Structural insights into substrate binding of brown spider venom class ii phospholipases d

Current Protein and Peptide Science

Volumn 16, Issue 8, 2015, Pages 768-774

  Coronado, M A ^a   Ullah, A ^a   da Silva, L S ^a   Chaves Moreira, D ^b   Vuitika, L ^b   Chaim, O M ^b   Veiga, S S ^b   Chahine, J ^a   Murakami, M T ^c   Arni, R K ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b FEDERAL UNIVERSITY OF PARANÁ   (Brazil)

^c BRAZILIAN CENTER FOR RESEARCH IN ENERGY AND MATERIALS CNPEM   (Brazil)

Author keywords

Loxoscele; Myo inositol 1 phosphate; Phospholipase D; Sphingomyelin

Indexed keywords

PHOSPHOLIPASE D; SPIDER VENOM; INOSITOL 1-PHOSPHATE; INOSITOL PHOSPHATE; LOXOSCELES VENOM; MUTANT PROTEIN; OCTANOIC ACID; OCTANOIC ACID DERIVATIVE; PHOSPHODIESTERASE;

AMINO ACID SEQUENCE; ARTICLE; CRYSTALLIZATION; DATA PROCESSING; ENZYME SUBSTRATE COMPLEX; MOLECULAR DYNAMICS; MUTAGENESIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIMULATION; X RAY DIFFRACTION; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM; MOLECULAR GENETICS; SPIDER; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CAPRYLATES; CRYSTALLOGRAPHY, X-RAY; INOSITOL PHOSPHATES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; PHOSPHOLIPASE D; PHOSPHORIC DIESTER HYDROLASES; SEQUENCE ALIGNMENT; SPIDER VENOMS; SPIDERS; SUBSTRATE SPECIFICITY;

EID: 84942086723     PISSN: 13892037     EISSN: 18755550     Source Type: Journal    
DOI: 10.2174/1389203716666150505231625     Document Type: Article

References (29)

