Skip to main content Accessibility help
×
×
Home

Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding

  • Thomas A. Steitz (a1)

Extract

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, the E. coli catabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKay et al. 1982; Weber & Steitz, 1987), a cro repressor from phage λ (Anderson et al. 1981), and the DNA-binding proteolytic fragment of λcI repressor protein (Pabo & Lewis, 1982) Although crystallographic studies of the E. coli lac repressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitz et al. 1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure of λcro repressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP, λcro, λcI repressor fragment, 434 repressor fragment (Anderson et al. 1987), 434 cro repressor (Wolberger et al. 1988), E. coli trp repressor (Schevitz et al. 1985), E. coli met repressor (Rafferty et al. 1989)], EcoR I restriction endonuclease (McClarin et al. 1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfull et al. 1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment of E. coli DNA polymerase I (Ollis et al. 1985) and the E. coli Hu protein (Tanaka et al., 1984)].

Copyright

References

Hide All
Abdel-Meguid, S. S., Grindley, N. D. F., Smyth Templeton, N. & Steitz, T. A. (1984). Cleavage of the site-specific recombination protein γδ resolvase: the smaller of two fragments binds DNA specifically. Proc. natn. Acad. Sci. USA 81, 20012005.
Abdel-Meguid, S. S., Murthy, H. M. K. & Steitz, T. A. (1986). Preliminary X-ray diffraction studies of the putative catalytic domain of γδ resolvase from Escherichia coli. J. biol. Chem. 261, 1593415935.
Adler, K., Beyreuther, K., Fanning, E., Geisler, N., Gronenborn, B., Klemm, A., Müller-Hill, B., Pfahl, M., Schmitz, A. (1972). How Lac repressor binds to DNA. Nature 237, 322326.
Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 99–07.
Aiba, H. (1983). Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene. Cell 32, 141149.
Aiba, H., Fujimoto, S. & Ozaki, N. (1982). Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucl. Acids Res. 10, 1345.
Aiba, H., Nakamura, T., Mitani, H. & Mori, H. (1985). Mutations that alter the allosteric nature of cAMP receptor protein of Escherichia coli. EMBO. J. 4, 33293332.
Anderson, J., Ptashne, M. & Harrison, S. C. (1984). Co-crystals of the DNA-binding domain of phage 434 repressor and a synthetic phage 434 operator. Proc. natn. Acad. Sci. USA 81, 13071311.
Anderson, J. E., Ptashne, M. & Harrison, S. C. (1985). A phage repressor-operator complex at 7 Å resolution. Nature 316, 596601.
Anderson, J. E., Ptashne, M. & Harrison, S. C. (1987). Structure of the repressor-operator complex of bacteriophage 434. Nature 326, 846852.
Anderson, W. F., Cygler, M., Vandonselaar, M., Ohlendorf, D. H., Matthews, B. W., Kim, J. & Takeda, Y. (1983). Crystallographic data for complexes of the cro repressor with DNA. J. molec. Biol. 168, 903906.
Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981). Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature 290, 754758.
Anderson, W. F., Takeda, Y., Ohlendorf, D. H. & Matthews, B. W. (1982). Proposed α-helical super-secondary structure associated with protein-DNA recognition. J. molec. Biol. 159, 745751.
Benson, N., Sugiono, P. & Yonderian, P. (1988). DNA sequence determinants of λ repressor binding in vivo. Genetics 118, 2129.
Berg, J. M. (1988). Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc. natn. Acad. Sci. USA 85, 99102.
Besse, M., Von Wilcken-Bergmann, B. & Müller-Hill, B. (1986). Synthetic lac operator mediates repression through lac repressor when introduced upstream and downstram from lac repressor. EMBO J. 5, 13771381.
Bhat, T. N., Blow, D. M. & Brick, P. (1982). Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold. J. molec. Biol. 158, 699709.
Boelens, R., Scheek, R. M., Van Boom, J. H. & Kaptein, R. (1987). Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance. J. molec. Biol. 193, 213216.
Bogenhagen, D. F., Sakonju, S. & Brown, D. D. (1980). A control region in the centre of the 5S RNA gene directs specific initiation of transcription: the 3′ border of the region. Cell 19, 2735.
Brayer, G. D. & Mcpherson, A. (1983). Refined structure of the gene 5 DNA binding protein from bacteriophage fd. J. molec. Biol. 169, 565596.
