From synthetic coiled coils to functional proteins: Automated design of a receptor for the calmodulin-binding domain of calcineurin

Giovanna Ghirlanda, James D. Lear, Angela Lombardi, William F. Degrado

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

A series of synthetic receptors capable of binding to the calmodulin-binding domain of calcineurin (CN393-414) was designed, synthesized and characterized. The design was accomplished by docking CN393-414 against a two-helix receptor, using an idealized three-stranded coiled coil as a starting geometry. The sequence of the receptor was chosen using a side-chain re-packing program, which employed a genetic algorithm to select potential binders from a total of 7.5 x 106 possible sequences. A total of 25 receptors were prepared, representing 13 sequences predicted by the algorithm as well as 12 related sequences that were not predicted. The receptors were characterized by CD spectroscopy, analytical ultracentrifugation, and binding assays. The receptors predicted by the algorithm bound CN393-414 with apparent dissociation constants ranging from 0.2 μM to > 50 μM. Many of the receptors that were not predicted by the algorithm also bound to CN393-414. Methods to circumvent this problem and to improve the automated design of functional proteins are discussed.

Original languageEnglish
Pages (from-to)379-391
Number of pages13
JournalJournal of Molecular Biology
Volume281
Issue number2
DOIs
Publication statusPublished - Aug 14 1998

Keywords

  • Calmodulin mimetic
  • De novo design
  • Molecular recognition
  • Peptide binding
  • Three-helix bundle

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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