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Volumn 44, Issue 20, 2005, Pages 7469-7478

Relationship between folding and function in a sequence-specific miniature DNA-binding protein

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; HYDROPHOBICITY; POLYPEPTIDES; PROTEINS;

EID: 18844367477     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050121h     Document Type: Article
Times cited : (13)

References (53)
  • 1
    • 0035233367 scopus 로고    scopus 로고
    • Recent advances in chemical approaches to the study of biological systems
    • Shogren-Knaak, M. A., Alaimo, P. J., and Shokat, K. M. (2001) Recent advances in chemical approaches to the study of biological systems, Annu. Rev. Cell Dev. Biol. 17, 405-433.
    • (2001) Annu. Rev. Cell Dev. Biol. , vol.17 , pp. 405-433
    • Shogren-Knaak, M.A.1    Alaimo, P.J.2    Shokat, K.M.3
  • 2
    • 0033636402 scopus 로고    scopus 로고
    • Small-molecule inhibitors of cell signaling
    • McCormick, F. (2000) Small-molecule inhibitors of cell signaling, Curr. Opin. Biotechnol. 11, 593-597.
    • (2000) Curr. Opin. Biotechnol. , vol.11 , pp. 593-597
    • McCormick, F.1
  • 3
    • 0034130734 scopus 로고    scopus 로고
    • Structural chemistry and therapeutic intervention of protein-protein interactions in immune response, human immunodeficiency virus entry, and apoptosis
    • Huang, Z. (2000) Structural chemistry and therapeutic intervention of protein-protein interactions in immune response, human immunodeficiency virus entry, and apoptosis, Pharmacol. Ther. 86, 201-215.
    • (2000) Pharmacol. Ther. , vol.86 , pp. 201-215
    • Huang, Z.1
  • 4
    • 0033612729 scopus 로고    scopus 로고
    • Highly specific DNA recognition by a designed miniature protein
    • Zondlo, N. J., and Schepartz, A. (1999) Highly specific DNA recognition by a designed miniature protein, J. Am. Chem. Soc. 121, 6938-6939.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 6938-6939
    • Zondlo, N.J.1    Schepartz, A.2
  • 5
    • 0034811833 scopus 로고    scopus 로고
    • Concerted evolution of structure and function in a miniature protein
    • Chin, J. W., and Schepartz, A. (2001) Concerted evolution of structure and function in a miniature protein, J. Am. Chem. Soc. 123, 2929-2930.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 2929-2930
    • Chin, J.W.1    Schepartz, A.2
  • 6
    • 0035886913 scopus 로고    scopus 로고
    • Design and Evolution of a Miniature Bcl-2 Binding Protein
    • Chin, J. W., and Schepartz, A. (2001) Design and Evolution of a Miniature Bcl-2 Binding Protein, Angew. Chem., Int. Ed. Engl. 20, 3806-3809.
    • (2001) Angew. Chem., Int. Ed. Engl. , vol.20 , pp. 3806-3809
    • Chin, J.W.1    Schepartz, A.2
  • 7
    • 0037467384 scopus 로고    scopus 로고
    • Miniature homeodomains: High specificity without an N-terminal arm
    • Montclare, J. K., and Schepartz, A. (2003) Miniature homeodomains: high specificity without an N-terminal arm, J. Am. Chem. Soc. 125, 3416-3417.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 3416-3417
    • Montclare, J.K.1    Schepartz, A.2
  • 8
    • 0344443346 scopus 로고    scopus 로고
    • Molecular recognition of protein surfaces: High affinity ligands for the CBP KIX domain
    • Rutledge, S. E., Volkman, H. M., and Schepartz, A. (2003) Molecular recognition of protein surfaces: high affinity ligands for the CBP KIX domain, J. Am. Chem. Soc. 125, 14336-14347.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14336-14347
    • Rutledge, S.E.1    Volkman, H.M.2    Schepartz, A.3
  • 12
    • 0019413468 scopus 로고
    • X-ray analysis (1.4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone
    • Blundell, T. L., Pitts, J. E., Tickle, I. J., Wood, S. P., and Wu, C.-W. (1981) X-ray analysis (1.4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone, Proc. Natl. Acad. Sci. U.S.A. 78, 4175-4179.