Brennan, R. G., Takeda, Y., Kim, J., Anderson, W. F. & Matthews, B. W. (1986). Crystallization of a complex of cro repressor with a 17 base-pair operator. J. molec. Biol. 188, 115118.
Brick, P., Bhat, T. N. & Blow, D. M. (1989). Structure of tyrosyl-tRNA synthetase refined at 2·3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. molec. Biol, in press.
Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallogr. A32, 832.
Brunie, S., Mellot, P., Zelwer, C., Risler, J.-L., Blanquet, S. & Fayat, G. (1987). Structure-activity relationships of methionyl-tRNA synthetase: graphics modelling and genetic engineering. J. molec. Graphics 5, 1828.
Brutlag, D., Atkinson, M. R., Setlow, P. & Kornberg, A. (1969). An active fragment of DNA polymerase produced by proteolytic cleavage. Biochem. biophys. Res. Comm. 37, 982989.
Brutlag, D. & Kornberg, A. (1972). Enzymatic synthesis of doexyribonucleic acid. J. biol. Chem. 247, 241248.
Burlingame, R. W., Love, W. E., Wang, B.-C., Hamlin, R., Xuong, N. H. & Moudrianankis, E. N. (1985). Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3·3 Å. Science 228, 546553.
Carter, C. W. & Kraut, J. (1974). A proposed model for interaction of polypeptides with RNA. Proc. natn. Acad. Sci. USA 71, 283287.
Charlier, B. M., Maurizot, J. C. & Zaccui, G. (1980). Neutron scattering studies of lac repressor. Nature (London) 286, 423425.
Church, G. M., Sussman, J. L. & Kim, S.-H. (1977). Secondary structure complementarity between DNA and proteins. Proc. natn. Acad. Sci. USA 74, 14581462.
Coll, M., Frederick, C. A., Wang, A. H.-J. & Rich, A. (1987). A bifurcated hydrogen-bonded conformation in the d(AT) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. natn. Acad. Sci. USA 84, 83858389.
Cossart, P. & Gicquel-Sanzey, B. (1982). Cloning and sequence of the crp gene of Escherichia coli K12. Nucl. Acids Res. 10, 13631378.
La Cour, T. F. M., Nyborg, J., Thirup, S. & Clark, B. F. C. (1985). Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studies by X-ray crystallography. EMBO J. 4, 23852388.
Crick, F. H. C. & Klug, A. (1975). Kinky helix. Nature 255, 530533.
De Crombrugghe, B., Busby, S. & Buc, H. (1984). Cyclic AMP receptor protein: role in transcription activation. Science 224, 831838.
Delarue, M. & Moras, D. (1989). RNA structure. In Nucleic Acids and Molecular biology, vol. 3 (ed. Eckstein, F. and Lilley, D. M. J.), pp. 182196. Springer-Verlag.
Derbyshire, V., Freemont, P. S., Sanderson, M. R., Beese, L. S., Friedman, J. M., Steitz, T. A. & Joyce, C. M. (1988). Genetic and crystallographic studies of the 3′,5′-exonucleolytic site of DNA polymerase I. Science 240, 199201.
Diakun, G. P., Fairall, L. & Klug, A. (1986). EXAFS study of the zinc-binding sites in the protein transcription factor IIIA. Nature 324, 698699.
Dickerson, R. E. (1983). Base sequence and helix structure variation in B- and A-DNA. J. molec. Biol. 166, 419441.
Dickerson, R. E. & Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. molec. Biol. 149, 761786.
Dickson, R. C., Abelson, J., Barnes, W. M. & Reznikoff, W. S. (1975). Genetic regulation: the lac control region. Science 187, 2735.
Digabriele, A. D., Sanderson, M. R. & Steitz, T. A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. natn. Acad. Sci. USA 85, 18161820.
Drew, H. R. & Travers, A. A. (1984). DNA structural variations in the E. coli tyr T promoter. Cell 37, 491502.
Ebright, R. H., Cossart, P., Gicquel-Sanzey, B. & Beckwith, J. (1984). Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature 311, 232235.
Ebright, R. H., Kolb, A., Buc, H., Kunkel, T. A., Krakow, J. S. & Beckwith, J. (1987). Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP. Proc. natn. Acad. Sci. USA 84, 60836087.
Ebright, R. H., Le Grice, S. F. J., Miller, J. P. & Krakow, J. S. (1985). Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA. J. molec. Biol. 182, 92107.
Fersht, A. (1985). Enzyme Structure and Mechanism, 2nd ed.New York: W. H. Freeman & Co.
