Systematic analysis snake neurotoxins' functional classification using a data warehousing approach

Bioinformatics

Volumn 20, Issue 18, 2004, Pages 3466-3480

  Siew, Joyce Phui Yee ^a   Khan, Asif M ^a,b   Tan, Paul T J ^a,b   Koh, Judice L Y ^b   Seah, Seng Hong ^b   Koo, Chuay Yeng ^a   Chai, Siaw Ching ^a   Armugam, Arunmozhiarasi ^a   Brusic, Vladimir ^b   Jeyaseelan, Kandiah ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

NEUROTOXIN; SNAKE VENOM;

ARTICLE; CLASSIFICATION; DATA ANALYSIS; DATA BASE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; SNAKE; STRUCTURE ACTIVITY RELATION; UNINDEXED SEQUENCE;

SERPENTES;

EID: 19944433570     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth430     Document Type: Article

References (43)

1. Aiken,S.P., Sellin,L.C., Schmidt,J.J., Weinstein,S.A. and McArdle,J.J. (1992) A novel peptide toxin from Trimeresurus wagleri acts pre- and post-synaptically to block transmission at the rat neuromuscular junction. Pharmacol. Toxicol., 70, 459-462.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller, W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Antil,S., Servent,D. and Menez,A. (1999) Variability among the sites by which curaremimetic toxins bind to torpedo acetylcholine receptor, as revealed by identification of the functional residues of alpha-cobratoxin. J. Biol. Chem., 274, 34851-34858.
4. Bassett,D.E., Eisen,M.B. and Boguski,M.S. (1999) Gene expression informatics - it's all in your mine. Nat. Genet., 21 51-55.
5. Bon,C., Changeux,J.P., Jeng,T.W. and Fraenkel-Conrat,H. (1979) Postsynaptic effects of crotoxin and of its isolated subunits. Eur. J. Biochem., 99, 471-481.
6. Brown,N.P., Leroy,C. and Sander,C., (1998) MView: a web-compatible database search or multiple alignment viewer. Bioinformatics, 14, 380-381.
7. Chang,C.C., Huang,T.Y., Kuo,K.W., Chen,S.W., Huang,K.F. and Chiou,S.H. (1993) Sequence characterization of a novel alpha-neurotoxin from the king cobra (Ophiophagus hannah) venom. Biochem. Biophys. Res. Commun., 191, 214-223.
8. Dewan,J.C., Grant,G.A. and Sacchettini,J.C. (1994) Crystal structure of kappa-bungarotoxin at 2.3-Å resolution. Biochemistry 33, 13147-13154.
9. Dufton,M.J. (1984) Classification of elapid snake neurotoxins and cytotoxins according to chain length: evolutionary implications, J. Mol. Evol., 20, 128-134.
10. Dufton,M.J. and Hider,R.C. (1983) Conformational properties of the neurotoxins and cytotoxins isolated from Elapid snake venoms. CRC Crit. Rev. Biochem., 14, 113-171.
11. Endo,T. and Tamiya,N. (1991) Structure-function relationships of postsynaptic neurotoxins. In HarveyA.L. (ed.), Snake Toxins. Pergamon Press, New York, pp. 165-222.
12. Faure,G., Boulain,J.C., Bouet,F., Montenay-Garestier,T., Fromageot,P., and Menez,A. (1983) Role of indole and amino groups in the structure and function of Naja nigricollis toxin alpha. Biochemistry, 22, 2068-2076.
13. Felsenstein,J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
14. Felsenstein,J. (2001) The troubled growth of statistical phylogenetics. Syst. Biol., 50, 465-467.
15. Fiordalisi,J.J., al-Rabiee,R., Chiappinelli,V.A. and Grant,G.A. (1994) Affinity of native kappa-bungarotoxin and site-directed mutants the muscle nicotinic acetylcholine receptor. Biochemistry, 33, 12962-12967.
16. Francis,B., Coffield,J.A., Simpson,L.L. and Kaiser,I.I. (1995) Amino acid sequence of a new type of toxic phospholipase A2 from the venom of the Australian tiger snake (Notechis scutatus scutatus). Arch. Biochem. Biophys., 318, 481-488.
17. Fry,B., Wuster,W., Kini,R.M., Brusic,V., Khan,A., Venkataraman,D. and Rooney,A.P. (2003) Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J. Mol. Evol., 57, 110-129.
18. Gong,N.L., Armugam,A. and Jeyaseelan,K. (1999) Postsynaptic short-chain neurotoxins from Pseudonaja textilis: cDNA cloning, expression and protein characterization. Eur. J. Biochem., 265 982-989.
19. Gong,N.L., Armugam,A. and Jeyaseelan,K. (2000) Molecular cloning, characterization and evolution of the genes encoding a new group of short-chain alpha-neurotoxins in an Australian elapid, Pseudonaja textilis. FEBS Lett., 473, 303-310.
20. Grant,G.A., Frazier,M.W. and Chiappinelli,V.A. (1988) Amino acid sequence of kappa-flavitoxin: establishment of a new family of snake venom neurotoxins. Biochemistry, 27, 3794-3798.
