Insights into the substrate specificity of a novel snake venom serine peptidase by molecular modeling

Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology

Volumn 144, Issue 3, 2006, Pages 334-342

  Vitorino Cardoso, Ana Flávia ^a   Pereira Ramos, Oscar Henrique ^b   Homsi Brandeburgo, Maria Inês ^a   Selistre de Araujo, Heloisa Sobreiro ^b  

^a FEDERAL UNIVERSITY OF UBERLÂNDIA   (Brazil)

^b FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

Author keywords

Bothrops alternatus; cDNA cloning; cDNA sequencing; Comparative analysis; Homology modeling; Recombinant serine peptidase; Snake venom; Thrombin like enzymes

Indexed keywords

ARGININE; ASPARTIC ACID; BOTHROPS ALTERNATUS THROMBIN LIKE ENZYME; BRIDGED COMPOUND; CALCIUM; COMPLEMENTARY DNA; GLYCINE; LIGAND; PHENYLALANINE; PLASMINOGEN ACTIVATOR; PROTEIN DERIVATIVE; SNAKE VENOM; SNAKE VENOM SERINE PEPTIDASE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; DNA SEQUENCE; ENZYME CONFORMATION; ENZYME SPECIFICITY; GENE CLUSTER; GENE SEQUENCE; HEMOSTASIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMINOGEN ACTIVATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

BOTHROPS ALTERNATUS; VIRIDOVIPERA STEJNEGERI;

EID: 33745235785     PISSN: 10964959     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpb.2006.03.010     Document Type: Article