    • (1981) Proc. Natl. Acad. Sci. U.S.A. , vol.78 , pp. 4175-4179
    • Blundell, T.L.1    Pitts, J.E.2    Tickle, I.J.3    Wood, S.P.4    Wu, C.-W.5
  • 13
    • 0020584172 scopus 로고
    • Conformational flexibility in a small globular hormone: X-ray analysis of avian pancreatic polypeptide at 0.98-Å resolution
    • Glover, I., Haneef, I., Pitts, J., Wood, S., Moss, D., Tickle, I., and Blundell, T. (1983) Conformational flexibility in a small globular hormone: X-ray analysis of avian pancreatic polypeptide at 0.98-Å resolution, Biopolymers 22, 293-304.
    • (1983) Biopolymers , vol.22 , pp. 293-304
    • Glover, I.1    Haneef, I.2    Pitts, J.3    Wood, S.4    Moss, D.5    Tickle, I.6    Blundell, T.7
  • 14
    • 2642581493 scopus 로고    scopus 로고
    • Herpesvirus protease inhibition by dimer disruption
    • Shimba, N., Nomura, A. M., Marnett, A. B., and Craik, C. S. (2004) Herpesvirus protease inhibition by dimer disruption, J. Virol. 78, 6657-6665.
    • (2004) J. Virol. , vol.78 , pp. 6657-6665
    • Shimba, N.1    Nomura, A.M.2    Marnett, A.B.3    Craik, C.S.4
  • 15
    • 4143072539 scopus 로고    scopus 로고
    • A miniprotein scaffold used to assemble the polyproline II binding epitope recognized by SH3 domains
    • Cobos, E. S., Pisabarro, M. T., Vega, M. C., Lacroix, E., Serrano, L., Ruiz-Sanz, J., and Martinez, J. C. (2004) A miniprotein scaffold used to assemble the polyproline II binding epitope recognized by SH3 domains, J. Mol. Biol. 342, 355-365.
    • (2004) J. Mol. Biol. , vol.342 , pp. 355-365
    • Cobos, E.S.1    Pisabarro, M.T.2    Vega, M.C.3    Lacroix, E.4    Serrano, L.5    Ruiz-Sanz, J.6    Martinez, J.C.7
  • 16
    • 0027049805 scopus 로고
    • The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: Crystal structure of the protein-DNA complex
    • Ellenberger, T. E., Brandi, C. J., Struhl, K., and Harrison, S. C. (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: Crystal structure of the protein-DNA complex, Cell 71, 1223-1237.
    • (1992) Cell , vol.71 , pp. 1223-1237
    • Ellenberger, T.E.1    Brandi, C.J.2    Struhl, K.3    Harrison, S.C.4
  • 17
    • 0027377202 scopus 로고
    • The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility
    • Konig, P., and Richmond, T. J. (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.
    • (1993) J. Mol. Biol. , vol.233 , pp. 139-154
    • Konig, P.1    Richmond, T.J.2
  • 18
    • 0029563634 scopus 로고
    • Crystal structure of a bZIP/DNA complex at 2.2 Å: Determinants of DNA specific recognition
    • Keller, W., König, P., and Richmond, T. (1995) Crystal structure of a bZIP/DNA complex at 2.2 Å: Determinants of DNA specific recognition, J. Mol. Biol. 254, 657-667.
    • (1995) J. Mol. Biol. , vol.254 , pp. 657-667
    • Keller, W.1    König, P.2    Richmond, T.3
  • 20
    • 0035907464 scopus 로고    scopus 로고
    • Methodology for optimizing functional miniature proteins based on avian pancreatic polypeptide using phage display
    • Chin, J. W., Grotzfeld, R. M., Fabian, M. A., and Schepartz, A. (2001) Methodology for optimizing functional miniature proteins based on avian pancreatic polypeptide using phage display, Bioorg. Med. Chem. Lett. 11, 1501-1505.
    • (2001) Bioorg. Med. Chem. Lett. , vol.11 , pp. 1501-1505
    • Chin, J.W.1    Grotzfeld, R.M.2    Fabian, M.A.3    Schepartz, A.4
  • 22
    • 0031053362 scopus 로고    scopus 로고
    • A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites
    • Greisman, H. A., and Pabo, C. O. (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites, Science 275, 657-661.
