DOI: 10.1006/jmbi.1999.3406. DNA-induced α-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2-His2 zinc fingers

DNA-induced α-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2-His2 zinc fingers

10.1006/jmbi.1999.3406

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Laity, J. H., Dyson, H. J., & Wright, P. E. (2000). DNA-induced Î±-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2-His2 zinc fingers. Journal of Molecular Biology, 295(4), 719â727.

Authors 3

John H Laity (first)
H.Jane Dyson (additional)
Peter E Wright (additional)

References 35 Referenced 138

10.1128/MCB.17.4.2116 / Mol. Cell. Biol. / Human and mouse MOK2 proteins are associated with nuclear ribonucleoprotein components and bind specifically to RNA and DNA through their zinc finger domains by Arranz (1997)
10.1126/science.8178170 / Science / Rules for α-helix termination by glycine by Aurora (1994)
10.1021/bi00129a006 / Biochemistry / Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59 by Bell (1992)
10.1089/dna.1.1989.8.377 / DNA / The human genome contains hundreds of genes coding for finger proteins of the Krüppel type by Bellefroid (1989)
10.1073/pnas.93.15.7562 / Proc. Natl Acad. Sci. USA / RNA binding by the Wilms tumor suppressor zinc finger proteins by Caricasole (1996)
10.1093/nar/21.15.3341 / Nucl. Acids Res. / A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA by Choo (1993)
10.1126/science.8475383 / Science / Molecular basis for specific recognition of both RNA and DNA by a zinc finger proteins by Clemens (1993)
10.1006/jmbi.1994.1701 / J. Mol. Biol. / Relative contributions of the zinc fingers of transcription factor IIIA to the energetics of DNA binding by Clemens (1994)
10.1073/pnas.88.18.7923 / Proc. Natl Acad. Sci. USA / A cluster of related zinc finger protein genes is deleted in the mouse embroyonic lethal mutation tw18 by Crossley (1991)
10.1016/S0969-2126(96)00125-6 / Structure / Zif268 protein-DNA complex refined at 1.6 Å by Elrod-Erickson (1996)
10.1038/366483a0 / Nature / The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition by Fairall (1993)
10.1023/A:1008290631575 / J. Biomol. NMR / Chemical shift as a probe of molecular interfaces by Foster (1998)
10.1038/nsb0897-605 / Nature Struct. Biol. / Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA by Foster (1997)
10.1007/BF00179351 / J. Biomol. NMR / Identification of N-terminal helix capping boxes by means of 13C chemical shifts by Gronenborn (1994)
10.1021/bi9717993 / Biochemistry / Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1 by Hamilton (1998)
10.1073/pnas.93.24.13577 / Proc. Natl Acad. Sci. USA / Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator by Houbaviy (1996)
10.1002/j.1460-2075.1992.tb05552.x / EMBO J. / Determination of the base recognition positions of zinc fingers from sequence analysis by Jacobs (1992)
10.1016/0092-8674(90)90809-S / Cell / A finger protein structurally similar to TFIIIA that binds exclusively to 5S RNA in Xenopus by Joho (1990)
10.1038/nsb1196-940 / Nature Struct. Biol. / A 2.2 Å resolution crystal structure of a designed zinc finger protein bound to DNA by Kim (1996)
10.1126/science.2503871 / Science / Three-dimensional solution structure of a single zinc finger binding domain by Lee (1989)
10.1021/bi00053a006 / Biochemistry / Capping interactions in isolated α helices by Lyu (1993)
{'key': '10.1006/jmbi.1999.3406_BIB22', 'series-title': 'Molecular Modeling of Nucleic Acids', 'first-page': '379', 'article-title': 'Modeling unusual nucleic acid structures', 'author': 'Macke', 'year': '1998'} / Molecular Modeling of Nucleic Acids / Modeling unusual nucleic acid structures by Macke (1998)
10.1073/pnas.95.6.2938 / Proc. Natl Acad. Sci. USA / Differing roles for zinc fingers in DNA recognition by Nolte (1998)
10.1126/science.3047872 / Science / Zinc-dependent structure of a single-finger domain of yeast ADR1 by Parraga (1988)
10.1126/science.2028256 / Science / Zinc-finger-DNA recognition by Pavletich (1991)
10.1126/science.8378770 / Science / Crystal structure of a five-finger GLI-DNA complex by Pavletich (1993)
10.1126/science.3381086 / Science / Amino acid preferences for specific locations at the ends of α helices by Richardson (1988)
{'key': '10.1006/jmbi.1999.3406_BIB28', 'series-title': 'Protein Folding', 'first-page': '53', 'article-title': 'The α-conformation at the ends of helices', 'author': 'Schellman', 'year': '1980'} / Protein Folding / The α-conformation at the ends of helices by Schellman (1980)
10.1038/342296a0 / Nature / Capping and α-helix stability by Serrano (1989)
10.1126/science.7536342 / Science / Specific DNA-RNA hybrid binding by zinc finger proteins by Shi (1995)
10.1021/ja00014a071 / J. Am. Chem. Soc. / Empirical correlation between protein backbone conformation and Cα and Cβ 13C nuclear magnetic resonance chemical shifts by Spera (1991)
10.1016/0022-2836(91)90214-Q / J. Mol. Biol. / Relationship between nuclear magnetic resonance chemical shift and protein secondary structure by Wishart (1991)
10.1006/jmbi.1997.1291 / J. Mol. Biol. / Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence by Wuttke (1997)
10.1021/ja00082a049 / J. Am. Chem. Soc. / Structure of a C-terminal α-helix cap in a synthetic peptide by Zhou (1994)
10.1063/1.1730390 / J. Chem. Phys. / Theory of the phase transition between helix and random coil by Zimm (1959)

Dates

Type	When
Created	22 years, 10 months ago (Oct. 7, 2002, 3:12 a.m.)
Deposited	5 years, 8 months ago (Dec. 17, 2019, 7:34 p.m.)
Indexed	2 months ago (July 2, 2025, 10:18 a.m.)
Issued	25 years, 8 months ago (Jan. 1, 2000)
Published	25 years, 8 months ago (Jan. 1, 2000)
Published Print	25 years, 8 months ago (Jan. 1, 2000)

Funders 0

None

BibTeX

@article{Laity_2000, title={DNA-induced α-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2-His2 zinc fingers}, volume={295}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.1999.3406}, DOI={10.1006/jmbi.1999.3406}, number={4}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Laity, John H and Dyson, H.Jane and Wright, Peter E}, year={2000}, month=jan, pages={719–727} }

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      "author": "Choo",
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      "author": "Fairall",
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      "author": "Hamilton",
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      "volume": "93",
      "author": "Houbaviy",
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      "author": "Jacobs",
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      "author": "Joho",
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      "journal-title": "Cell"
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      "first-page": "940",
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      "author": "Lee",
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      "first-page": "421",
      "DOI": "10.1021/bi00053a006",
      "article-title": "Capping interactions in isolated \u03b1 helices",
      "volume": "32",
      "author": "Lyu",
      "year": "1993",
      "journal-title": "Biochemistry"
    },
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      "series-title": "Molecular Modeling of Nucleic Acids",
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      "article-title": "Modeling unusual nucleic acid structures",
      "author": "Macke",
      "year": "1998"
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      "first-page": "2938",
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      "volume": "95",
      "author": "Nolte",
      "year": "1998",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
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      "first-page": "1489",
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      "article-title": "Zinc-dependent structure of a single-finger domain of yeast ADR1",
      "volume": "241",
      "author": "Parraga",
      "year": "1988",
      "journal-title": "Science"
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      "first-page": "809",
      "DOI": "10.1126/science.2028256",
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      "author": "Pavletich",
      "year": "1991",
      "journal-title": "Science"
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      "first-page": "1701",
      "DOI": "10.1126/science.8378770",
      "article-title": "Crystal structure of a five-finger GLI-DNA complex",
      "volume": "261",
      "author": "Pavletich",
      "year": "1993",
      "journal-title": "Science"
    },
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      "first-page": "1648",
      "DOI": "10.1126/science.3381086",
      "article-title": "Amino acid preferences for specific locations at the ends of \u03b1 helices",
      "volume": "240",
      "author": "Richardson",
      "year": "1988",
      "journal-title": "Science"
    },
    {
      "key": "10.1006/jmbi.1999.3406_BIB28",
      "series-title": "Protein Folding",
      "first-page": "53",
      "article-title": "The \u03b1-conformation at the ends of helices",
      "author": "Schellman",
      "year": "1980"
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      "first-page": "296",
      "DOI": "10.1038/342296a0",
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      "volume": "342",
      "author": "Serrano",
      "year": "1989",
      "journal-title": "Nature"
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      "first-page": "282",
      "DOI": "10.1126/science.7536342",
      "article-title": "Specific DNA-RNA hybrid binding by zinc finger proteins",
      "volume": "268",
      "author": "Shi",
      "year": "1995",
      "journal-title": "Science"
    },
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      "first-page": "5490",
      "DOI": "10.1021/ja00014a071",
      "article-title": "Empirical correlation between protein backbone conformation and C\u03b1 and C\u03b2 13C nuclear magnetic resonance chemical shifts",
      "volume": "113",
      "author": "Spera",
      "year": "1991",
      "journal-title": "J. Am. Chem. Soc."
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      "first-page": "311",
      "DOI": "10.1016/0022-2836(91)90214-Q",
      "article-title": "Relationship between nuclear magnetic resonance chemical shift and protein secondary structure",
      "volume": "222",
      "author": "Wishart",
      "year": "1991",
      "journal-title": "J. Mol. Biol."
    },
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      "DOI": "10.1006/jmbi.1997.1291",
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      "volume": "273",
      "author": "Wuttke",
      "year": "1997",
      "journal-title": "J. Mol. Biol."
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      "volume": "116",
      "author": "Zhou",
      "year": "1994",
      "journal-title": "J. Am. Chem. Soc."
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      "first-page": "526",
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      "article-title": "Theory of the phase transition between helix and random coil",
      "volume": "31",
      "author": "Zimm",
      "year": "1959",
      "journal-title": "J. Chem. Phys."
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