Files, J. G. & Weber, K. (1976). Limited proteolytic digestion of lac repressor by trypsin. J. biol. Chem. 251, 33863391.
Frankel, A. D. & Pabo, C. O. (1988). Fingering too many proteins. Cell 53, 675.
Frederick, C. A., Grable, J., Melia, M., Samudzi, C., Jen-Jacobson, L., Wang, B.-C., Greene, P. J., Boyer, H. W. & Rosenberg, J. M. (1984). Kinked DNA in crystalline complex with EcoRI endonuclease. Nature 309, 327331.
Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R. & Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. natn. Acad. Sci. USA 85, 89248928.
Freemont, P. S., Ollis, D. L., Steitz, T. A. & Joyce, C. M. (1986). A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity. Proteins 1, 6673.
Friedman, D. I. (1988). Integration host factor: a protein for all reasons. Cell 55, 545554.
Garges, S. & Adhya, S. (1985). Sites of allosteric shift in the structure of the cyclic AMP receptor protein. Cell 41, 745751.
Gartenberg, M. R. & Crothers, D. M. (1988). DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature 333, 824829.
Gent, M. E., Gronenborn, A. M., Davies, T. W. & Clore, G. M. (1987). Biochem. J. 242, 645653.
Geisler, N. & Weber, K. (1977). Isolation of the amino-terminal fragment of lactose repressor necessary for DNA binding Biochemistry 16, 938943.
Grindley, N. D. F. (1983). Transposition of Tn3 and related transposons. Cell 32, 35.
Gronenborn, A. M. & Clore, G. M. (1982). Proton nuclear magnetic resonance studies on cyclic nucleotide binding to the Escherichia coli adenosine cyclic 3′,5′-phosphate receptor protein. Biochemistry 21, 40404048.
Gronenborn, A. M., Nermut, M. V., Eason, P. & Clore, G. M. (1984). Visualization of cAMP receptor protein-induced DNA kinking by electron microscopy. J. molec. Biol. 179, 751–575.
Hatfull, G. F. & Grindley, N. D. F. (1988). Genetic Recombination (ed. Smith, G. and Kucharlapati, R.), pp. 357564. Washington, D.C.: American Society for Microbiology.
Hatfull, G. F., Sanderson, M. R., Freemont, P. S., Raccuia, P. R., Grindley, N. D. F. & Steitz, T. A. (1989). Preparation of heavy atom derivatives using site-directed mutagenesis: introduction of cysteine residues into γδ resolvase. J. molec. Biol. 208, 661667.
Hecht, M. H., Nelson, H. C. M. & Sauer, R. T. (1983). Mutations in λ repressor's amino-terminal domain: implications for protein stability and DNA binding. Proc. natn. Acad. Sci. USA 80, 26762680.
Hochschild, A. & Ptashne, M. (1986 a). Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix. Cell 44, 681687.
Hochschild, A. & Ptashne, M. (1986 b). Homologous interactions of λ repressor and λ cro with the λ operator. Cell 44, 925933.
Hol, W. G. S. (1985). The role of the α-helix dipole in protein function and structure. Prog. Biophys. molec. Biol. 45, 149195.
Hooper, M. L., Russell, R. L. & Smith, J. D. (1972). Mischarging in mutant tyrosine transfer RNAs. FEBS Lett. 22, 149.
Irwin, N. & Ptashne, M. (1987). Mutants of the catabolite activator protein of Escherichia coli that are specifically deficient in the gene-activation function. Proc. natn. Acad. Sci. USA 84, 83158319.
Johnson, L. N. & Phillips, D. C. (1965). Structure of some crystalline lysozyme-inhibitor complexes determined by X-ray analysis at 6 Å resolution. Nature 206, 760763.
Jordan, R. S. & Pabo, C. O. (1988). Structure of the λ complex at 2·5 Å resolution: details of the repressor-operator interactions. Science 242, 893899.
Jordan, S. R., Whitcombe, T. V., Berg, J. M. & Pabo, C. O. (1985). Systematic variation in DNA length yields highly ordered repressor-operator co-crystals. Science 230, 1383.
Joyce, C. M., Ollis, D. L., Rush, J., Steitz, T. A., Konigsberg, W. H. & Grindley, N. D. F. (1986). In: Protein Structure, Folding and Design, UCLA Symposia on Molecular and Cellular Biology (ed. Oxender, D.), pp. 197205. New York: Liss.
