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BioMed Research International
Volume 2013 (2013), Article ID 471636, 10 pages
http://dx.doi.org/10.1155/2013/471636
Research Article

In Silico Modeling and Functional Interpretations of Cry1Ab15 Toxin from Bacillus thuringiensis BtB-Hm-16

National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Maunath Bhanjan, Uttar Pradesh 275101, India

Received 4 April 2013; Accepted 19 August 2013

Academic Editor: H. C. Van der Mei

Copyright © 2013 Sudhanshu Kashyap. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. Y. Roh, J. Y. Choi, M. S. Li, B. R. Jin, and Y. H. Je, “Bacillus thuringiensis as a specific, safe, and effective tool for insect pest control,” Journal of Microbiology and Biotechnology, vol. 17, no. 4, pp. 547–559, 2007. View at Scopus
  2. C. Hofmann, H. Vanderbruggen, H. Hofte, J. van Rie, S. Jansens, and H. van Mellaert, “Specificity of Bacillus thuringiensisδ-endotoxins is correlated with the presence of high-affinity binding sites in the brush border membrane of target insect midguts,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 21, pp. 7844–7848, 1988. View at Scopus
  3. P. Boonserm, P. Davis, D. J. Ellar, and J. Li, “Crystal structure of the mosquito-larvicidal toxin Cry4Ba and its biological implications,” Journal of Molecular Biology, vol. 348, no. 2, pp. 363–382, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. P. Boonserm, M. Mo, C. Angsuthanasombat, and J. Lescar, “Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution,” Journal of Bacteriology, vol. 188, no. 9, pp. 3391–3401, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. D. J. Derbyshire, D. J. Ellar, and J. Li, “Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine,” Acta Crystallographica D, vol. 57, no. 12, pp. 1938–1944, 2001. View at Publisher · View at Google Scholar · View at Scopus
  6. N. Galitsky, V. Cody, A. Wojtczak et al., “Structure of the insecticidal bacterial δ-endotoxin Cry3Bb1 of Bacillus thuringiensis,” Acta Crystallographica D, vol. 57, no. 8, pp. 1101–1109, 2001. View at Publisher · View at Google Scholar · View at Scopus
  7. P. Grochulski, L. Masson, S. Borisova et al., “Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation,” Journal of Molecular Biology, vol. 254, no. 3, pp. 447–464, 1995. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Li, J. Carroll, and D. J. Ellar, “Crystal structure of insecticidal δ-endotoxin from Bacillus thuringiensis at 2.5 Å resolution,” Nature, vol. 353, no. 6347, pp. 815–821, 1991. View at Publisher · View at Google Scholar · View at Scopus
  9. R. J. Morse, T. Yamamoto, and R. M. Stroud, “Structure of Cry2Aa suggests an unexpected receptor binding epitope,” Structure, vol. 9, no. 5, pp. 409–417, 2001. View at Publisher · View at Google Scholar · View at Scopus
  10. P. Gutierrez, O. Alzate, and S. Orduz, “A theoretical model of the tridimensional structure of Bacillus thuringiensis subsp. medellin Cry 11Bb toxin deduced by homology modelling,” Memorias do Instituto Oswaldo Cruz, vol. 96, no. 3, pp. 357–364, 2001. View at Scopus
  11. Z. Xin-Min, X. Li-Qiu, D. Xue-Zhi, and W. Fa-Xiang, “The theoretical three-dimensional structure of Bacillus thuringiensis Cry5Aa and its biological implications,” Protein Journal, vol. 28, no. 2, pp. 104–110, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. L. Q. Xia, X. M. Zhao, X. Z. Ding, F. X. Wang, and Y. J. Sun, “The theoretical 3D structure of Bacillus thuringiensis Cry5Ba,” Journal of Molecular Modeling, vol. 14, no. 9, pp. 843–848, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000. View at Scopus
  14. D. W. A. Buchan, S. M. Ward, A. E. Lobley, T. C. O. Nugent, K. Bryson, and D. T. Jones, “Protein annotation and modelling servers at University College London,” Nucleic Acids Research, vol. 38, no. 2, pp. W563–W568, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, and M. Karplus, “Evaluation of comparative protein modeling by MODELLER,” Proteins, vol. 23, no. 3, pp. 318–326, 1995. View at Publisher · View at Google Scholar · View at Scopus