21. Harvey,A.L. and Anderson,A.J. (1991) Dendrotoxins: snake toxins that block potassium channels and facilitate neurotransmitter release. In Harvey,A.L. (ed.), Snake Toxins. Pergamon Press, New York, pp. 131-164.
22. Hori,H. and Tamiya,N. (1976) Preparation and activity of guanidinated or acetylated erabutoxins. Biochem. J., 153, 217-222.
23. Ishikawa,Y., Menez,A., Hori,H., Yoshida,H. and Tamiya,N. (1977) Structure of snake toxins and their affinity to the acetylcholine receptor of fish electric organ. Toxicon, 15, 477-488.
24. Kuhn,P., Deacon,A.M., Comsa,D.S., Rajaseger,G., Kini,R.M., Uson,I.I. and Kolatkar,P.R. (2000) The atomic resolution structure of bucandin, a novel toxin isolated from the Malayan krait, determined by direct methods. Acta Crystallogr. D., 56, 1401-1407.
25. Lenffer,J., Lai,P., El Mejaber,W., Khan,A.M., Koh,J.L., Tan,P.T., Seah,S.H. and Brusic,V. (2004) CysView: protein classification based on cysteine pairing patterns. Nucleic Acids Res., 32, W350-W355.
26. Liu,C.S., Hsiao,P.W., Chang,C.S., Tzeng,M.C. and Lo,T.B. (1989) Unusual amino acid sequence of fasciatoxin, a weak reversibly acting neurotoxin in the venom of the banded krait, Bungarus fasciatus. Biochem. J., 259, 153-158.
27. Marchot,P., Frachon,P. and Bougis,P.E. (1988) Selective distinction at equilibrium between the two alpha-neurotoxin binding sites of Torpedo acetylcholine receptor by microtitration. Eur. J. Biochem. 174, 537-542.
28. Meyer,E.M., Kuryatov,A., Gerzanich,V., Lindstrom,J. and Papke,R.L. (1998) Analysis of of 3-(4-hydroxy-, 2-methoxybenzylidene) anabaseine selectivity and activity at human and rat alpha-7 nicotinic receptors. J. Pharmacol. Exp. Ther., 287, 918-925.
29. Page,R.D. (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci., 12, 357-358.
30. Pillet,L., Tremeau,O., Ducancel,F., Drevet,P., Zinn-Justin,S., Pinkasfeld,S., Boulain,J.C. and Menez,A. (1993) Genetic engineering of snake toxins. Role of invariant residues in the structural and functional properties of a curaremimetic toxin, as probed by site-directed mutagenesis. J. Biol. Chem., 268, 909-916.
31. Poh,S.L., Mourier,G., Thai,R., Armugam,A., Molgo,J., Servent,D., Jeyaseelan,K. and Menez,A. (2002) A synthetic weak neurotoxin binds with low affinity to Torpedo and chicken alpha7 nicotinic acetylcholine receptors. Eur. J. Biochem., 269, 4247-4256.
32. Saitou,N. and Nei,M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Bio. Evol., 4, 406-425.
33. Schönbach,C., Kowalski-Saunders,P. and Brusic,V. (2000) Data warehousing in molecular biology. Brief Bioinform., 1, 190-198.
34. Servent,D., Winckler-Dietrich,V., Hu,H.Y., Kessler,P., Drevet,P., Bertrand,D. and Menez,A. (1997) Only snake curaremimetic toxins with a fifth disulfide bond have high affinity for the neuronal alpha7 nicotinic receptor. J. Biol. Chem., 272, 24279-24286.
35. Sorace,J.M. and Canfield,K. (1998) Collaborative bioinformatics: data warehouses for targeted experimental results. J. Interferon Cytokine Res., 18, 799-802.
36. Srinivasan,K.N., Gopalakrishnakone,P., Tan,P.T., Chew,K.C., Cheng,B., Kini,R.M., Koh,J.L., Seah,S.H., Brusic,V. (2002) SCORPION, a molecular database of scorpion toxins. Toxicon, 40, 23-31.
37. Strydom,D.J. (1977) Snake venom toxins. The amino-acid sequence of a short-neurotoxin homologue from Dendroaspis polylepis polylepis (black mamba) venom. Eur. J. Biochem., 76, 99-106.
38. Tan,P.T., Khan,A.M. and Brusic,V. (2003) Bioinformatics for venom and toxin sciences. Brief Bioinform., 4, 53-62.
39. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
40. Toyama,M.H., de Oliveira,D.G., Beriam,L.O., Novello,J.C., Rodrigues-Simioni,L. and Marangoni,S. (2003) Structural, enzymatic and biological properties of new PLA(2) isoform from Crotalus durissus terrificus venom. Toxicon, 41, 1033-1038.
41. Utkin,Y.N., Kukhtina,V.V., Kryukova,E.V., Chiodini,F., Bertrand,D., Methfessel,C. and Tsetlin,V.I. (2001) 'Weak toxin' from Naja kaouthia is a nontoxic antagonist of alpha 7 and muscle-type nicotinic acetylcholine receptors. J. Biol. Chem., 276, 15810-15815.
42. Weber,M. and Changeux,J.P. (1974) Binding of Naja nigricollis (3H) alpha-toxin to membrane fragments from Electrophorus and Torpedo electric organs. I. Binding of the tritiated alpha-neurotoxin in the absence of effector. Mol. Pharmacol., 10, 1-14.
43. Yasuda,O., Morimoto,S., Jiang,B., Kuroda,H., Kimura,T., Sakakibara,S., Fukuo,K., Chen,S., Tamatani,M. and Ogihara,T. (1994) FS2: a mamba venom toxin, is a specific blocker of the L-type calcium channels. Artery, 21, 287-302.