DNA-binding ability of GAGA zinc finger depends on the nature of amino acids present in the β-hairpin

Biochemistry

Volumn 46, Issue 25, 2007, Pages 7506-7513

  Dhanasekaran, Muthu ^a,c   Negi, Shigeru ^a   Imanishi, Miki ^b   Sugiura, Yukio ^a  

^a Doshisha Women's University   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH NIPER   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING ABILITY; DROSOPHILA MELANOGASTER; GAGA ZINC FINGERS; MUTANT PEPTIDES;

ABSORPTION SPECTROSCOPY; AMINES; DNA; GELS; MUTAGENESIS; PEPTIDES; ZINC;

AMINO ACIDS;

AMINO ACID; AROMATIC AMINO ACID; DNA; DNA BINDING PROTEIN; DROSOPHILA PROTEIN; GAGA FACTOR; METAL; MUTANT PROTEIN; PHENYLALANINE; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ABSORPTION SPECTROSCOPY; AMINO ACID COMPOSITION; ARTICLE; BETA CHAIN; BETA HAIRPIN; CALORIMETRY; CIRCULAR DICHROISM; CONSENSUS SEQUENCE; DROSOPHILA MELANOGASTER; GEL MOBILITY SHIFT ASSAY; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; ZINC FINGER MOTIF;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; CIRCULAR DICHROISM; DNA-BINDING PROTEINS; DROSOPHILA MELANOGASTER; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHENYLALANINE; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROPHOTOMETRY, ULTRAVIOLET; SUBSTRATE SPECIFICITY; ZINC FINGERS;

DROSOPHILA MELANOGASTER;

EID: 34250882693     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi700009q     Document Type: Article

References (38)