1. Gremski, L.H.; da Silveira, R.B.; Chaim, O.M.; Probst, C.M.; Ferrer, V.P.; Nowatzki, J.; Weinschutz, H.C.; Madeira, H.M.; Gremski, W.; Nader, H.B.; Senff-Ribeiro, A.; Veiga, S.S. A novel expression profile of the Loxosceles intermedia spider venomous gland revealed by transcriptome analysis. Mol Biosyst., 2010, 6(12), 2403-2416.
2. Gremski, L.H.; Trevisan-Silva, D.; Ferrer, V.P.; Matsubara, F.H.; Meissner, G.O.; Wille, A.C.; Vuitika, L.; Dias-Lopes, C.; Ullah, A.; de Moraes, F.R.; Chavez-Olortegui, C.; Barbaro, K.C.; Murakami, M.T.; Arni, R.K.; Senff-Ribeiro, A.; Chaim, O.M.; Veiga, S.S. Recent advances in the understanding of brown spider venoms: From the biology of spiders to the molecular mechanisms of toxins. Toxicon, 2014, 83, 91-120.
3. Chaim, O.M.; Trevisan-Silva, D.; Chaves-Moreira, D.; Wille, A.C.; Ferrer, V.P.; Matsubara, F.H.; Mangil,i O.C.; da Silveira, R.B.; Gremsk,i L.H.; Gremski, W.; Senff-Ribeiro, A.; Veiga, S.S. Brown spider (Loxosceles genus) venom toxins: tools for biological purposes. Toxins (Basel), 2011, 3(3), 309-344.
4. Chaves-Moreira, D.; Souza, F.N.; Fogaca, R.T.; Mangili, O.C.; Gremski, W.; Senff-Ribeiro, A.; Chaim, O.M.; Veiga, S.S. The relationship between calcium and the metabolism of plasma membrane phospholipids in hemolysis induced by brown spider venom phospholipase-D toxin. J Cell Biochem., 2011, 112(9), 2529-2540.
5. van Meeteren, L.A.; Frederiks, F.; Giepmans, B.N.; Pedrosa, M.F.; Billington, S.J.; Jost, B.H.; Tambourgi, D.V.; Moolenaar, W.H. Spider and bacterial sphingomyelinases D target cellular lysophosphatidic acid receptors by hydrolyzing lysophosphatidylcholine. J. Biol. Chem., 2004, 279(12), 10833-10836.
6. van Meeteren, D.M.; Zobel-Thropp, P.A.; Kumirov, V.K.; Bandarian, V.; Binford, G.J.; Cordes, M.H. Phospholipase D toxins of brown spider venom convert lysophosphatidylcholine and sphingomyelin to cyclic phosphates. PLoS One, 2013, 8(8), e72372.
7. Lajoie, D.M.; Zobel-Thropp, P.A.; Kumirov, V.K.; Bandarian, V.; Binford, G.J.; Cordes, M.H. Phospholipase D toxins of brown spider venom convert lysophosphatidylcholine and sphingomyelin to cyclic phosphates. PLoS One, 2013, 8(8), e72372.
8. Dragulev, B.; Bao, Y.; Ramos-Cerrillo, B.; Vazquez, H.; Olvera, A.; Stock, R.; Algaron, A.; Fox, J.W. Upregulation of IL-6, IL-8, CXCL1, and CXCL2 dominates gene expression in human fibroblast cells exposed to Loxosceles reclusa sphingomyelinase D: insights into spider venom dermonecrosis. J. Invest. Dermatol., 2007, 127(5), 1264-1266.
9. Brown, H.A.; Henage, L.G.; Preininger, A.M.; Xiang, Y.; Exton, J.H. Biochemical analysis of phospholipase D. Methods Enzymol., 2007, 434, 49-87.
10. Murakami, M.T.; Fernandes-Pedrosa, M.F.; de Andrade, S.A.; Gabdoulkhakov, A.; Betzel, C.; Tambourgi, D.V.; Arni, R.K. Structural insights into catalytic mechanism of sphingomyelinase D and evolutionary relationship to glycerophosphodiester phosphodiesterases. Biochem. Biophys. Res. Commun., 2006, 342(1), 323-329.
11. Giuseppe, P.O.; Ullah, A.; Trevisan-Silva, D.; Gremski, L.H.; Wille, A.C.M.; Chaves-Moreira, D.; Ribeiro, A.S.; MeiriCHain, O.; Murakam,i M.T.; Veiga, S.S.; Arni, R.K. Structure of a novel class II phospholipase D: Catalytic cleftis modified by a disulphide bridge. Biochem. Biophys. Res. Commun., 2011, 409, 622-627.
12. Chaves-Moreira, D.; Chaim, O.M.; Sade, Y.B.; Paludo, K.S.; Gremski, L.H.; Donatti, L.; de Moura, J.; Mangili, O.C.; Gremski, W.; da Silveira, R.B.; Senff-Ribeiro, A.; Veiga, S.S. Identification of a direct hemolytic effect dependent on the catalytic activity induced by phospholipase-D (dermonecrotic toxin) from brown spider venom. J. Cell Biochem., 2009, 107(4), 655-666.
13. Ullah, A.; Giuseppe, P.O.; Murakami, M.T.; Trevisan-Silva, D.; Wille, A.C.M.; Chaves-Moreira, D.; Gremski, L.H.; da Silveira, R.B.; Sennf-Ribeiro, A.; Chaim, O.M.; Veiga, S.S.; Arni, R.K. Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom. Acta Crystallogr. F, 2011, 67, 234-236.
