Comparative analysis of the catalytic domain of hemorrhagic and non-hemorrhagic snake venom metallopeptidases using bioinformatic tools

Toxicon

Volumn 44, Issue 5, 2004, Pages 529-538

  Ramos, O H P ^a   Selistre De Araujo, H S ^a  

^a FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

Author keywords

Bioinformatics; Comparative analysis; Hemorrhagic; Molecular model; Non hemorrhagic; Structure; SVMPs

Indexed keywords

ASPARTIC ACID DERIVATIVE; METALLOPROTEINASE; SERINE DERIVATIVE; VENOM;

ARTICLE; BIOINFORMATICS; BLEEDING; CATALYSIS; CATALYST; COMPARATIVE STUDY; CONTROLLED STUDY; ENZYME ACTIVE SITE; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STABILITY; SEQUENCE ANALYSIS; SNAKE; STRUCTURE ANALYSIS; TECHNIQUE; TOXICOLOGY;

ANIMALS; BINDING SITES; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; HEMORRHAGE; HEMOSTASIS; METALLOENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; SNAKE VENOMS;

SERPENTES;

EID: 4644372665     PISSN: 00410101     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.toxicon.2004.07.005     Document Type: Article

References (35)

1. J.B. Bjarnason, and J.W. Fox Hemorrhagic metallopeptidases from snake venoms Pharmacol.Ther. 62 1994 325 372
2. J.U. Bowie, R. Luthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 253 1991 164 170
3. J. Castresana Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 17 2000 540 552
4. E. Daoud, A.T. Tu, and M.F. el Asmar Isolation and characterization of an anticoagulant proteinase, cerastase F-4, from Cerastes cerastes (Egyptian sand viper) venom Thromb. Res. 42 1986 55 62
5. J. Felsenstein PHYLIP - phylogeny inference package (Version 3.2) Cladistics 5 1989 164 166
6. J. Felsenstein An alternating least squares approach to inferring phylogenies from pairwise distances Syst. Biol. 46 1997 101 111
7. L.T. García, L.T. Parreiras-Silva, O.H.P. Ramos, A.K. Carmona, P.A. Bersanetti, and H.S. Selistre-de-Araujo The effect of post-translational modifications on the hemorrhagic activity of snake venom metalloproteases Comp. Biochem. Physiol. 138 2004 23 32
8. A. Gasmi, N. Srairi, H. Karoui, and M. El Ayeb Amino acid sequence of VlF: identification in the C-terminal domain of residues common to non-hemorrhagic metalloproteinases from snake venoms Biochim. Biophys. Acta 1481 2000 209 212
9. A. Gattiker, E. Gasteiger, and A. Bairoch ScanProsite: a reference implementation of a PROSITE scanning tool Appl. Bioinf. 1 2002 107 108
10. N. Guex, and M.C. Peitsch Swiss-Pdb Viewer: A Fast and Easy-to-use PDB Viewer for Macintosh and PC, Protein Data Bank Quaterly Newsletter 7 1996 pp. 7
11. K. Guruprasad, B.V. Reddy, and M.W. Pandit Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence Protein Eng. 4 1990 155 161
12. N. Hulo, C.J. Sigrist, V. LeSaux, P.S. Langendijk-Genevaux, L. Bordoli, A. Gattiker, E. De Castro, P. Bucher, and A. Bairoch Recent improvements to the PROSITE database Nucleic Acids Res. 32 2004 134 137
13. A. Ikai Thermostability and aliphatic index of globular proteins J. Biochem. 88 1980 1895 1898
14. E.K. Johnson, and C.L. Ownby Isolation of a hemorrhagic toxin from the venom of Agkistrodon contortrix laticinctus (broad-banded copperhead) and pathogenesis of the hemorrhage induced by the toxin in mice Int. J. Biochem. 25 1993 267 278
15. H. Kondo, S. Kondo, H. Ikezawa, and R. Murata Studies on the quantitative method for determination of hemorrhagic activity of Habu snake venom Jpn. J. Med. Sci. Biol. 13 1960 43 52
