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Literature DB >> 14681383

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

Jean-Christophe Gelly¹, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, Laurent Chiche.

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.

Entities: Chemical

Mesh：

Substances：

Year: 2004 PMID： 14681383 PMCID： PMC308750 DOI： 10.1093/nar/gkh015

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

20 in total

1. Min-21 and min-23, the smallest peptides that fold like a cystine-stabilized beta-sheet motif: design, solution structure, and thermal stability.

Authors: A Heitz; D Le-Nguyen; L Chiche
Journal: Biochemistry Date: 1999-08-10 Impact factor: 3.162

Review 2. The cystine knot motif in toxins and implications for drug design.

Authors: D J Craik; N L Daly; C Waine
Journal: Toxicon Date: 2001-01 Impact factor: 3.033

3. Discovery and characterization of a family of insecticidal neurotoxins with a rare vicinal disulfide bridge.

Authors: X Wang; M Connor; R Smith; M W Maciejewski; M E Howden; G M Nicholson; M J Christie; G F King
Journal: Nat Struct Biol Date: 2000-06

Review 4. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains.

Authors: Marie-Paule Lefranc; Christelle Pommié; Manuel Ruiz; Véronique Giudicelli; Elodie Foulquier; Lisa Truong; Valérie Thouvenin-Contet; Gérard Lefranc
Journal: Dev Comp Immunol Date: 2003-01 Impact factor: 3.636

5. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.

Authors: Brigitte Boeckmann; Amos Bairoch; Rolf Apweiler; Marie-Claude Blatter; Anne Estreicher; Elisabeth Gasteiger; Maria J Martin; Karine Michoud; Claire O'Donovan; Isabelle Phan; Sandrine Pilbout; Michel Schneider
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. IMGT, the international ImMunoGeneTics database.

Authors: M P Lefranc; V Giudicelli; C Ginestoux; J Bodmer; W Müller; R Bontrop; M Lemaitre; A Malik; V Barbié; D Chaume
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

7. The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-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.

Authors: W Bode; H J Greyling; R Huber; J Otlewski; T Wilusz
Journal: FEBS Lett Date: 1989-01-02 Impact factor: 4.124

8. Crystallization and preliminary X-ray analysis of the complex of porcine pancreatic elastase and a hybrid squash inhibitor.

Authors: Kai Hilpert; Jens Schneider-Mergener; Jacqueline Aÿ
Journal: Acta Crystallogr D Biol Crystallogr Date: 2002-03-22

9. Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 A resolution.

Authors: D C Rees; W N Lipscomb
Journal: J Mol Biol Date: 1982-09-25 Impact factor: 5.469

10. Identification of epitope-like consensus motifs using mRNA display.

Authors: Rick Baggio; Petra Burgstaller; Stephen P Hale; Andrew R Putney; Meghan Lane; Dasa Lipovsek; Martin C Wright; Richard W Roberts; Rihe Liu; Jack W Szostak; Richard W Wagner
Journal: J Mol Recognit Date: 2002 May-Jun Impact factor: 2.137

41 in total

1. Site-specific effects of diselenide bridges on the oxidative folding of a cystine knot peptide, omega-selenoconotoxin GVIA.

Authors: Konkallu Hanumae Gowd; Viktor Yarotskyy; Keith S Elmslie; Jack J Skalicky; Baldomero M Olivera; Grzegorz Bulaj
Journal: Biochemistry Date: 2010-03-30 Impact factor: 3.162

Review 2. A new generation of protein display scaffolds for molecular recognition.

Authors: Ralf J Hosse; Achim Rothe; Barbara E Power
Journal: Protein Sci Date: 2006-01 Impact factor: 6.725

Review 3. Plant cystine-knot peptides: pharmacological perspectives.

Authors: Barbara Molesini; Davide Treggiari; Andrea Dalbeni; Pietro Minuz; Tiziana Pandolfini
Journal: Br J Clin Pharmacol Date: 2016-04-22 Impact factor: 4.335

4. Molecular cloning and in silico characterization of knottin peptide, U2-SCRTX-Lit2, from brown spider (Loxosceles intermedia) venom glands.

Authors: Gabriel Otto Meissner; Pedro Túlio de Resende Lara; Luis Paulo Barbour Scott; Antônio Sérgio Kimus Braz; Daniele Chaves-Moreira; Fernando Hitomi Matsubara; Eduardo Mendonça Soares; Dilza Trevisan-Silva; Luiza Helena Gremski; Silvio Sanches Veiga; Olga Meiri Chaim
Journal: J Mol Model Date: 2016-08-03 Impact factor: 1.810

10. Interrogating and predicting tolerated sequence diversity in protein folds: application to E. elaterium trypsin inhibitor-II cystine-knot miniprotein.

Authors: Jennifer L Lahti; Adam P Silverman; Jennifer R Cochran
Journal: PLoS Comput Biol Date: 2009-09-04 Impact factor: 4.475