Joyce, C. M. & Steitz, T. A. (1987). DNA polymerase. I. From crystal structure to function via genetics. Trends Biochem. Sci. 12, 288292.
Jurnak, F. (1985). Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. Science 230, 3236.
Kaptain, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. & Van Gunsterne, W. F. (1985). A protein structure from nuclear magnetic resonance data. J. molec. Biol. 182, 179182.
Kennard, O. & Hunter, W. N. (1989). Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies. Q. Reviews of Biophys. 22, 327379.
Kim, R., Modrich, P. & Kim, S.-H. (1984). ‘Interactive’ recognition in EcoR I restriction enzyme-DNA complex. Nucl. Acids Res. 12, 72857292.
Kim, S. H., Suddath, F. L., Quigley, G. J., McPherson, A., Sussman, J. L., Wang, A. H. J., Seeman, N. C. & Rich, A. (1974). Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185, 435440.
Klenow, H. & Henningson, I. (1970). Selective elimination of the exonuclease activity of the DNA polymerase from E. coli B by a limited proteolysis. Proc. natn. Acad. Sci. USA 65, 168.
Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z. & Steitz, T. A. (1979). A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. molec. Biol. 131, 669680.
Kolb, A. & Buc, H. (1982). Is DNA unwound by the cyclic AMP receptor protein? Nucl. Acids Res. 10, 473485.
Koo, H.-S., Wu, H.-M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501506.
Koudelka, G. B., Harrison, S. C. & Ptashne, M. (1987). Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro. Nature 326, 886888.
Koudelka, G. B., Harbury, P., Harrison, S. C. & Ptashne, M. (1988). DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc. natn. Acad. Sci. USA 85, 46334637.
Kramer, H., Niemoller, M., Ampuyal, M., Revet, B., Von Wilcken-Bergmann, B. & Müller-Hill, B. (1987). lac repressor forms loops with linear DNA carrying two suitably spaced lac operators EMBO J. 6, 14811491.
Landschultz, W. H., Johnson, P. R. & Mcknight, S. L. (1988). The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 17591764.
Laughon, A. & Scott, M. P. (1984). Sequence of a Drosophila segmentation gene; protein structure homology with DNA-binding proteins. Nature 310, 2531.
Lawson, C. L., Zhang, R.-G., Schevitz, R. W., Otwinowski, Z., Joachimiak, A. & Sigler, P. B. (1988). Flexibility of the DNA-binding domains of trp repressor. Proteins 3, 1831.
Leahy, M. C. (1982). The binding of lac repressor to DNA substituted with nucleotide analogs. Ph.D. thesis, Yale University, New Haven, Connecticut.
Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., Wright, P. E. (1989). Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635637.
Lehming, N., Sartorius, J., Niemöller, M., Genenger, G., Wilcken-Bergmann, B.V. & Müller-Hill, B. (1987). The interaction of the recognition helix of lac repressor with lac operator. EMBO J. 6, 31453153.
Lewis, M., Wang, J. & Pabo, C. (1985). Structure of the operator binding domain of lambda repressor. In: Biological Macromolecules and Assemblies, vol. 2 (ed. Jurnak, F. A. and McPherson, A.), New York: John Wiley & Sons.
Liu-Johnson, H.-N., Gartenberg, M. R. & Grothers, D. M. (1986). The DNA binding domain and bending angle of E. coli CAP protein. Cell 47, 9951005.
Lomonossoff, G. P., Butler, P. J. G. & Klug, A. (1981). Sequence-dependent variation in the conformation of DNA. J. molec. Biol. 149, 745760.
Majors, J. (1977). Dissertation (Harvard University, Cambridge, MA).
McCall, M., Brown, T., Hunter, W. N. & Kennard, O. (1986). The crystal structure of d(GGATGGGAG) form an essential part of the binding site for TFIIIA. Nature 332, 661664.
Martin, K., Huo, L. & Schleif, R. F. (1986). The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc. natn. Acad. Sci. USA 83, 36543658.
Matthews, B. W. (1988). No code for recognition. Nature 335, 294295.
Matthews, B. W., Ohlendorf, D. H., Anderson, W. F. & Takeda, Y. (1982). Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor. Proc. natn. Acad. Sci. USA 79, 1428.
McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grable, J. & Rosenberg, J. M. (1986). Structure of the DNA-ECoR I endonuclease recognition complex at 3 Å resolution. Science 234, 15261541.