14. Otwinowskiand, Z.; Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode, Methods in Enzymology. Macromolecular Crystallography, part A. 276, 307-326, C.W. Carter, Jr. & R.M. Sweet, Eds. Academic Press. 1997.
15. Vagin, A.; Teplyakov, A. MOLREP: An Automated Program for Molecular Replacement. J. Appl. Crystallogr., 1997, 30, 1022-1025.
16. Murshudov, G.N.; Skubak, P.; Lebedev, A.A.; Pannu, N.S.; Steiner, R.A.; Nicholls, R.A.; Winn, M.D.; Long, F.; Vagin, A.A. REFMAC for the refinement of macromolecular crystal structure. Acta Cryst. D., 2011, 67, 355-367.
17. Emsley. P.; Cowtan. K. Coot: model-building tools for molecular graphics. Acta Cryst. D-Bio Cryst,. 2004, 60, 2126-2132.
18. Hanwell, M.D.; Curtis, D.E.; Lonie, D.C.; Vandermeersch, T.; Zurek, E.; Hutchison, G.R. Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J. Cheminformatics, 2012, 4, 17.
19. Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollamn, P.A.; Case, D.A. Development and testing of a general Amber force field. J. Comput. Chem., 2004, 25, 1157-1174.
20. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani G.; Barone, V.; Mennucci, B.; Petersson, G.A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H.P.; Izmaylov, A.F.; Bloino, J.; Zheng, G.; Sonnenberg, J.L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai H.; Vreven, R.; Montgomery, J.A.; Peralta, J.E.; Ogliaro, F.; Bearpark, M.; Heyd, J.J.; Brothers, Kudin, K.N.; Staroverov, V.N.; Kobayashi, R.; Normand J.; Raghavachari, K.; Rendell, A.; Burant, J.C.; Iyengar, S.S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J.M.; Klene, M.; Knox, J.E.; Cross, J.B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R.E.; Yazyev, O.; Austin, A.J.; Cammi, R.; Pomelli, C.; Ochterski, J.W.; Martin, R.L.; Morokuma, K.; Zakrzewski, V.G.; Voth, G.A.; Salvador, P.; Dannenberg, J.J.; Dapprich, S.; Daniels, A.D.; Farkas, O.; Foresman, J.B.; Ortiz, J.V.; Cioslowski, J.; Fox, D.J. Gaussian, Inc., Wallingford CT, Gaussian 09, Revision A.02, 2009.
21. Case, D.A.; Darden, T.A.; Cheatham, T.E.; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Walker, R.C.; Zhang, W.; Merz, K.M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K.F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S.R.; Steinbrecher T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.J.; Cui, G.; Roe, D.R.; Mathews, D.H.; Seetin, M.G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P.A. AMBER 11, San Francisco, 2010.
22. Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.; Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 1983, 79, 926-935.
23. Martyna, G.J.; Klein, M.L.; Tuckerman, M. Nosie-Hoover chains: The canonical ensemble via continuous dynamics. J. Chem. Phys., 1992, 97, 2635.
24. Cerutti, D.S.; Case, D.A. Multi-Level Ewald: A Hybrid Multigrid/ Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem. J. Chem. Theory Comput., 2010, 6, 443-458.
25. Ryckaert, J.P.; Ciccotti, G.; Berendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys., 1977, 23, 327-341.
26. Anandakrishnan, R.; Aguilar, B.; Onufriev, A.V. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulation. Nucleic Acids Res., 2012, 40, 537-541.
27. Chaim, O.M.; Sade, Y.B.; da Silveira, R.B.; Toma, L.; Kalapothakis, E.; Chavez-Olortegui, C.; Mangili, O.C.; Gremski, W.; von Dietrich, C.P.; Nader, H.B.; Veiga, S.S. Brown spider dermonecrotic toxin directly induces nephrotoxicity. Toxicol .Appl. Pharmacol., 2006, 211(1), 64-77.
28. Bruntz, R.C.; Lindsley, C.W.; Brown, H.A. Phospholipase D Signaling Pathways and Phosphatidic Acid as Therapeutic Targets in Cancer. Pharmacol. Rev., 2014, 66, 1033-1079.
29. Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera-a visualization system for exploratory researchand analysis. J. Comput. Chem., 2004, 2(13), 1605-1612.