    • (1997) Science , vol.275 , pp. 657-661
    • Greisman, H.A.1    Pabo, C.O.2
  • 23
    • 0025940099 scopus 로고
    • Highly conserved residues in the bZIP domain of yeast GCN4 are not essential for DNA binding
    • Pu, W. T., and Struhl, K. (1991) Highly conserved residues in the bZIP domain of yeast GCN4 are not essential for DNA binding, Mol. Cell. Biol. 11, 4918-4926.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 4918-4926
    • Pu, W.T.1    Struhl, K.2
  • 24
    • 0026523148 scopus 로고
    • Mutations in the bZIP domain of yeast GCN4 that alter DNA-binding specificity
    • Tzamarias, D., Pu, W. T., and Struhl, K. (1992) Mutations in the bZIP domain of yeast GCN4 that alter DNA-binding specificity, Proc. Natl. Acad. Sci. U.S.A. 89, 2007-2011.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 2007-2011
    • Tzamarias, D.1    Pu, W.T.2    Struhl, K.3
  • 25
    • 0028020101 scopus 로고
    • Replacement of invariant bZip residues within the basic region of the yeast transcriptional activator GCN4 can change its DNA binding specificity
    • Suckow, M., Schwamborn, K., Kisters-Woike, B., von Wilcken-Bergmann, B., and Müller-Hill, B. (1994) Replacement of invariant bZip residues within the basic region of the yeast transcriptional activator GCN4 can change its DNA binding specificity, Nucleic Acids Res. 22, 4395-4404.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4395-4404
    • Suckow, M.1    Schwamborn, K.2    Kisters-Woike, B.3    Von Wilcken-Bergmann, B.4    Müller-Hill, B.5
  • 26
  • 27
    • 0037026871 scopus 로고    scopus 로고
    • Sequence-specific recognition of DNA by hydrophobic, alanine-rich mutants of the basic region/leucine zipper motif investigated by fluorescence anisotropy
    • Bird, G. H., Lajmi, A. R., and Shin, J. A. (2002) Sequence-specific recognition of DNA by hydrophobic, alanine-rich mutants of the basic region/leucine zipper motif investigated by fluorescence anisotropy, Biopolymers 65, 10-20.
    • (2002) Biopolymers , vol.65 , pp. 10-20
    • Bird, G.H.1    Lajmi, A.R.2    Shin, J.A.3
  • 28
    • 0027479165 scopus 로고
    • Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding
    • Suckow, M., von Wilcken-Bergmann, B., and Müller-Hill, B. (1993) Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding, EMBO J. 12, 1193-1200.
    • (1993) EMBO J. , vol.12 , pp. 1193-1200
    • Suckow, M.1    Von Wilcken-Bergmann, B.2    Müller-Hill, B.3
  • 30
    • 0028894384 scopus 로고
    • Crystal-structure of the heterodimeric Bzip transcription factor C-Fos-C-Jun bound to DNA
    • Glover, J. N. M., and Harrison, S. C. (1995) Crystal-structure of the heterodimeric Bzip transcription factor C-Fos-C-Jun bound to DNA, Nature 373, 257-261.
    • (1995) Nature , vol.373 , pp. 257-261
    • Glover, J.N.M.1    Harrison, S.C.2
  • 31
    • 0025182484 scopus 로고
    • Design of DNA-binding peptides based on the leucine zipper motif
    • O'Neil, K. T., Hoess, R. H., and DeGrado, W. F. (1990) Design of DNA-binding peptides based on the leucine zipper motif, Science 249, 774-778.
    • (1990) Science , vol.249 , pp. 774-778
    • O'Neil, K.T.1    Hoess, R.H.2    DeGrado, W.F.3
  • 32
    • 0025991706 scopus 로고
    • DNA-induced increase in the alpha-helical content of C/EBP and GCN4
    • O'Neil, K. T., Shuman, J. D., Arape, C., and DeGrado, W. F. (1991) DNA-induced increase in the alpha-helical content of C/EBP and GCN4, Biochemistry 30, 9030-9034.
    • (1991) Biochemistry , vol.30 , pp. 9030-9034
    • O'Neil, K.T.1    Shuman, J.D.2    Arape, C.3    DeGrado, W.F.4
  • 33
    • 0024988083 scopus 로고
    • Sequence-specific DNA binding by a short peptide dimer
    • Talanian, R. V., McKnight, C. J., and Kim, P. S. (1990) Sequence-specific DNA binding by a short peptide dimer, Science 249, 769-771.
    • (1990) Science , vol.249 , pp. 769-771
    • Talanian, R.V.1    McKnight, C.J.2    Kim, P.S.3
  • 34
    • 0026687589 scopus 로고
    • Minimum length of a sequence-specific DNA binding peptide
    • Talanian, R. V., McKnight, C. J., Rutkowski, R., and Kim, P. S. (1992) Minimum length of a sequence-specific DNA binding peptide, Biochemistry 31, 6871-6875.