16. J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
17. R.A. Laskowski PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
18. M.C. Manning Sequence analysis of fibrolase, a fibrinolytic metalloproteinase from Agkistrodon contortrix contortrix Toxicon 33 1995 1189 1200
19. M.J. Paine, H.P. Desmond, R.D. Theakston, and J.M. Crampton Purification, cloning, and molecular characterization of a high molecular weight hemorrhagic metalloprotease, jararhagin, from Bothrops jararaca venom. Insights into the disintegrin gene family J. Biol. Chem. 267 1992 22869 22876
20. A. Rucavado, B. Lomonte, M. Ovadia, and J.M. Gutierrez Local tissue damage induced by BaP1, a metalloproteinase isolated from Bothrops asper (Terciopelo) snake venom Exp. Mol. Pathol. 63 1995 186 199
21. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
22. C.J. Sigrist, L. Cerutti, N. Hulo, A. Gattiker, L. Falquet, M. Pagni, A. Bairoch, and P. Bucher PROSITE: a documented database using patterns and profiles as motif descriptors Brief. Bioinf. 3 2002 265 274
23. E. Siigur, A.T. Aaspôllu, A.T. Tu, and J. Siigur cDNA cloning and deduced amino acid sequence of fibrinolytic enzyme (lebetase) from Vipera lebetina snake venom Biochem. Biophys. Res. Commun. 224 1996 229 336
24. M.D. Sternlicht, and Z. Werb How matrix metalloproteinases regulate cell behavior Annu. Rev. Cell Dev. Biol. 17 2001 463 516
25. D.L. Swofford, P.J. Waddell, J.P. Huelsenbeck, P.G. Foster, P.O. Lewis, and J.S. Rogers Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods Syst. Biol. 50 2001 525 539
26. H. Takeya, M. Arakawa, T. Miyata, S. Iwanaga, and T. Omori-Satoh Primary structure of H2-proteinase, a non-hemorrhagic metalloproteinase, isolated from the venom of the habu snake, Trimeresurus flavoviridis J. Biochem. 106 1989 151 157
27. H. Takeya, H. Takeya, K. Oda, T. Miyata, T. Omori-Satoh, and S. Iwanaga The complete amino acid sequence of the high molecular mass hemorrhagic protein HR1B isolated from the venom of Trimeresurus flavoviridis J. Biol. Chem. 265 1990 16068 16073
28. H. Takeya, K. Oda, A. Onikura, T. Miyata, S. Iwanaga, T. Nikai, H. Sugihara, and T. Omori-Satoh The structure and function relationships of hemorrhagic factors isolated from the venoms of Trimeresurus flavoviridis and Crotalus ruber ruber Jpn. J. Med. Sci. Biol. 43 1990 252 253
29. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
30. K. Trummal, H. Vija, J. Subbi, and J. Siigur MALDI-TOF mass spectrometry analysis of substrate specificity of lebetase, a direct-acting fibrinolytic metalloproteinase from Vipera lebetina snake venom Biochim. Biophys. Acta 1476 2000 331 336
31. I.H. Tsai, Y.M. Wang, T.Y. Chiang, Y.L. Chen, and R.J. Huang Purification, cloning and sequence analyses for pro-metalloprotease-disintegrin variants from Deinagkistrodon acutus venom and subclassification of the small venom metalloproteases Eur. J. Biochem. 267 2000 1359 1367
32. O.V. Tsodikov, M.T. Record Jr., and Y.V. Sergeev Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature J. Comput. Chem. 23 2002 600 609
33. G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56
34. L. Watanabe, J.D. Shannon, R.H. Valente, A. Rucavado, A. Alape-Giron, A.S. Kamiguti, R.D. Theakston, J.W. Fox, and J.M. Gutierrez Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities Protein Sci. 12 2003 2273 2281
35. X. Xu, C. Wang, J. Liu, and Z. Lu Purification and characterization of hemorrhagic components from Agkistrodon acutus (hundred pace snake) venom Toxicon 19 1981 633 644