The structural characterization of a complex of α-bungarotoxin with a recombinant antibody fragment that mimics the acetylcholine receptor was achieved using docking simulation procedures. To drive the computer simulation towards a limited set of solutions with biological significance, a filter, incorporating general considerations of antigen–antibody interactions, specificity of the selected antibody fragment and results from α-bungarotoxin epitope mapping, was adopted. Two similar structures were obtained for the complex, both of them stabilized by cation-π and hydrophobic interactions due to tyrosilyl residues of the antibody fragment. Site-directed mutagenesis studies, removing each of the latter aromatic residues and causing full inactivation of the interaction process between the antibody fragment and the neurotoxin, support the validity of the calculated structure of the complex.
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April 2003
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Research Article|
April 15 2003
Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin
Luisa BRACCI;
Luisa BRACCI
1
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
1To whom correspondence should be addressed (e-mail braccil@unisi.it).
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Alessandro PINI;
Alessandro PINI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Andrea BERNINI;
Andrea BERNINI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
†Biomolecular Structure Research Centre, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Barbara LELLI;
Barbara LELLI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Claudia RICCI;
Claudia RICCI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Maria SCARSELLI;
Maria SCARSELLI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
†Biomolecular Structure Research Centre, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Neri NICCOLAI;
Neri NICCOLAI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
†Biomolecular Structure Research Centre, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Paolo NERI
Paolo NERI
∗Department of Molecular Biology, University of Siena, Via Fiorentina 1, I-53100 Siena, Italy
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Publisher: Portland Press Ltd
Received:
September 02 2002
Revision Received:
January 02 2003
Accepted:
January 09 2003
Accepted Manuscript online:
January 09 2003
Online ISSN: 1470-8728
Print ISSN: 0264-6021
The Biochemical Society, London ©2003
2003
Biochem J (2003) 371 (2): 423–427.
Article history
Received:
September 02 2002
Revision Received:
January 02 2003
Accepted:
January 09 2003
Accepted Manuscript online:
January 09 2003
Citation
Luisa BRACCI, Alessandro PINI, Andrea BERNINI, Barbara LELLI, Claudia RICCI, Maria SCARSELLI, Neri NICCOLAI, Paolo NERI; Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. Biochem J 15 April 2003; 371 (2): 423–427. doi: https://doi.org/10.1042/bj20021369
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