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Determining the Structures of the Snake and Spider Toxins by X-Rays

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2068)

Abstract

Snake and spider venom is a complex mixture that contains proteins, peptides, and small organic and inorganic compounds. In contrast to spider venom, snake venom proteins are well known both functionally and structurally. This work describes methods for purification and crystallization of snake and spider venom toxins and their three-dimensional structure determination by X-ray crystallography.

Key words

Snake and spider venom toxins Purification Crystallization Three-dimensional structure determination 

References

  1. 1.
    Kang TS, Georgieva D et al (2011) Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis. FEBS J 278:4544–4576CrossRefPubMedGoogle Scholar
  2. 2.
    Ullah A, Masood R, Ali I, Ullah K, Ali H, Akbar H, Betzel C (2018) Thrombin-like enzymes from snake venom: structural characterization and mechanism of action. Int J Biol Macromol 114:788–811CrossRefPubMedGoogle Scholar
  3. 3.
    Gremski LH, Trevisan-Silva D et al (2014) Recent advances in the understanding of brown spider venoms: from the biology of spiders to the molecular mechanisms of toxins. Toxicon 83:91–120CrossRefPubMedGoogle Scholar
  4. 4.
    Fernandes-Pedrosa MF, Junqueira-de-Azevedo ILM, Gonçalves-de-Andrade RM et al (2008) Transcriptome analysis of Loxosceles laeta (Araneae, Sicariidae) spider venomous gland using expressed sequence tags. BMC Genomics 9:279CrossRefPubMedCentralGoogle Scholar
  5. 5.
    Ullah A, Souza TA et al (2013) Crystal structure of Jararacussin-I: the highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes. Protein Sci 22:128–132CrossRefPubMedGoogle Scholar
  6. 6.
    Zhu Z, Liang Z et al (2005) Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases. J Biol Chem 280:10524–10529CrossRefPubMedGoogle Scholar
  7. 7.
    Ullah A, Souza TA, Abrego JR, Betzel C, Murakami MT, Arni RK (2012) Structural insights into selectivity and cofactor binding in snake venom L-amino acid oxidases. Biochem Biophys Res Commun 421:124–128CrossRefPubMedGoogle Scholar
  8. 8.
    Ullah A, Souza TA, Betzel C, Murakami MT, Arni RK (2012) Crystallographic portrayal of different conformational states of a Lys49 phospholipase A2 homologue: insights into structural determinants for myotoxicity and dimeric configuration. Int J Biol Macromol 51:209–214CrossRefPubMedGoogle Scholar
  9. 9.
    de Giuseppe PO, Ullah A et al (2011) Structure of a novel class II phospholipase D: catalytic cleft is modified by a disulphide bridge. Biochem Biophys Res Commun 409:622–627CrossRefPubMedGoogle Scholar
  10. 10.
    Murakami MT, Fernandes-Pedrosa MF et al (2006) Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases. Biochem Biophys Res Commun 342:323–329CrossRefPubMedGoogle Scholar
  11. 11.
    Ullah A, Magalhães GS, Masood R, Mariutti RB, Coronado MA, Murakami MT, Barbaro KC, Arni RK (2014) Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom. Acta Crystallogr F Struct Biol Commun 70:1418–1420CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Ullah A, Masood R, Spencer PJ, Murakami MT, Arni RK (2014) Crystallization and preliminary X-ray diffraction studies of an L-amino-acid oxidase from Lachesis muta venom. Acta Crystallogr F Struct Biol Commun 70:1556–1559CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Ullah A, de Souza Tde A, Masood R, Murakami MT, Arni RK (2012) Purification, crystallization and preliminary X-ray diffraction analysis of a class P-III metalloproteinase (BmMP-III) from the venom of Bothrops moojeni. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:1222–1225CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Fernandes de Oliveira LM, Ullah A, Masood R, Zelanis A, Spencer PJ, Serrano SM, Arni RK (2013) Rapid purification of serine proteinases from Bothrops alternatus and Bothrops moojeni venoms. Toxicon 76:282–290CrossRefPubMedGoogle Scholar
  15. 15.
    Coronado MA, Georgieva D, Buck F, Gabdoulkhakov AH et al (2012) Purification, crystallization and preliminary X-ray diffraction analysis of crotamine, a myotoxic polypeptide from the Brazilian snake Crotalus durissus terrificus. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:1052–1054CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Coronado MA, Ullah A, da Silva LS et al (2015) Structural insights into substrate binding of brown spider venom class II phospholipases D. Curr Protein Pept Sci 16:768–774CrossRefPubMedGoogle Scholar
  17. 17.
    Masood R, Ullah K, Ali H, Ali I, Betzel C, Ullah A (2018) Spider’s venom phospholipases D: a structural review. Int J Biol Macromol 107(Pt A):1054–1065CrossRefPubMedGoogle Scholar
  18. 18.
    Berejnov V, Husseini NS, Alsaied OA, Thorne RE (2006) Effects of cryoprotectant concentration and cooling rate on vitrification of aqueous solutions. J Appl Crystallogr 39:244–251CrossRefGoogle Scholar
  19. 19.
    Otwinowski Z, Minor W (1997) Macromolecular crystallography. Part A. Academic Press, New York, pp 307–326CrossRefGoogle Scholar
  20. 20.
    Battye TGG, Kontogiannis L, Johnson O, Powell HR, Leslie AGW (2011) iMosflm: a new graphical interface for diffraction-image processing with MOSFLM. Acta Cryst D67:271–281Google Scholar
  21. 21.
    Kabsch W (2010) XDS. Acta Cryst D66:125–132Google Scholar
  22. 22.
    Vagin AA, Teplyakov A (1997) Molrep: an automated program for molecular replacement. J Appl Crystallogr 30:1022–1025CrossRefGoogle Scholar
  23. 23.
    Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San CarlosGoogle Scholar
  25. 25.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of BiosciencesCOMSATS UniversityIslamabadPakistan
  2. 2.Department of BiochemistryShaheed Benazir Bhutto Women UniversityPeshawarPakistan

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