Mckay, D. B., Pickover, C. A. & Steitz, T. A. (1982 a). E. coli lac repressor is elongated with its DNA binding domains located at both ends. J. molec. Biol. 156, 175183.
Mckay, D. B. & Steitz, T. A. (1981). Structure of catabolite gene activator protein at 2·9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744749.
McKay, D. B., Weber, I. T. & Steitz, T. A. (1982 b). Structure of catabolite gene activator protein at 2·9 Å resolution: Incorporation of amino-acid sequence and interactions with c-AMP. J. biol. Chem. 257, 95189524.
Miller, J. H. (1978). The lacI gene: its role in lac operon control and its use as a genetic system. In The Operon (ed. Miller, J. H. and Reznikoff, W. S.). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.
Miller, J., McLachlan, A. D. & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 16091614.
Moore, S. (1981). The Enzymes, 3rd edn, vol. 14 (ed. Boyer, P. D.), pp. 281296. New York: Academic Press.
Moras, D., Comarmond, M. B., Fischer, J., Theirry, J. C., Ebel, J. P. & Giegé, R. (1980). Crystal structure of tRNAAsp. Nature 288, 669674.
Müller-Hill, B. (1975). lac repressor and lac operator. Prog. Biophys. molec. Biol. 30, 227252.
Müller-Hill, B. (1983). Sequence homology between lac and gal repressors and three sugar-binding periplasmic proteins. Nature 302, 163164.
Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature 330, 221226.
Nelson, H. C. M. & Sauer, R. T. (1986). Interaction of mutant λ repressors with operator and non-operator DNA. J. molec. Biol. 192, 2238.
Normanly, J. & Abelson, J. (1989). tRNA Identity. Ann. Rev. Biochem. 58, 10291049.
Oefner, C. & Suck, D. (1986). Crystallographic refinement and structure of DNase I at 2 Å resolution. J. molec. Biol. 192, 605632.
Ogata, R. T. & Gilbert, W. (1979). DNA-binding site of lac repressor probed by dimethylsulfate methylation of lac operator. J. molec. Biol. 132, 709728.
Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y. & Matthews, B. W. (1982). The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature 298, 718723.
Ohlendorf, D. H., Anderson, W. F., Lewis, M., Pabo, C. O. & Matthews, B. W. (1983). Comparison of the structures of cro and λ repressor protein from bacteriophage λ. J. molec. Biol. 169, 757769.
Ohlendorf, D. H., Anderson, W. F., Takeda, Y. & Matthews, B. W. (1983). High resolution structural studies of cro repressor protein and implications for DNA recognition. J. biomol. Struct. Design 1, 553563.
Ohlendorf, D. H. & Matthews, B. W. (1983). Structural studies of protein-nucleic acid interactions. Ann. Rev. Biophys. Bioeng. 12, 259284.
Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G. & Steitz, T. A. (1985). Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313, 762766.
O'Shea, E. K., Ruttkowski, R. & Kim, P. S. (1989). Evidence that the leucine zipper is a coiled coil. Science 243, 538542.
Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmostein, R. Q., Luisi, B. F. & Sigler, P. B. (1988). Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321329.
Pabo, C. O. (1983). DNA-protein interactions. In Proceedings of The Robert A. Welch Foundation Conferences on Chemical Research, XXVII, Stereospecificity in Chemistry and Biochemistry, ch. 7, pp. 223255. Houston, Texas.
Pabo, C. O., Krovatin, W., Jeffrey, A. & Sauer, R. T. (1982). The N-terminal arms of λ repressor wrap around the operator DNA. Nature 298, 441443.
Pabo, C. O. & Lewis, M. (1982). The operator-binding domain of λ repressor: structure and DNA recognition. Nature 298, 443447.
Pabo, C. O. & Sauer, R. T. (1984). Protein-DNA recognition. Ann. Rev. Biochem. 53, 293321.
Pabo, C. O., Sauer, R. T., Sturtevant, J. M. & Ptashne, M. (1979). The λ repressor contains two domains. Proc. natn. Acad. Sci. USA 76, 16081612.
Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L., Young, E. T. & Klevit, R. E. (1988). Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241, 14891492.
Perona, J. J., Swanson, R. N., Rould, M. A., Steitz, T. A. & Söll, D. (1989). Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science 246, 11521154.
Pflugrath, J. W. & Quiocho, F. A. (1985). Sulphate sequestered in the sulphate-binding protein of Salmonella typhimurium is bound solely by hydrogen bonds. Nature 314, 257.
