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. 2004 Jan 1;32(Database issue):D156-9.
doi: 10.1093/nar/gkh015.

The KNOTTIN website and database: a new information system dedicated to the knottin scaffold

Jean-Christophe Gelly  1 , Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, Laurent Chiche
Affiliations

The KNOTTIN website and database: a new information system dedicated to the knottin scaffold

Jean-Christophe Gelly et al. Nucleic Acids Res. .

Abstract

The KNOTTIN website and database organize information about knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology. Thanks to their small size and high stability, knottins provide appealing scaffolds for protein engineering and drug design. Static pages present the main historical and recent results about knottin discoveries, sequences, structures, folding, functions, applications and bibliography. Database searches provide dynamically generated tabular reports or sequence alignments for knottin three-dimensional structures or sequences. BLAST/HMM searches are also available. A simple nomenclature, based on loop lengths between cysteines, is proposed and is complemented by a uniform numbering scheme. This standardization is applied to all knottin structures in the database, facilitating comparisons. Renumbered and structurally fitted knottin PDB files are available for download. The standardized numbering is used for automatic drawing of two-dimensional Colliers de Perles. The KNOTTIN website and database are available at http://knottin.cbs.cnrs.fr and http://knottin.com.

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Figures

Figure 1
Figure 1
Schematic representation of knottins with an indication of nomenclature and unique numbering. The arrows indicate the triple-stranded β-sheet present in many knottins. The cysteines involved in the knot are labeled with roman numbers according to the sequence order. The letters a–f indicate the loop lengths between cysteines and are used to build the nomenclature. The C–N link in macrocyclic knottins is shown as a dashed line and is labeled with a gray letter. The new cysteine numbering is shown as white numbers on black circles.
Figure 2
Figure 2
Two-dimensional Collier de Perles representation. Fixed residues are shown on a light blue background (residues 38–40, 60–61, 79–81 and 99–100). Their positions in the Colliers de Perles conform to the proximities in the 3D structures. As an example, cysteines 80 and 100 face each other in the β-hairpin with residues 81 and 99 being hydrogen bonded. Other residues are inserted according to the knottin numbering. Cysteines and disulfide bridges of the knot are shown as red letters and orange thick lines, respectively. Prolines are shown on a yellow background.
Figure 3
Figure 3
Main flow chart and content of the KNOTTIN database.
See this image and copyright information in PMC

References

    1. Rees D.C. and Lipscomb,W.N. (1982) Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 Å resolution. J. Mol. Biol., 160, 475–498. - PubMed
    1. Bode W., Greyling,H.J., Huber,R., Otlewski,J. and Wilusz,T. (1989) The refined 2.0 Å X-ray crystal structure of the complex formed between bovine β-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes. FEBS Lett., 242, 285–292. - PubMed
    1. Chiche L., Gaboriaud,C., Heitz,A., Mornon,J.P., Castro,B. and Kollman,P.A. (1989) Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins, 6, 405–417. - PubMed
    1. Heitz A., Chiche,L., Le-Nguyen,D. and Castro,B. (1989) 1H 2D NMR and distance geometry study of the folding of Ecballium elaterium trypsin inhibitor, a member of the squash inhibitors family. Biochemistry, 28, 2392–2398. - PubMed
    1. Davis J.H., Bradley,E.K., Miljanich,G.P., Nadasdi,L., Ramachandran,J. and Basus,V.J. (1993) Solution structure of ω-conotoxin GVIA using 2-D NMR spectroscopy and relaxation matrix analysis. Biochemistry, 32, 7396–7405. - PubMed

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