Zn(II) binding and DNA binding properties of ligand-substituted CXHH-type zinc finger proteins

Biochemistry

Volumn 51, Issue 16, 2012, Pages 3342-3348

  Imanishi, Miki ^a   Matsumura, Kazushi ^a   Tsuji, Shogo ^a   Nakaya, Tomohiro ^a   Negi, Shigeru ^b   Futaki, Shiroh ^a   Sugiura, Yukio ^b  

^a KYOTO UNIVERSITY   (Japan)

^b Doshisha Women's College of Liberal Arts   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RESIDUES; ASPARTIC ACIDS; BINDING AFFINITIES; CONFORMATIONAL CHANGE; CYSTEINE RESIDUES; DIVERSE RANGE; DNA BINDING; DNA BINDING ABILITY; DNA BINDING AFFINITY; DNA BINDING SEQUENCE; DNA-BINDING DOMAIN; DNA-BINDING PROPERTIES; GEL MOBILITY SHIFT ASSAY; GLUTAMIC ACID; LIGAND SUBSTITUTION; METAL COORDINATION; SECOND LIGAND; WILD TYPES; ZINC FINGER; ZINC FINGER PEPTIDES; ZINC FINGER PROTEIN;

AMINO ACIDS; BINDING ENERGY; LIGANDS; PEPTIDES; TRANSCRIPTION FACTORS; ZINC COMPOUNDS;

ZINC;

ASPARTIC ACID; CYSTEINE; DNA; GLUTAMIC ACID; HISTIDINE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ZIF268; UNCLASSIFIED DRUG; ZINC; ZINC FINGER PROTEIN;

ARTICLE; BINDING AFFINITY; CONCENTRATION (PARAMETERS); CONFORMATIONAL TRANSITION; DISSOCIATION; DNA BINDING; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; PRIORITY JOURNAL; PROTEIN DOMAIN; THERMOSTABILITY;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; CYSTEINE; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; KINETICS; LIGANDS; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; ZINC; ZINC FINGERS;

EID: 84860147811     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300236m     Document Type: Article

References (30)

1. Klug, A. (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation Annu. Rev. Biochem. 79, 213-231
2. 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
3. Frankel, A. D., Berg, J. M., and Pabo, C. O. (1987) Metal-dependent folding of a single zinc finger from transcription factor IIIA Proc. Natl. Acad. Sci. U.S.A. 84, 4841-4845
4. Imanishi, M., Nakaya, T., Morisaki, T., Noshiro, D., Futaki, S., and Sugiura, Y. (2010) Metal-stimulated regulation of transcription by an artificial zinc-finger protein ChemBioChem 11, 1653-1655
5. Rebar, E. J. and Pabo, C. O. (1994) Zinc finger phage: Affinity selection of fingers with new DNA-binding specificities Science 263, 671-673
6. Beerli, R. R., Segal, D. J., Dreier, B., and Barbas, C. F., III (1998) Toward controlling gene expression at will: Specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks Proc. Natl. Acad. Sci. U.S.A. 95, 14628-14633
7. Segal, D. J., Dreier, B., Beerli, R. R., and Barbas, C. F., III. (1999) Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences Proc. Natl. Acad. Sci. U.S.A. 96, 2758-2763
8. Maeder, M. L., Thibodeau-Beganny, S., Sander, J. D., Voytas, D. F., and Joung, J. K. (2009) Oligomerized pool engineering (OPEN): An 'open-source' protocol for making customized zinc-finger arrays Nat. Protoc. 4, 1471-1501
9. 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
10. Blancafort, P., Segal, D. J., and Barbas, C. F., III (2004) Designing transcription factor architectures for drug discovery Mol. Pharmacol. 66, 1361-1371
11. Patel, K., Kumar, A., and Durani, S. (2007) Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures Biochim. Biophys. Acta 1774, 1247-1253
12. Sousa, S. F., Lopes, A. B., Fernandes, P. A., and Ramos, M. J. (2009) The zinc proteome: A tale of stability and functionality Dalton Trans., 38, 7946-7956
13. Green, A. and Sarkar, B. (1998) Alteration of zif268 zinc-finger motifs gives rise to non-native zinc-co-ordination sites but preserves wild-type DNA recognition Biochem. J. 333, 85-90
14. Negi, S., Itazu, M., Imanishi, M., Nomura, A., and Sugiura, Y. (2004) Creation and characteristics of unnatural CysHis3-type zinc finger protein Biochem. Biophys. Res. Commun. 325, 421-425
15. 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
16. Simpson, R. J., Cram, E. D., Czolij, R., Matthews, J. M., Crossley, M., and Mackay, J. P. (2003) CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions J. Biol. Chem. 278, 28011-28018
17. Sénèque, O. and Latour, J. M. (2010) Coordination properties of zinc finger peptides revisited: Ligand competition studies reveal higher affinities for zinc and cobalt J. Am. Chem. Soc. 132, 17760-17774
18. Morisaki, T., Imanishi, M., Futaki, S., and Sugiura, Y. (2008) Rapid transcriptional activity in vivo and slow DNA binding in vitro by an artificial multi-zinc finger protein Biochemistry 47, 10171-10177
19. 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 metalloprotein Proc. Natl. Acad. Sci. U.S.A. 83, 8452-8456
20. May, S. W. and Kuo, J. Y. (1978) Preparation and properties of cobalt(II) rubredoxin Biochemistry 17, 3333-3338
21. Vasák, M., Kägi, J. H., Holmquist, B., and Vallee, B. L. (1981) Spectral studies of cobalt(II)- and nickel(II)-metallothionein Biochemistry 20, 6659-6664
22. Bertini, I. and Luchinat, C. (1984) High spin cobalt(II) as a probe for the investigation of metalloproteins Adv. Inorg. Biochem. 6, 71-111
23. Negi, S., Imanishi, M., Sasaki, M., Tatsutani, K., Futaki, S., and Sugiura, Y. (2011) An arginine residue instead of a conserved leucine residue in the recognition helix of the finger 3 of Zif268 stabilizes the domain structure and mediates DNA binding Biochemistry 50, 6266-6272
24. Dhanasekaran, M., Negi, S., Imanishi, M., Suzuki, M., and Sugiura, Y. (2008) 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 47, 11717-11724
25. 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
26. Elrod-Erickson, M., Benson, T. E., and Pabo, C. O. (1998) High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition Structure 6, 451-464
27. Elrod-Erickson, M. and Pabo, C. O. (1999) Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex J. Biol. Chem. 274, 19281-19285
28. Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays Proc. Natl. Acad. Sci. U.S.A. 98, 7158-7163
29. Swirnoff, A. H. and Milbrandt, J. (1995) DNA-binding specificity of NGFI-A and related zinc finger transcription factors Mol. Cell. Biol. 15, 2275-2287
30. Sigrist, C. J., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., and Hulo, N. (2010) PROSITE, a protein domain database for functional characterization and annotation Nucleic Acids Res. 38, D161-D166