Phillips, S. E. V., Manfield, I., Parsons, I., Davidson, B. E., Rafferty, J. B., Somers, W. S., Margarita, D., Cohen, G. N., Saint-Girons, I. & Stockley, P. S. (1989). Cooperative tandem binding of met repressor of Escherichia coli. Nature 341, 711715.
Platt, T., Files, J. G. & Weber, K. (1973). lac repressor. J. biol. Chem. 248, 110121.
Porschke, D., Hillen, W. & Takahashi, M. (1984). The change of DNA structure by specific binding of the cAMP receptor protein from rotation diffusion and dichroism measurements. EMBO J. 3, 28732878.
Price, P. A. (1975). The essential role of Ca2+ in the activity of bovine pancreatic deoxyribonuclease. J. biol. Chem. 250, 19811986.
Ptashne, M. (1986). A Genetic Switch. Cambridge, MA: Cell Press.
Ptashne, M. (1986). Gene regulation by proteins acting nearby and at a distance. Nature 322, 697701.
Qian, Y. Q., Billeter, M., Otting, G., Müller, M., Gehring, W. J. & Wüthrich, K. (1989). The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: Comparison with prokaryotic repressors. Cell 59, 573580.
Que, B. G., Downey, K. M. & So, A. (1978). Mechanism of selective inhibition of 3′ to 5′ exonuclease activity of E. coli DNA polymerase I by nucleoside 5′-monophosphates. Biochemistry 17, 1603.
Rafferty, J. B., Somers, W. S., St.-Girons, I. & Phillips, S. E. V. (1989). Three-dimensional crystal structures of E. coli met repressor with and without corepressor. Nature 341, 705710.
Richmond, T. J., Finch, J. T., Rushton, B., Rhodes, D. & Klug, A. (1984). Structure a of the nucleosome core particle at 7 Å resolution. Nature 311, 532537.
Richmond, T. J. & Steitz, T. A. (1976). Protein-DNA interaction investigated by binding E. coli lac repressor protein to poly[d(A·U-HgX)]. J. molec. Biol. 103, 2538.
Robertus, J. D., Ladner, J. E., Finch, J. T., Rhodes, D., Brown, R. S., Clark, B. F. C. & Klug, A. (1974). Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250, 546551.
Rossman, M. G., Liljas, A., Branden, C.-I. & Banaszak, L. J. (1975). Evolutionary and structural relationships among dehydrogenases. In The Enzymes, vol II (ed. P. Boyer), pp. 61102.
Rould, M. A., Perona, J. J., Söll, D. & Steitz, T. A. (1989). Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2·8 Å resolution: implications for tRNA discrimination. Science 246, 11351142.
Rouvière-Yaniv, J. & Yaniv, M. (1979). E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell 17, 265274.
Satchwell, S. C., Drew, H. R., Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. molec. Biol. 191, 659675.
Sauer, R. T., Jordan, S. R., Pabo, C. O. (1990). λ repressor: A model system for understanding protein-DNA interactions and protein stability. Adv. Prot. Chem. (in the press).
Sauer, R. T., Pabo, C. O., Meyer, B. J., Ptashne, M. & Backman, K. C. (1979). Regulatory functions of the λ repressor reside in the amino-terminal domain. Nature 279, 396400.
Sauer, R. T., Yocum, R. R., Doolittle, R. F., Lewis, M. & Pabo, C. O. (1982). Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298, 447451.
Scheffler, I. E., Elson, E. L. & Baldwin, R. L. (1968). Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J. molec. Biol. 36, 291304.
Schevitz, R. W., Otwinowski, Z., Joanchimiak, A., Lawson, C. L. & Sigler, P. B. (1985). The three-dimensional structure of trp repressor. Nature 317, 782786.
Scholübbers, H.-G., Van Knippenberg, P. H., Baraniak, J., Stec, W. J., Morr, M. & Jastorff, B. (1983). Investigations of stimulation of lac transcription in vivo in Escherichia coli by cAMP analogues. Eur. J. Biochem. 138, 101109.
Schulman, L. H. & Abelson, J. (1988). Recent excitement in understanding transfer RNA identity. Science 240, 15911592.
Schulman, L. H. & Pelka, H. (1985). In vitro conversion of a methionine to a glutamine-acceptor tRNA. Biochemistry 24, 73097314.
