. Holbrook, S R and Kim, S H. (1985) Crystallisation and heavy-atom derivatives of polynucleotides. Methods Enzymol 114, 167–176

    CAS  Google Scholar 

  99. Laemmli, U (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685

    CAS  Google Scholar 

  100. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilising the principle of protein-dye binding. Anal Biochem 72, 248–254

    CAS  Google Scholar 

  101. Goldman, A, Ollis, D L, and Steitz, T A (1987) Crystal structure of muconate lactonising enzyme at 3 Å resolution. J Mol Biol 194, 143–153

    CAS  Google Scholar 

  102. Matthews, B. W. (1985) Determination of protein molecular weights, hydration, and packing from crystal density. Methods Enzymol 114, 176–187

    CAS  Google Scholar 

  103. Westbrook, E M (1985) Crystal density measurements using aqueous ficoll solutions. Methods Enzymol 114, 187–196

    CAS  Google Scholar 

  104. Matthews, B.W. (1968) Solvent content of protein crystals. J Mol Biol 33, 491–497

    CAS  Google Scholar 

  105. Wyckoff, H. W., Hirs, C. H. W., and Timasheff, S. N. (eds.) (1985) Diffraction methods for biological macromolecules. Methods Enzymol 115

    Google Scholar 

  106. Lattman, E D (1985) Use of rotation and translation functions. Methods Enzymol 115, 55–77.

    CAS  Google Scholar 

  107. Wang, B.-C. (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol 115, 90–112

    CAS  Google Scholar 

  108. Sussman, J L (1985) Constrained-restrained least squares (CORELS) refinement of proteins and nucleic acids. Methods Enzymol 115, 271–303.

    CAS  Google Scholar 

  109. Hendrickson, W. A. (1985) Stereochemically restrained refinement of macromolecular structures. Methods Enzymol 115, 252–270

    CAS  Google Scholar 

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Authors and Affiliations

  1. Randall Institute, King’s College, University of London, UK

    David G. Brown

  2. Protein Structure Laboratory, Imperial Cancer Research Fund, London, UK

    Paul S. Freemont

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  1. David G. Brown
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  2. Paul S. Freemont
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Editors and Affiliations

  1. National Institute for Biological Standards and Control, Potters Bar, UK

    Christopher Jones  & Barbara Mulloy  & 

  2. Department of Biophysics, King’s College, London, UK

    Mark R. Sanderson

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Brown, D.G., Freemont, P.S. (1996). Crystallography in the Study of Protein-DNA Interactions. In: Jones, C., Mulloy, B., Sanderson, M.R. (eds) Crystallographic Methods and Protocols. Methods in Molecular Biology™, vol 56. Humana Press. https://doi.org/10.1385/0-89603-259-0:293

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  • DOI: https://doi.org/10.1385/0-89603-259-0:293

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