1. Jantz, D., Amann, B. T., Gatto, G. J., Jr., and Berg, J. M. (2004) The design of functional DNA-binding proteins based on zinc finger domains, Chem. Rev. 104, 789-799.
2. Durai, S., Mani, M., Kandavelou, K., Wu, J., Porteus, M. H., and Chandrasegaran, S. (2005) Zinc finger nucleases: Custom-designed molecular scissors for genome engineering of plant and mammalian cells, Nucleic Acids Res. 33, 5978-5990.
3. Dhanasekaran, M., Negi, S., and Sugiura, Y. (2006) Designer zinc finger proteins: Tools for creating artificial DNA-binding functional proteins, Acc. Chem. Res. 39, 45-52.
4. Jamieson, A. C., Miller, J. C., and Pabo, C. O. (2003) Drug discovery with engineered zinc-finger proteins, Nat. Rev. Drug Discovery 2, 361-368.
5. Blancafort, P., Segal, D. J., and Barbas, C. F., III (2004) Designing transcription factor architectures for drug discovery, Mol. Pharmacol. 66, 1361-1371.
6. Klug, A. (2005) Towards therapeutic applications of engineered zinc finger proteins, FEBS Lett. 579, 892-894.
7. 2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding, Proc. Natl. Acad. Sci. U.S.A 93, 2822-2826.
8. 2 zinc finger proteins, Cell. Mol. Life Sci. 58, 625-635.
9. Omichinski, J. G., Pedone, P. V., Felsenfeld, G., Gronenborn, A. M., and Clore, G. M. (1997) The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode, Nat. Struct. Biol. 4, 122-132.
10. Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., and Baldwin, R. L. (1990) Relative helix-forming tendencies of nonpolar amino acids, Nature 344, 268-270.
11. O'Neil, K. T., and DeGrado, W. (1990) A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids, Science 250, 646-651.
12. Berg, J., and Godwin, H. A. (1997) Lessons from zinc-binding peptides, Annu. Rev. Biophys. Biomol. Struct. 26, 357-371.
13. Struthers, M. D., Cheng, R. P., and Imperiali, B. (1996) Design of a monomeric 23-residue polypeptide with defined tertiary structure, Science 271, 342-345.
14. Dahiyat, B. I., and Mayo, S. T. (1997) De novo protein design; Fully automated sequence selection, Science 278, 82-87.
15. Weiss, M. A., and Keutmann, H. (1990) Alternating zinc finger motifs in the male-associated protein ZFY: Defining architectural rules by mutagenesis and design of an "aromatic swap" second-site revertant, Biochemistry 29, 9808-9813.
16. Lachenmann, M. J., Ladbury, J. E., Philips, N. B., Narayana, N., Qian, X., and Weiss, M. A. (2002) The hidden thermodynamics of a zinc finger, J. Mol. Biol. 316, 969-989.
17. 2 zinc fingers, FEBS Lett. 296, 11-15.
18. 2-type zinc finger peptides, Biochemistry 44, 2523-2528.
19. Negi, S., Dhanasekaran, M., Urata, H., and Sugiura, Y. (2006) Biomolecular mirror-image recognition: Reciprocal chiral-specific DNA binding of synthetic enantiomers of zinc finger domain from GAGA factor, Chirality 18, 254-258.
20. Nokihara, K., Nagawa, Y., Hong, S.-P., and Nakanishi, H. (1997) Efficient solid-phase synthesis of a large peptide by a single coupling protocol with a single HPLC purification step, Lett. Pept. Sci. 4, 141-146.
21. Uno, Y., Matsushita, K., Nagaoka, M., and Sugiura, Y. (2001) Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition, Biochemistry 40, 1787-1795.
22. Shiraishi, Y., Imanishi, M., and Sugiura, Y. (2004) Exchange of histidine spacing between Sp1 and GiI zinc fingers: distinct effect of histidine spacing-linker region on DNA binding, Biochemistry 43, 6352-6359.
23. Frankel, A. D., Berg, J. M., and Pabo, C. O. (1987) Metal-dependent folding of a single zinc finger from transcriptional IIIA, Proc. Natl. Acad. Sci. U.S.A. 84, 4841-4845.
24. Nomura, A., and Sugiura, Y. (2002) Contribution of individual zinc ligands to metal binding and peptide folding of zinc finger peptides, Inorg. Chem. 41, 3693-3698.
25. Giedroc, D. P., Keating, K. M., Williams, K. R., Konigsberg, W. H., Coleman, J. E. (1986) Gene 32 protein, the single-stranded DNA binding protein from bacteriophage T4, is a zinc metalloprotein, Proc. Natl. Acad. Sci. U.S.A. 83, 8452-8456.
26. May, S. W., and Kuo, J.-Y. (1978) Preparation and properties of cobalt(II) rubredoxin, Biochemistry 17, 3333-3338.
27. Vašák, M., Kägi, J. H. R., Holmquist, B., Vallee, B. L.(1981) Spectral studies of cobalt(II)- and nickel(II)-metallothionein, Biochemistry 20, 6659-6664.
28. Bertini, I., and Luchinat, C. (1984) High spin cobalt(II) as a probe for the investigation of metalloproteins, Adv. Inorg. Biochem. 6, 71-111.
29. Berg, J. M., and Merkle, D. L. (1989) On the metal ion specificity of "zinc finger" proteins, J. Am. Chem. Soc. 111, 3759-3761.
30. Woody, R. W. (1995) Circular dichroism, Methods Enzymol. 246, 34-71.
31. Gray, D. M., Ratliff, R. L., and Vaughan, M. R. (1992) Circular dichroism spectroscopy of DNA, Methods Enzymol. 211, 389-406.
32. Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L, Young, E. T., and Klevit, R. E. (1988) Zinc-dependent structure of a single-finger domain of yeast ADR1, Science 241, 1489-1492.
33. Elrod-Erickson, M., Rould, M. A., Nekludova, L., and Pabo, C. O. (1996) Zif268 protein-DNA complex refined at 1.6 Å: A model system for understanding zinc finger-DNA interactions. Structure 4, 1171-1180.
34. 2 zinc finger peptide, Proc. Natl. Acad. Sci. U.S.A. 89, 4796-4800.
35. Kim, C. A., and Berg, J. M. (1993) Thermodynamic β-sheet propensities measured using a zinc-finger host peptide, Nature 362, 267-270.
36. Kochoyan, M., Keutmann, H. T., and Weiss, M. A. (1991) Architectural rules of the zinc-finger motif: Comparative two-dimentional NMR studies of native and "aromatic-swap" domains define a "weakly polar switch", Proc. Natl. Acad. Sci. U.S.A 88, 8455-8459.
37. 2 zinc finger/TATA box complexes, Structure 9, 717-723.
38. Miller, J. C., and Pabo, C. O. (2001) Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition, J. Mol. Biol. 313, 309-315.