References (47)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped blast and PSI-blast: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Barrett A.J., and Rawlings R.D. Families and clans of serine peptidases. Arch. Biochem. Biophys. 318 (1995) 247-250
3. Bode W., Turk D., and Karshikov A. The refined 1.9-Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human [α]-thrombin: structure analysis, overall structure, eletrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci. 1 (1992) 426-471
4. Bowie J.U., Luthy R., and Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 (1991) 164-170
5. Brandstetter H., Bauer M., Huber R., Lollar P., and Bode W. X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 9796-9800
6. Braud S., Bon C., and Wisner A. Snake venom proteins acting on hemostasis. Biochimie 82 (2000) 851-859
7. Braud S., Parry M.A.A., Maroun R., Bon C., and Wisner A. The contribution of residues 192 and 193 to the specificity of snake venom serine proteinases. J. Biol. Chem. 275 (2000) 1823-1828
8. Braud S., Le Bonniec B.F., Bon C., and Wisner A. The stratagem utilized by the plasminogen activator of Trimeresurus stejnegeri to escape serpins. Biochemistry 41 (2002) 8478-8484
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
10. Castro H.C., Silva D.M., Craik C., and Zingali R.B. Structural features of a snake venom thrombin-like enzyme: primary structure and evidence for a fibrinogen recognition exosite different from thrombin. Biochim. Biophys. Acta 1547 (2001) 183-195
11. Castro H.C., Zingali R.B., Albuquerque M.G., Pujol-Luz M., and Rodrigues C.R. Snake venom thrombin-like enzymes: from reptilase to now. Cell. Mol. Life Sci. 61 (2004) 843-856
12. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16 (1988) 10881-10890
13. Felsenstein J. PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5 (1989) 164-166
14. Guex N., and Peitsch M.C. Swiss PDB-Viewer: a fast and easy-to-use PDB viewer for Macintosh and PC. Protein Data Bank Quarterly Newsletter vol. 77 (1996) 7
15. Guinto E.R., Caccia S., Rose T., Futterer K., Waksman G., and Di Cera E. Unexpected crucial role of residue 225 in serine proteases. Proc. Natl. Acad. Sci. U. S. A. 93 (1999) 10653-10656
16. Komori Y., and Nikai T. Chemistry and biochemistry of kallikrein-like enzyme from snake venoms. J. Toxicol., Toxin Rev. 17 (1998) 261-277
17. Krem M.M., and Di Cera H. Molecular markers of serine protease evolution. EMBO J. 20 (2001) 3036-3045
18. Laskowski R.A. Procheck: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
19. Lesk A.M., and Fordham W.D. Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J. Mol. Biol. 258 (1996) 501-537
20. Magalhaes A., Ferreira R.N., Richardson M., Gontijo S., Yarleque A., Magalhaes H.P.B., Bloch C., and Sanchez E.F. Coagulant thrombin-like enzymes from the venoms of Brazilian and Peruvian bushmaster (Lachesis muta muta) snakes. Comp. Biochem. Physiol., B 136 (2003) 255-266
21. Markland F. Snake venoms and the hemostatic system. Toxicon 36 (1998) 1749-1800
22. Maroun R.C., and Serrano S.M. Identification of the substrate-binding exosites of two snake venom serine proteinases: molecular basis for the partition of two essential functions of thrombin. J. Mol. Recognit. 17 (2004) 51-61
23. Matsui T., Fujimura Y., and Titani K. Snake venom proteases affecting hemostasis and thrombosis. Biochim. Biophys. Acta 1477 (2000) 146-156
24. McGrath M.E., Vasquez J.R., Craik C.S., Yang A.S., Honig B., and Fletterick R.J. Perturbing the polar environment of Asp102 in trypsin: consequences of replacing conserved Ser214. Biochemistry 31 (1992) 3059-3064
25. Ouyang C., Teng C., and Huang T. Characterization of snake venom components acting on blood coagulation and platelet function. Toxicon 30 (1992) 945-966
26. Oyama E., and Takahashi H. Purification and characterization of a thrombin-like enzyme, elegaxobin II, with Lysbradykinin releasing activity from the venom of Trimeresurus elegans (Sakishima-Habu). Toxicon 41 (2003) 559-568
27. Padmanabhan K., Padmanabhan K.P., Tulinsky A., Park C.H., Bode W., Huber R., Blankenship D.T., Cardin A.D., and Kisiel W. Structure of human des(1-45) factor Xa at 2.2 Å resolution. J. Mol. Biol. 232 (1993) 947-966
28. Parry M.A., Jacob U., Huber R., Wisner A., Bon C., and Bode W. The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases. Structure 6 (1998) 1195-1206
29. Perona J.J., and Craik C.S. Structural basis of substrate specificity in the serine proteases. Protein Sci. 4 (1995) 337-360
30. Perona J.J., and Craik C.S. Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold. J. Biol. Chem. 272 (1997) 29987-29990
31. Pinho F.M.O., and Pereira I.D. Ofidismo. Rev. Assoc. Med. Bras. 47 (2001) 24-29
32. Pletnev V.Z., Zamolodchikova T.S., Pangborn W.A., and Duax W.L. Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities. Proteins 41 (2000) 8-16
33. Rocha M.M.T., and Furtado M.F.D. Individual characterization of Bothrops alternatus Duméril, Bibron & Duméril venoms, according to their geographic distribution in Brazil (Serpentes, Viperidae). Rev. Bras. Zool. 22 2 (2005) 383-393
34. Sali A., and Blundell T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
35. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning. A Laboratory Manual (1989), Cold Spring Harbor, Laboratory Press, New York
36. Sanger F., Nicklen S., and Coulson A.R. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 5463-5467
37. Serrano S.M.T., and Maroun R.C. Snake venom serine proteinases: sequence homology vs. substrate specificity, a paradox to be solved. Toxicon 45 (2005) 1115-1132
38. Serrano S.M., Mentele R., Sampaio C.A., and Fink E. Purification, characterization, and amino acid sequence of a serine proteinase, PA-BJ, with platelet-aggregating activity from the venom of Bothrops jararaca. Biochemistry 34 (1995) 7186-7193
39. Silva Jr. F.P., and De-Simone S.G. S1 subsite in snake venom thrombin-like enzymes: can S1 subsite lypophilicity be used to sort binding affinities of trypsin-like enzymes to small-molecule inhibitors?. Bioorg. Med. Chem. 12 (2004) 2571-2587
40. Smolka M.B., Marangoni S., Oliveira B., and Novello J.C. Purification and partial characterization of a thrombin-like enzyme, balterobin, from the venom of Bothrops alternatus. Toxicon 36 (1998) 1059-1063
41. Swofford D.L., Waddell P.J., Huelsenback J.P., Foster P.G., Lewis P.O., and Rogers J.S. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50 (2001) 525-539
42. Thompson J.D., Higgins D.G., and Gibson T.J. 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
43. Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56
44. Wisner A., Braud S., and Bon C. Snake venom proteinases as tools in hemostasis studies: structure-function relationship of a plasminogen activator purified from Trimeresurus stejnegeri venom. Haemostasis 31 (2001) 133-140
45. You W.K., Choi W.S., Koh Y.S., Shin H.C., Jang Y., and Chung K.H. Functional characterization of recombinant batroxobin, a snake venom thrombin-like enzyme, expressed from Pichia pastoris. FEBS Lett. 571 (2004) 67-73
46. Zhang Y., Wisner A., Xiong Y., and Bon C. A novel plasminogen activator from snake venom. Purification, characterization, and molecular cloning. J. Biol. Chem. 270 (1995) 10246-10255
47. Zhang Y., Wisner A., Maroun R.C., Chournet V., Xiong Y., and Bon C. Trimeresurus stejnegeri snake venom plasminogen activator. Site-directed mutagenesis and molecular modeling. J. Biol. Chem. 272 (1997) 20531-20537