SKN-1 domain folding and basic region monomer stabilization upon DNA binding

Genes and Development

Volumn 11, Issue 17, 1997, Pages 2227-2238

  Carroll, Adam S ^a   Gilbert, Dara E ^a   Liu, Xiaoying ^a   Cheung, Jim W ^a   Michnowicz, Jennifer E ^a   Wagner, Gerhard ^a   Ellenberger, Tom E ^a   Blackwell, T Keith ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Basic region; BZIP; DNA binding; Molten globule; SKN 1; helix

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CAENORHABDITIS ELEGANS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

CAENORHABDITIS ELEGANS;

EID: 0030886314     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.17.2227     Document Type: Article

References (68)

1. Anthony-Cahill, S.J., P.A. Benfield, R. Fairman, Z.R. Wasserman, S.L. Brenner, W.F. Stafford, C. Altenbach, W.L. Hubbell, and W.F. DeGrado. 1992. Molecular characterization of helix-loop-helix peptides. Science 255: 979-983.
2. Aurora, R., R. Srinivasan, and G.D. Rose. 1994. Rules for α-helix termination by glycine. Science 264: 1126-1130.
3. Berg, J.M. and Y. Shi. 1996. The galvanization of biology: A growing appreciation for the roles of zinc. Science 271: 1081-1085.
4. Blackwell, T.K., B. Bowerman, J. Priess, and H. Weintraub. 1994. Formation of a monomeric DNA binding domain by Skn-1 bZIP and homeodomain elements. Science 266: 621-628.
5. Boniface, J.J., D.S. Lyons, D.A. Wettstein, N.L. Allbritton, and M.M. Davis. 1996. Evidence for a conformational change in a class II major histocompatibility complex molecule occurring in the same pH range where antigen binding is enhanced. J. Exp. Med. 183: 119-126.
6. Bowerman, B., B.A. Eaton, and J.R. Priess. 1992. skn-1, a maternally expressed gene required to specify the fate of ventral blastomeres in the early C. elegans embryo. Cell 68: 1061-1075.
7. Bowerman, B., B.W. Draper, C. Mello, and J. Priess. 1993. The maternal gene skn-1 encodes a protein that is distributed unequally in early C. elegans embryos. Cell 74: 443-452.
8. Bradley, E.K., J.F. Thomason, F.E. Cohen, P.A. Kosen, and I.D. Kuntz. 1990. Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. J. Mol. Biol. 215: 607-622.
9. Carey, J. 1991. Gel retardation. Methods Enzymol 208: 103-117.
10. Cuenoud, B. and A. Schepartz. 1993a. Altered specificity of DNA-binding proteins with transition metal dimerization domains. Science 259: 510-513.
11. _. 1993b. Design of a metallo-bZIP protein that discriminates between CRE and AP1 target sites: Selection against AP1. Proc. Natl. Acad. Sci. 90: 1154-1159.
12. De Filippis, V., P. Polverino de Laureto, N. Toniutti, and A. Fontana. 1996. Acid-induced molten globule state of a fully active mutant of human interleukin-6. Biochemistry 35: 11503-11511.
13. Dixon, W., J.J. Hayes, J.R. Levin, M.F. Weidner, B.A. Dombrowski, and T.D. Tullius. 1991. Hydroxyl radical footprinting. Methods Enzymol. 208: 380-413.
14. Edelhoch, H. 1967. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6: 1948-1954.
15. Ellenberger, T.E. 1994. Getting a grip on DNA recognition: Structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains. Curr. Opin. Struct. Biol. 4: 12-21.
16. Ellenberger, T.E., C.J. Brandi, K. Struhl, and S.C. Harrison. 1992. The GCN4 BR-leucine zipper binds DNA as a dimer of uninterrupted α-helices: Crystal structure of the protein-DNA complex. Cell 71: 1223-1237.
17. Evans, L.J.A., M.L. Goble, K.A. Hales, and J.H. Lakey. 1996. Different sensitivities to acid denaturation within a family of proteins: Implications for acid unfolding and membrane translocation. Biochemistry 35: 13180-13185.
18. Gehring, W.J., Y.Q. Qian, M. Billeter, K. Furukubo-Tokunaka, A.F. Schier, D. Resendez-Perez, M. Affolter, G. Otting, and K. Wuthrich. 1994. Homeodomain-DNA recognition. Cell 78: 211-223.