    • (1992) Biochemistry , vol.31 , pp. 6871-6875
    • Talanian, R.V.1    McKnight, C.J.2    Rutkowski, R.3    Kim, P.S.4
  • 35
    • 0025045635 scopus 로고
    • Thermal unfolding studies of a leucine zipper domain and its specific DNA complex: Implications for scissor's grip recognition
    • Weiss, M. A. (1990) Thermal unfolding studies of a leucine zipper domain and its specific DNA complex: implications for scissor's grip recognition, Biochemistry 29, 8020-8024.
    • (1990) Biochemistry , vol.29 , pp. 8020-8024
    • Weiss, M.A.1
  • 36
    • 0025155512 scopus 로고
    • Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA
    • Weiss, M. A., Ellenberger, T., Wobbe, C. R., Lee, J. P., Harrison, S. C., and Struhl, K. (1990) Folding transition in the DNA-binding domain of GCN4 on specific binding to DNA, Nature 347, 575-578.
    • (1990) Nature , vol.347 , pp. 575-578
    • Weiss, M.A.1    Ellenberger, T.2    Wobbe, C.R.3    Lee, J.P.4    Harrison, S.C.5    Struhl, K.6
  • 37
    • 0025865320 scopus 로고
    • Solution structure of the basic region from the transcriptional activator GCN4
    • Saudek, V., Pasley, H. S., Gibson, T., Gausepohl, H., Frank, R., and Pastore, A. (1991) Solution structure of the basic region from the transcriptional activator GCN4, Biochemistry 30, 1310-1317.
    • (1991) Biochemistry , vol.30 , pp. 1310-1317
    • Saudek, V.1    Pasley, H.S.2    Gibson, T.3    Gausepohl, H.4    Frank, R.5    Pastore, A.6
  • 38
    • 0027458868 scopus 로고
    • Design of a metallo-bZIP protein that discriminates between CRE and API target sites: Selection against API
    • Cuenoud, B., and Schepartz, A. (1993) Design of a metallo-bZIP protein that discriminates between CRE and API target sites: Selection against API, Proc. Natl. Acad. Sci. U.S.A. 90, 1154-1159.
    • (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , pp. 1154-1159
    • Cuenoud, B.1    Schepartz, A.2
  • 39
    • 0027339727 scopus 로고
    • Altered specificity of DNA-binding proteins with transition metal dimerization domains
    • Cuenoud, B., and Schepartz, A. (1993) Altered specificity of DNA-binding proteins with transition metal dimerization domains, Science 259, 510-513.
    • (1993) Science , vol.259 , pp. 510-513
    • Cuenoud, B.1    Schepartz, A.2
  • 40
    • 0033525126 scopus 로고    scopus 로고
    • Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA
    • Bracken, C., Can, P. A., Cavanagh, J., and Palmer, A. G., III (1999) Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA, J. Mol. Biol 285, 2133-2146.
    • (1999) J. Mol. Biol , vol.285 , pp. 2133-2146
    • Bracken, C.1    Can, P.A.2    Cavanagh, J.3    Palmer III, A.G.4
  • 41
    • 0019335168 scopus 로고
    • Reversible dimerization of avian pancreatic polypeptide
    • Chang, P. J., Noelken, M. E., and Kimmel, J. R. (1980) Reversible dimerization of avian pancreatic polypeptide, Biochemistry 19, 1844-1849.
    • (1980) Biochemistry , vol.19 , pp. 1844-1849
    • Chang, P.J.1    Noelken, M.E.2    Kimmel, J.R.3
  • 42
    • 0036194480 scopus 로고    scopus 로고
    • The effect of C-terminal helix stabilization on specific DNA binding by monomeric GCN4 peptides
    • Zhang, M., Wu, B., Zhao, H., and Taylor, J. W. (2002) The effect of C-terminal helix stabilization on specific DNA binding by monomeric GCN4 peptides, J. Pept. Sci. 8, 125-136.
    • (2002) J. Pept. Sci. , vol.8 , pp. 125-136
    • Zhang, M.1    Wu, B.2    Zhao, H.3    Taylor, J.W.4
  • 43
    • 0037133141 scopus 로고    scopus 로고
    • Structure-based design of a leucine zipper protein with new DNA contacting region
    • Morii, T., Sato, S., Hagihara, M., Mori, Y., Imoto, K., and Makino, K. (2002) Structure-based design of a leucine zipper protein with new DNA contacting region, Biochemistry 41, 2177-2183.