Schultz, S. C., Shields, G. C. & Steitz, T. A. (1990). Crystallization of E. coli CAP with its operator DNA: the use of modular DNA. J. molec. Biol (in the press).
Seeman, N. C., Rosenberg, J. M., Rich, A. (1976). Sequence-specific recognition of double helical nucleic acids by proteins. Proc. natn. Acad. Sci. USA 73, 804808.
Seong, B. L., Lee, C.-P. & Rajbhandary, U. L. (1989). Supression of amber codons in vivo as evidence that mutants derived fro Escherichia coli initiator tRNA can act at the step of elongation in protein synthesis. J. biol. Chem. 264, 6504.
Shepherd, J. C. W., Mcginnis, W., Carrasco, A. E., De Roberts, E. M., & Gehring, W. J. (1984). Fly and frog homoeo domains show homologies with yeast mating type regulatory proteins. Nature 310, 5972, 7071.
Shimura, Y., Aono, H., Ozeki, H., Sarabhai, A., Lamform, H. & Abelson, J. (1972). Mutant tyrosine tRNA of altered amino acid specificity. FEBS Lett. 22, 144148.
Simpson, R. B. (1980). Interaction of the cAMP receptor protein with the lac promoter. Nucl. Acids Res. 8, 759.
Steitz, T. A., Beese, L., Freemont, P. S., Friedman, J. & Sanderson, M. R. (1987). Structural studies of Klenow fragment: an enzyme with two active sites. Cold Spring Harbor Symposia on Quantitative Biology, ch. 52, pp. 465471. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Steitz, T. A., Ohlendorf, D. H., McKay, D. B., Anderson, W. F. & Matthews, B. W. (1982). Structural similarity in the DNA binding domains of catabolite gene activator and cro repressor proteins. Proc. natn. Acad. Sci. USA 79, 30973100.
Steitz, T. A., Richmond, T. J., Wise, D. & Engelman, D. M. (1974). The lac repressor protein: molecular shape, subunit structure and proposed model for operator interaction based on structural studies of micro-crystals. Proc. natn. Acad. Sci. USA 72, 53.
Steitz, T. A., Stenkamp, R. E., Geisler, N., Weber, K. & Finch, J. (1979). X-ray and electron microscopic studies of crystals of core lac repressor protein. In Biomolecular Structure, Conformation, Function and Evolution (ed. Srinivasan, R.)., Oxford: Pergamon Press.
Steitz, T. A. & Weber, I. T. (1985). Structure of catabolite gene activator protein. In Biological Macromolecules and Assemblies, 2nd edn (ed. McPherson, A. and Jurnak, F.), pp. 290321. New York: John Wiley.
Steitz, T. A., Weber, I. T., Ollis, D. & Brick, P. (1983). Crystallographic studies of protein-nucleic acid interaction: catabolite gene activator protein and the large fragment of DNA polymerase I. J. biomolec. Struct. Dyn. 1, 10231037.
Suck, D., Lahm, A. & Oefner, C. (1988). Structure refined to 2 Å of a nickel DNA octanucleotide complex with DNase I. Nature 332, 6163, 465468.
Suck, D. & Oefner, C.(1986). Structure of DNase I at 2·0 Å resolution suggests a mechanism for binding to and cutting DNA. Nature 321, 620625.
Suck, D., Oefner, C. & Kabsch, W. (1984). Three-dimensional structure of bovine pancreatic DNase I at 2·5 Å resolution. EMBO J. 3, 24232430.
Sung, M. T. & Dixon, G. H. (1970). Modification of histones during spermiogenesis in trout: a molecular mechanism of altering histone binding to DNA. Proc. natn. Acad. Sci. USA 67, 16161623.
Takeda, Y., Ohlendorf, D. H., Anderson, W. F. & Matthews, B. W. (1983). DNA-binding proteins. Science 221, 10201026.
Tanaka, I., Appelt, K., Dij, K. L., White, S. W. & Wilson, K. S. (1984). 3 Å resolution structure of a protein with histone-like properties in prokaryotes. Nature 310, 376381.
Vyas, N. K., Vyas, M. N., & Quiocho, F. A. (1988). Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242, 12901295.
Wang, B.-C. (1987). Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymol. 115, 90111.
Warrant, R. W. & Kim, S. -H. (1978). α-Helix-double helix interaction shown in the structure of a protamine-transfer RNA complex and a nucleoprotamine model. Nature 271, 130135.
Warwicker, J., Engelman, B. P. & Steitz, T. A. (1987). Electrostatic calculations and model building suggest that DNA bound to CAP is sharply bent. Proteins 2, 283289.