19. Glover, J.N. and S.C. Harrison. 1995. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature 373: 257-261.
20. González-Mañas, J.M., J.H. Lakey, and F. Pattus. 1992. Brominated phospholipids as a tool for monitoring the membrane insertion of colicin A. Biochemistry 31: 7294-7300.
21. Harada, K., S.S. Martin, and A.D. Frankel. 1996. Selection of RNA-binding peptides in vivo. Nature 380: 175-179.
22. Harper, E.T. and G.D. Rose. 1993. Helix stop signals in proteins and peptides: The capping box. Biochemistry 32: 7605-7609.
23. Harrison, S.C. 1991. A structural taxonomy of DNA-binding proteins. Nature 353: 715-719.
24. Jennings, P.A. and P.E. Wright. 1993. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262: 892-896.
25. Johnson, P.F. 1993. Identification of C/EBP basic region residues involved in DNA sequence recognition and half-site spacing preference. Mol. Cell. Biol. 13: 6919-6930.
26. Johnson, W.C. 1988. Secondary structure of proteins through circular dichroism spectroscopy. Annu. Rev. Biophys. Biophys. Chem. 17: 145-166.
27. Kay, M.S. and R.L. Baldwin. 1996. Packing interactions in the apomyoglobin folding intermediate. Nature Struct. Biol. 3: 439-445.
28. Keller, W., P. König, and T.J. Richmond. 1995. Crystal structure of a bZIP/DNA complex at 2.2å: Determinants of DNA specific recognition. J. Mol. Biol. 254: 657-667.
29. Kissinger, C.R., B. Liu, E. Martin-Blanco, T.B. Kornberg, and C. Pabo. 1990. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions. Cell 63: 579-580.
30. König, P. and T.J. Richmond. 1993. The x-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility. J. Mol. Biol. 233: 139-154.
31. Krebs, D., B. Dahmani, S. El Antri, M. Monnot, O. Convert, O. Mauffret, F. Troalen, and S. Fermandjian. 1995. The basic subdomain of the c-Jun oncoprotein: A joint CD, Fourier-transform infrared and NMR study. Eur. J. Biochem. 231: 370-380.
32. Kuwajima, K. 1989. The molten globule as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins: Struct. Function Genet. 6: 87-103.
33. Landschulz, W.H., P.F. Johnson, E.Y. Adashi, B.J. Graves, and S.L. McKnight. 1988. Isolation of a recombinant copy of the gene encoding C/EBP. Genes & Dev. 2: 786-800.
34. Mach, H. and C.R. Middaugh. 1995. Interaction of partially structured states of acidic fibroblast growth factor with phospholipid membranes. Biochemistry 34: 9913-9920.
35. Metallo, S.J. and A. Schepartz. 1997. Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA. Nature Struct. Biol. 4: 115-117.
36. O'Neil, K.T., R.H. Hoess, and W.F. DeGrado. 1990. Design of DNA-binding peptides based on the leucine zipper motif. Science 249: 774-778.
37. O'Shea, E.K., R. Rutkowski, and P.S. Kim. 1989. Evidence that the leucine zipper is a coiled coil. Science 243: 538-542.
38. Park, C., J.L. Campbell, and W.A.I. Goddard. 1992. Protein stitchery: Design of a protein for selective binding to a specific DNA sequence. Proc. Natl. Acad. Sci. 89: 9094-9096.
39. _. 1996. Can the monomer of the leucine zipper proteins recognize the dimer binding site without dimerization? J. Am. Chem. Soc. 118: 4235-4239.
40. Patel, L., C. Abate, and T. Curran. 1990. Altered protein conformation on DNA binding by Fos and Jun. Nature 347: 572-575.
41. Pellegrini, M. and R.H. Ebright. 1996. Artificial sequence-specific DNA binding peptides: Branched-chain basic regions. J. Am. Chem. Soc. 118: 5831-5835.
42. Peng, Z.-Y., L.C. Wu, B.A. Schulman, and P.S. Kim. 1995. Does the molten globule have a native-like tertiary fold? Phil. Trans. R. Soc. Lond. B 348: 43-47.
43. Percival-Smith, A., M. Müller, M. Affolter, and W.J. Gehring. 1990. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J. 9: 3967-3974.
