Effects of bulkiness and hydrophobicity of an aliphatic amino acid in the recognition helix of the GAGA zinc finger on the stability of the hydrophobic core and DNA binding affinity

Biochemistry

Volumn 47, Issue 45, 2008, Pages 11717-11724

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

^a DOSHISHA WOMEN'S COLLEGE OF LIBERAL ARTS   (Japan)

^b University of Arizona   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; BINDING ENERGY; COLLOIDS; CONFORMATIONS; DNA; GELATION; GENES; HYDROPHOBICITY; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; PROBABILITY DENSITY FUNCTION; ULTRAVIOLET SPECTROSCOPY; ZINC;

ALIPHATIC AMINO ACIDS; ALIPHATIC RESIDUES; CD MEASUREMENTS; DNA BINDING AFFINITIES; DNA BINDINGS; DROSOPHILA MELANOGASTER; GAGA ZINC FINGERS; GEL MOBILITY SHIFT ASSAYS; HYDROPHOBIC CORES; METAL BINDINGS; NMR SPECTROSCOPIES; PEPTIDE CONFORMATIONS; SECONDARY STRUCTURES; SIDE CHAIN LENGTHS; SYSTEMATIC STUDIES; TERNARY STRUCTURES; VIS SPECTROSCOPIES; WILD TYPES; ZINC FINGERS;

ORGANIC ACIDS;

AMINO ACID; CYSTEINE; HISTIDINE; ISOLEUCINE; LEUCINE; VALINE; ZINC FINGER PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; GEL MOBILITY SHIFT ASSAY; HYDROPHOBICITY; METAL BINDING; MOLECULAR RECOGNITION; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; ULTRAVIOLET SPECTROSCOPY; WILD TYPE;

AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; BASE SEQUENCE; BINDING SITES; CIRCULAR DICHROISM; DNA; DNA-BINDING PROTEINS; DROSOPHILA PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HYDROPHOBICITY; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SPECTROPHOTOMETRY; SPECTROPHOTOMETRY, ULTRAVIOLET; STRUCTURE-ACTIVITY RELATIONSHIP; ZINC FINGERS;

DROSOPHILA MELANOGASTER;

EID: 55849141927     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801306d     Document Type: Article

References (34)

1. 2 zinc finger proteins. Cell. Mol. Life Sci. 58, 625-635.
2. Tupler, R., Perini, G., and Green, M. R. (2001) Expressing the human genome. Nature 409, 832-833.
3. Granok, H., Leibovitch, B. A., Shaffer, C. D., and Elgin, S. C. R. (1995) Chromatin: Ga-ga over GAGA factor. Curr. Biol. 5, 238-241.
4. 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.
5. 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.
6. Dhanasekaran, M., Negi, S., Imanishi, M., and Sugiura, Y. (2007) DNA-binding ability of GAGA zinc finger depends on the nature of amino acids present in the β-hairpin. Biochemistry 46, 7506-7513.
7. 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 of zinc-finger/DNA recognition. Nature 366, 483-487.
8. 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, 809-816.
9. Pavletich, 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.
10. Urnov, F. D., Miller, J. C., Lee, Y. L., Beausejour, C. M., Rock, J. M., and Augustus, S. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646-651.
11. Segal, D. J., Crotty, J. W., Bhakta, M. S., Barbas, C. F., III, and Horton, N. C. (2006) Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J. Mol. Biol. 363, 405-421.
12. Vonderfecht, T. R., Schroyer, D. C., Schenck, B. L., McDonough, V. M., and Pikaart, M. J. (2008) Substitution of DNA-contacting amino acids with functional variants in the Gata-1 zinc finger: A structurally and phylogenetically guided mutagenesis. Biochem. Biophys. Res. Commun. 369, 1052-1056.
13. Imperiali, B., and Ottesen, J. J. (1998) Design strategies for the construction of independently folded polypeptide motifs. Biopolymers 47, 23-29.
14. Struthers, M. D., Cheng, R. P., and Imperiali, B. (1996) Economy in protein design: Evolution of a metal-independent ββα motif based on the zinc finger domains. J. Am. Chem. Soc. 118, 3073-3081.
15. Dahiyat, B. I., and Mayo, S. L. (1997) De novo protein design: Fully automated sequence selection. Science 278, 82-87.
16. Negi, S., Imanishi, M., Matsumoto, M., and Sugiura, Y. (2008) New redesigned zinc-finger proteins: Design strategy and its application. Chem. - Eur. J. 14, 3236-3249.
17. Wu, J., Kandavelou, K., and Chandrasegaran, S. (2007) Custom-designed zinc finger nucleases: What is next? Cell. Mol. Life Sci. 64, 2933-2944.
18. Dhanasekaran, M., Negi, S., and Sugiura, Y. (2006) Designer zinc finger proteins: Tools for artificial DNA-binding functional proteins. Acc. Chem. Res. 39, 45-52.
19. Klug, A. (2005) Towards therapeutic applications of engineered zinc finger proteins. FEBS Lett. 579, 892-894.
20. Blancafort, P., Segal, D. J., and Barbas, C. F. (2004) Designing transcription factor architectures for drug-discovery. Mol. Pharmacol. 66, 1361-1371.
21. 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.
22. 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.
23. Piotto, M., Saudek, V., and Sklenár, V. (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR. 2, 661-665.
24. 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.
25. 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.
26. Giedroc, D. P., Keating, K. M., Williams, K. R., Konigsberg, W. H., and Coleman, J. E. (1986) Gene 32 protein, the single-stranded DNA binding protein from bacteriophage T4, is a zinc metallo-protein. Proc. Natl. Acad. Sci. U.S.A. 83, 8452-8456.
27. May, S. W., and Kuo, J.-Y. (1978) Preparation and properties of cobalt(II) rubredoxin. Biochemistry 17, 3333-3338.
28. Vašák, M., Kägi, J. H. R., Holmquist, B., and Vallee, B. L. (1981) Spectral studies of cobalt(II)- and nickel(II)-metallothionein. Biochemistry 20, 6659-6664.
29. Bertini, I., and Luchinat, C. (1984) High spin cobalt(II) as a probe for the investigation of metalloproteins. Adv. Inorg. Biochem. 6, 71-111.
30. Berg, J. M., and Merkle, D. L. (1989) On the metal ion specificity of "zinc finger" proteins. J. Am. Chem. Soc. 111, 3759-3761.
31. Woody, R. W. (1995) Circular dichroism. Methods Enzymol. 246, 34-71.
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. 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.
34. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., and Wright, P. E. (1989) Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635-637.