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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Kang TS, Georgieva D et al (2011) Enzymatic toxins from snake venom: structural characterization and mechanism of catalysis. FEBS J 278:4544–4576
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 114:788–811
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 83:91–120
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 9:279
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 22:128–132
Zhu Z, Liang Z et al (2005) Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases. J Biol Chem 280:10524–10529
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 421:124–128
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 51:209–214
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 409:622–627
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 342:323–329
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 70:1418–1420
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 70:1556–1559
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 68:1222–1225
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 76:282–290
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 68:1052–1054
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 16:768–774
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):1054–1065
Berejnov V, Husseini NS, Alsaied OA, Thorne RE (2006) Effects of cryoprotectant concentration and cooling rate on vitrification of aqueous solutions. J Appl Crystallogr 39:244–251
Otwinowski Z, Minor W (1997) Macromolecular crystallography. Part A. Academic Press, New York, pp 307–326
Battye TGG, Kontogiannis L, Johnson O, Powell HR, Leslie AGW (2011) iMosflm: a new graphical interface for diffraction-image processing with MOSFLM. Acta Cryst D67:271–281
Kabsch W (2010) XDS. Acta Cryst D66:125–132
Vagin AA, Teplyakov A (1997) Molrep: an automated program for molecular replacement. J Appl Crystallogr 30:1022–1025
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501
DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos
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 25:1605–1612
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ullah, A., Masood, R., Hayat, Z., Hafeez, A. (2020). Determining the Structures of the Snake and Spider Toxins by X-Rays. In: Priel, A. (eds) Snake and Spider Toxins. Methods in Molecular Biology, vol 2068. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9845-6_8
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9845-6_8
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9844-9
Online ISBN: 978-1-4939-9845-6
eBook Packages: Springer Protocols