Weber, K. & Files, J. G. (1976). Limited proteolytic digestion of lac repressor by trypsin. J. biol. Chem. 251, 33863391.
Weber, I. T. & Steitz, T. Q. (1984). A model for non-specific binding of catabolite gene activator protein to DNA. Nucl. Acids Res. 12, 84758487.
Weber, I. T. & Steitz, T. A. (1984). Model of specific complex between CAP and B-DNA suggested by electrostatic complementarity. Proc. natn. Acad. Sci. USA 81, 39733977.
Weber, I. T. & Steitz, T. A. (1987). The structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2·5 Å resolution. J. molec. Biol. 198, 311326.
Weber, I. T., McKay, D. B. & Steitz, T. A. (1982 a). Two helix DNA binding motif of CAP found in lac repressor and gal repressor Nucl. Acids Res. 10, 50855102.
Weber, I. T., Steitz, T. A., Bubis, J. & Taylor, S. S. (1987). Predicted structures of cAMP binding domains of type I and II regulatory subunits of cAMP-dependent protein kinase. Biochemistry 26, 343351.
Weber, I. T., Takio, K., Titani, K. & Steitz, T. A. (1982 b). The cAMP-binding domains of the regulatory subunit of cAMP-dependent protein kinase and the catabolite gene activator proton are homologous. Proc. natn. Acad. Sci. USA 79, 76797683.
Weber, P. C., Ollis, D. L., Debrin, W. R., Abdel-Meguid, S. S. & Steitz, T. A. (1982 c). Crystallization of resolvase, a repressor which also catalyzes site-specific DNA recombination. J. biol. Chem. 157, 689690.
Wharton, R. (1985). Thesis, Harvard University, Cambridge, MA.
Wharton, R. P. & Ptashne, M. (1985). Changing the binding specificity of a repressor by redesigning an α-helix. Nature 316, 601605.
Wharton, R. P., Brown, E. L. & Ptashne, M. (1984). Substituting an α-helix switches the sequence-specific DNA interactions of a repressor. Cell 38, 361369.
Wolberger, C., Dong, Y., Ptashne, M. & Harrison, S. C. (1988). Structure of a phage 434 cro/DNA complex. Nature 335, 789795.
Woo, N. H., Roe, B. A. & Rich, A. (1980). Three-dimensional structure of Escherichia coli initiator tRNAfMet. Nature 286, 346351.
Woodbury, C. P., Hagenbüchle, O. & Von Hippel, P. H. (1980). DNA site recognition and reduced specificity of the Ecor I endonuclease. J. biol. Chem. 255, 1153411546.
Wu, H. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509513.
Yang, C. -C. & Nash, H. W. (1989). The interaction of E. coli IHF protein with its specific-binding sites. Cell 57, 869880.
Yaniv, M., Folk, W., Berg, P. & Soll, L. (1974). A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J. molec. Biol. 86, 245260.
Yarus, M. (1988). tRNA identity: a hair of the dogma that bit us. Cell 55, 739741.
Yarus, M., Knowlton, R. & Soll, L. (1977). Aminoacylation of the ambivalent Su + 7 amber suppressor tRNA. In Nucleic Acid-Protein Recognition (ed. Vogel, H. J.) pp. 391409. New York: Academic Press.
Yoon, C., Prive, G. G., Goodsell, D. S. & Dickerson, R. E. (1988). Structure of an alternating-B DNA helix and its relationship to A-tract DNA. Proc. natn. Acad. Sci. USA 85, 63326336.
Young, T. -S., Kim, S.-H., Modrich, P., Seth, A. & Jay, E. (1981). Preliminary X-ray diffraction studies of EcoR I restriction endonuclease-DNA complex. J. molec. Biol. 145, 607610.
Zelwer, C., Risler, J. L. & Brunie, S. (1982). Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2·5 Å resolution. J. molec. Biol. 115, 6381.
Zhang, R. -G., Joachimiak, A., Lawson, C. L., Schevitz, R. W., Otwinowski, Z. & Sigler, P. G. (1987). The crystal structure of trp aporepressor at 1·8 Å shows how binding tryptophan enhances DNA affinity. Nature 327, 591597.
Zubay, G. & Doty, P. J. (1959). The isolation and properties of deoxyribonucleoprotein particles containing single nucleic acid molecules. J. molec. Biol. 7, 120.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed