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Design, synthesis and structure of a zinc finger with an artificial beta-turn.

Viles JH, Patel SU, Mitchell JB, Moody CM, Justice DE, Uppenbrink J, Doyle PM, Harris CJ, Sadler PJ, Thornton JM
J Mol Biol 279 973-86 (1998)
Cited: 19 times
EuropePMC logo PMID: 9642075

Abstract

We have incorporated a bicyclic beta-turn mimetic (BTD; beta-turn dipeptide) into a zinc finger, creating a zinc finger with an artificial beta-turn. The designed peptide chelates zinc and has the same fold as the unmodified native zinc finger (finger 3 of the human YY1 protein). A combination of 1H NMR and structure calculations reveals that, in solution, this zinc finger has a fold similar to the known wild-type crystal structure and to other zinc fingers containing the consensus sequence X3-Cys-X4-Cys-X12-His-X3-His-X. The peptide was designed with BTD between the chelating cysteine residues, with BTD forming a type II' beta-turn linking the two strands of a distorted anti-parallel beta-sheet. The C-terminal portion of the peptide forms a helix with zinc co-ordinating histidine residues on successive turns of the helix. This work represents a step towards developing methods by which parts of a target protein may be replaced by peptide mimetics.

Articles - 1znm mentioned but not cited (1)

  1. Letter Native, sequential protein folding via anchored N and C protein termini. Alberti S. Proc Natl Acad Sci U S A 113 E3189-91 (2016)


Reviews citing this publication (3)

  1. Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure. Reinert ZE, Horne WS. Org. Biomol. Chem. 12 8796-8802 (2014)
  2. Proteomimetics as protein-inspired scaffolds with defined tertiary folding patterns. Horne WS, Grossmann TN. Nat Chem 12 331-337 (2020)
  3. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Santhouse JR, Rao SR, Horne WS. Methods Enzymol 656 93-122 (2021)

Articles citing this publication (15)

  1. Evaluating beta-turn mimics as beta-sheet folding nucleators. Fuller AA, Du D, Liu F, Davoren JE, Bhabha G, Kroon G, Case DA, Dyson HJ, Powers ET, Wipf P, Gruebele M, Kelly JW. Proc. Natl. Acad. Sci. U.S.A. 106 11067-11072 (2009)
  2. Protein-like tertiary folding behavior from heterogeneous backbones. Reinert ZE, Lengyel GA, Horne WS. J. Am. Chem. Soc. 135 12528-12531 (2013)
  3. Structure and dynamics of a primordial catalytic fold generated by in vitro evolution. Chao FA, Morelli A, Haugner JC, Churchfield L, Hagmann LN, Shi L, Masterson LR, Sarangi R, Veglia G, Seelig B. Nat. Chem. Biol. 9 81-83 (2013)
  4. Structural characterization of a beta-turn mimic within a protein-protein interface. Eckhardt B, Grosse W, Essen LO, Geyer A. Proc. Natl. Acad. Sci. U.S.A. 107 18336-18341 (2010)
  5. A SALL4 zinc finger missense mutation predicted to result in increased DNA binding affinity is associated with cranial midline defects and mild features of Okihiro syndrome. Miertus J, Borozdin W, Frecer V, Tonini G, Bertok S, Amoroso A, Miertus S, Kohlhase J. Hum. Genet. 119 154-161 (2006)
  6. Folding Thermodynamics of Protein-Like Oligomers with Heterogeneous Backbones. Reinert ZE, Horne WS. Chem Sci 5 3325-3330 (2014)
  7. Comparison of backbone modification in protein β-sheets by α→γ residue replacement and α-residue methylation. Lengyel GA, Reinert ZE, Griffith BD, Horne WS. Org. Biomol. Chem. 12 5375-5381 (2014)
  8. A PEG-based oligomer as a backbone replacement for surface-exposed loops in a protein tertiary structure. Reinert ZE, Musselman ED, Elcock AH, Horne WS. Chembiochem 13 1107-1111 (2012)
  9. Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure. George KL, Horne WS. J. Am. Chem. Soc. 139 7931-7938 (2017)
  10. Matching organic libraries with protein-substructures. Preissner R, Goede A, Rother K, Osterkamp F, Koert U, Froemmel C. J. Comput. Aided Mol. Des. 15 811-817 (2001)
  11. Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns. Rao SR, Horne WS. Pept Sci (Hoboken) 112 e24177 (2020)
  12. Evaluation of β-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure. Mortenson DE, Kreitler DF, Thomas NC, Guzei IA, Gellman SH, Forest KT. Chembiochem 19 604-612 (2018)
  13. Foldamer Tertiary Structure through Sequence-Guided Protein Backbone Alteration. George KL, Horne WS. Acc. Chem. Res. 51 1220-1228 (2018)
  14. High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins. Horx P, Geyer A. Chem Sci 12 11455-11463 (2021)
  15. Protein Backbone Alteration in Non-Hairpin β-Turns: Impacts on Tertiary Folded Structure and Folded Stability. Harmon TW, Horne WS. Chembiochem 24 e202300113 (2023)


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