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 language | English |
|---|---|
| Pages (from-to) | 379-391 |
| Number of pages | 13 |
| Journal | Journal of Molecular Biology |
| Volume | 281 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - Aug 14 1998 |
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Keywords
- Calmodulin mimetic
- De novo design
- Molecular recognition
- Peptide binding
- Three-helix bundle
ASJC Scopus subject areas
- Virology
Cite this
From synthetic coiled coils to functional proteins : Automated design of a receptor for the calmodulin-binding domain of calcineurin. / Ghirlanda, Giovanna; Lear, James D.; Lombardi, Angela; Degrado, William F.
In: Journal of Molecular Biology, Vol. 281, No. 2, 14.08.1998, p. 379-391.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - From synthetic coiled coils to functional proteins
T2 - Automated design of a receptor for the calmodulin-binding domain of calcineurin
AU - Ghirlanda, Giovanna
AU - Lear, James D.
AU - Lombardi, Angela
AU - Degrado, William F.
PY - 1998/8/14
Y1 - 1998/8/14
N2 - 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.
AB - 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.
KW - Calmodulin mimetic
KW - De novo design
KW - Molecular recognition
KW - Peptide binding
KW - Three-helix bundle
UR - http://www.scopus.com/inward/record.url?scp=0032516785&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0032516785&partnerID=8YFLogxK
U2 - 10.1006/jmbi.1998.1912
DO - 10.1006/jmbi.1998.1912
M3 - Article
C2 - 9698554
AN - SCOPUS:0032516785
VL - 281
SP - 379
EP - 391
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 2
ER -