44. Presta, L.G. and G.D. Rose. 1988. Helix signals in proteins. Science 240: 1632-1641.
45. Ptitsyn, O. 1996. How molten is the molten globule? Nature Struct. Biol. 3: 488-490.
46. Richardson, J.S. and D.C. Richardson. 1988. Amino acid preferences for specific locations at the ends of α helices. Science 240: 1648-1652.
47. Runnels, H.A., J.C. Moore, and P.E. Jensen. 1996. A structural transition in class II major histocompatibility complex proteins at mildly acidic pH. J. Exp. Med. 183: 127-136.
48. Saudek, V., H.S. Pasley, T. Gibson, H. Gausepohl, R. Frank, and A. Pastore. 1991. Solution structure of the basic region from the transcriptional activator GCN4. Biochemistry 30: 1310-1317.
49. Scholtz, J.M. and R.L. Baldwin. 1995. α-Helix formation by peptides in water. In Peptides: Synthesis, structures, and applications (ed. B. Gotte), pp. 171-192. Academic Press, San Diego, CA.
50. Seeley, S.K., R.M. Weis, and L.K. Thompson. 1996. The cytoplasmic fragment of the aspartate receptor displays globally dynamic behavior. Biochemistry 35: 5199-5206.
51. Serrano, L. and A.R. Fersht. 1989. Capping and α-helix stability. Nature 342: 296-299.
52. Shuman, J.D., C.R. Vinson, and S.L. McKnight. 1990. Evidence of changes in protease sensitivity and subunit exchange rate on DNA binding by C/EBP. Science 249: 771-774.
53. Sklenar, V., M. Piotto, R. Leppik, and V. Saudek. 1993. Gradient-tailored water suppression of 1H-15N HSQC experiments optimized to retain full sensitivity. J. Magnet. Res. 102: 241-245.
54. Spolar, R.S. and M.T. Record, Jr. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science 263: 777-784.
55. Stanojevic, D. and G.L. Verdine. 1995. Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex. Nature Struct. Biol. 2: 450-457.
56. Studier, F.W. 1991. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J. Mol. Biol. 219: 37-44.
57. Suckow, M., B. von Wilcken-Bergmann, and B. Muller-Hill. 1993. Identification of three residues in the BRs of the bZIP proteins GCN4, C/EBP, and TAF-1 that are involved in specific DNA-binding. EMBO J. 12: 1193-1200.
58. Talanian, R., C.J. McKnight, and P. Kim. 1990. Sequence-specific DNA binding by a short peptide dimer. Science 249: 769-771.
59. Talanian, R.V., C.J. McKnight, R. Rutkowski, and P.S. Kim. 1992. Minimum length of a sequence-specific DNA binding peptide. Biochemistry 31: 6871-6875.
60. Tan, R., L. Chen, J.A. Buettner, D. Hudson, and A.D. Frankel. 1993. RNA recognition by an isolated α-helix. Cell 73: 1031-1040.
61. Tortorella, D., D. Sesardic, C.S. Dawes, and E. London. 1995. Immunochemical analysis of the structure of diptheria toxin shows all three domains undergo structural changes at low pH. J. Biol. Chem. 270: 27439-27445.
62. van der Goot, F.G., J.M. González-Mañas, J.H. Lakey, and F. Pattus. 1991. A "molten-globule" membrane-insertion intermediate of the pore-forming domain of colicin A. Nature 354: 408-410.
63. Weiss, M.A. 1990. Thermal unfolding studies of a leucine zipper domain and its specific DNA complex: Implications for scissors grip recognition. Biochemistry 29: 8020-8024.
64. Weiss, M.A., T. Ellenherger, C.R. Wobbe, J.P. Lee, S.C. Harrison, and K. Struhl. 1990. Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA. Nature 347: 575-578.
65. Wishart, D.S., B.D. Sykes, and F.M. Richards. 1992. The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31: 1647-1651.
66. Wolberger, C., A.K. Vershon, B. Liu, A.D. Johnson, and C.O. Pabo. 1991. Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 67: 517-528.
67. Wu, L.C., B.A. Schulman, Z.-Y. Peng, and P.S. Kim. 1996. Disulfide determinants of calcium-induced packing in α-lactalbumin. Biochemistry 35: 859-863.
68. Zimm, B.H. and J.K. Bragg. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31: 526-535.