    • (2002) Biochemistry , vol.41 , pp. 2177-2183
    • Morii, T.1    Sato, S.2    Hagihara, M.3    Mori, Y.4    Imoto, K.5    Makino, K.6
  • 44
    • 1142293990 scopus 로고    scopus 로고
    • Controlling the DNA binding specificity of bHLH proteins through intramolecular interactions
    • Turner, E. C., Cureton, C. H., Weston, C. J., Smart, O. S., and Allemann, R. K. (2004) Controlling the DNA binding specificity of bHLH proteins through intramolecular interactions, Chem. Biol. 11, 69-77.
    • (2004) Chem. Biol. , vol.11 , pp. 69-77
    • Turner, E.C.1    Cureton, C.H.2    Weston, C.J.3    Smart, O.S.4    Allemann, R.K.5
  • 45
    • 0022381911 scopus 로고
    • GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences; implications for general control of amino acid biosynthetic genes in yeast
    • Hope, I. A., and Struhl, K. (1985) GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences; implications for general control of amino acid biosynthetic genes in yeast, Cell 43, 177-188.
    • (1985) Cell , vol.43 , pp. 177-188
    • Hope, I.A.1    Struhl, K.2
  • 46
    • 0030743625 scopus 로고    scopus 로고
    • The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA
    • Metallo, S. J., Paolella, D. N., and Schepartz, A. (1997) The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA, Nucleic Acids Res. 25, 2967-2972.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2967-2972
    • Metallo, S.J.1    Paolella, D.N.2    Schepartz, A.3
  • 48
    • 0036838776 scopus 로고    scopus 로고
    • The role of helix stabilizing residues in GCN4 basic region folding and DNA binding
    • Hollenbeck, J. J., McClain, D. L., and Oakley, M. G. (2002) The role of helix stabilizing residues in GCN4 basic region folding and DNA binding, Protein Sci. 11, 2740-2747.
    • (2002) Protein Sci. , vol.11 , pp. 2740-2747
    • Hollenbeck, J.J.1    McClain, D.L.2    Oakley, M.G.3
  • 49
    • 23444450909 scopus 로고
    • Coupling of local folding to site-specific binding of proteins to DNA
    • Spolar, R. S., and Record, M. T., Jr. (1994) Coupling of local folding to site-specific binding of proteins to DNA, Science 263, 777-784.
    • (1994) Science , vol.263 , pp. 777-784
    • Spolar, R.S.1    Record Jr., M.T.2
  • 50
    • 0028533280 scopus 로고
    • Distribution of labor among bZIP segments in the control of DNA affinity and specificity
    • Metallo, S. J., and Schepartz, A. (1994) Distribution of labor among bZIP segments in the control of DNA affinity and specificity, Chem. Biol. 1, 143-151.
    • (1994) Chem. Biol. , vol.1 , pp. 143-151
    • Metallo, S.J.1    Schepartz, A.2
  • 51
    • 84990085627 scopus 로고
    • The design of molecular hosts, guests, and their complexes
    • Cram, D. J. (1988) The design of molecular hosts, guests, and their complexes, Angew. Chem., Int. Ed. Engl. 27, 1009-1020.
    • (1988) Angew. Chem., Int. Ed. Engl. , vol.27 , pp. 1009-1020
    • Cram, D.J.1
  • 52
    • 0030821164 scopus 로고    scopus 로고
    • Structural insights into the evolution of an antibody combining site
    • Wedemayer, G. J., Patten, P. A., Wang, L. H., Schultz, P. G., and Stevens, R. C. (1997) Structural insights into the evolution of an antibody combining site, Science 276, 1665-1669.
    • (1997) Science , vol.276 , pp. 1665-1669
    • Wedemayer, G.J.1    Patten, P.A.2    Wang, L.H.3    Schultz, P.G.4    Stevens, R.C.5
  • 53
    • 0029379551 scopus 로고
    • Let's get specific: The relationship between specificity and affinity
    • Eaton, B. E., Gold, L., and Zichi, D. A. (1995) Let's get specific: the relationship between specificity and affinity, Chem. Biol. 2, 633-638.
    • (1995) Chem. Biol. , vol.2 , pp. 633-638
    • Eaton, B.E.1    Gold, L.2    Zichi, D.A.3


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