  17. C. M. Summa and M. Levitt, “Near-native structure refinement using in vacuo energy minimization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 9, pp. 3177–3182, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. I. W. Davis, A. Leaver-Fay, V. B. Chen et al., “MolProbity: all-atom contacts and structure validation for proteins and nucleic acids,” Nucleic Acids Research, vol. 35, pp. W375–W383, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. M. Wiederstein and M. J. Sippl, “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins,” Nucleic Acids Research, vol. 35, pp. W407–W410, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. R. Maiti, G. H. van Domselaar, H. Zhang, and D. S. Wishart, “SuperPose: a simple server for sophisticated structural superposition,” Nucleic Acids Research, vol. 32, pp. W590–W594, 2004. View at Publisher · View at Google Scholar · View at Scopus
  21. R. A. Laskowski, V. V. Chistyakov, and J. M. Thornton, “PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids,” Nucleic Acids Research, vol. 33, pp. D266–D268, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. D. Milburn, R. A. Laskowski, and J. M. Thornton, “Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis,” Protein Engineering, vol. 11, no. 10, pp. 855–859, 1998. View at Scopus
  23. E. F. Pettersen, T. D. Goddard, C. C. Huang et al., “UCSF Chimera—a visualization system for exploratory research and analysis,” Journal of Computational Chemistry, vol. 25, no. 13, pp. 1605–1612, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. The PyMOL Molecular Graphics System, “Version 1.2r3pre, PyMol was used for visualization of models,” Schrödinger, LLC.
  25. T. Castrignanò, P. D. De Meo, D. Cozzetto, I. G. Talamo, and A. Tramontano, “The PMDB protein model database,” Nucleic Acids Research, vol. 34, pp. D306–D309, 2006. View at Scopus
  26. C. Chothia and A. M. Lesk, “The relation between the divergence of sequence and structure in proteins,” The EMBO Journal, vol. 5, no. 4, pp. 823–826, 1986. View at Scopus
  27. C. Segura, F. Guzman, M. E. Patarroyo, and S. Orduz, “Activation pattern and toxicity of the Cry11 bb1 toxin of Bacillus thuringiensis subsp. medellin,” Journal of Invertebrate Pathology, vol. 76, no. 1, pp. 56–62, 2000. View at Publisher · View at Google Scholar · View at Scopus
  28. H. Lu, F. Rajamohan, and D. H. Dean, “Identification of amino acid residues of Bacillus thuringiensisδ-endotoxin CryIAa associated with membrane binding and toxicity to Bombyx mori,” Journal of Bacteriology, vol. 176, no. 17, pp. 5554–5559, 1994. View at Scopus
  29. D. Gerber and Y. Shai, “Insertion and organization within membranes of the δ-endotoxin pore-forming domain, helix 4-loop-helix 5, and inhibition of its activity by a mutant helix 4 peptide,” The Journal of Biological Chemistry, vol. 275, no. 31, pp. 23602–23607, 2000. View at Publisher · View at Google Scholar · View at Scopus
  30. E. Gazit, P. La Rocca, M. S. P. Sansom, and Y. Shai, “The structure and organization within the membrane of the helices composing the pore-forming domain of Bacillus thuringiensisδ-endotoxin are consistent with an “umbrella-like” structure of the pore,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 21, pp. 12289–12294, 1998. View at Scopus
  31. F. Girard, V. Vachon, G. Préfontaine et al., “Cysteine scanning mutagenesis of α4, a putative pore-lining helix of the Bacillus thuringiensis insecticidal toxin Cry1Aa,” Applied and Environmental Microbiology, vol. 74, no. 9, pp. 2565–2572, 2008. View at Publisher · View at Google Scholar · View at Scopus
  32. A. S. M. Kumar and A. I. Aronson, “Analysis of mutations in the pore-forming region essential for insecticidal activity of a Bacillus thuringiensisδ-endotoxin,” Journal of Bacteriology, vol. 181, no. 19, pp. 6103–6107, 1999. View at Scopus
  33. M. E. Nuez-Valdez, J. Sánchez, L. Lina, L. Güereca, and A. Bravo, “Structural and functional studies of α-helix 5 region from Bacillus thuringiensis Cry1Ab δ-endotoxin,” Biochimica et Biophysica Acta, vol. 1546, no. 1, pp. 122–131, 2001. View at Publisher · View at Google Scholar · View at Scopus
  34. F. Coux, V. Vachon, C. Rang et al., “Role of interdomain salt bridges in the pore-forming ability of the Bacillus thuringiensis toxins Cry1Aa and Cry1Ac,” The Journal of Biological Chemistry, vol. 276, no. 38, pp. 35546–35551, 2001. View at Publisher · View at Google Scholar · View at Scopus
  35. L. Masson, B. E. Tabashnik, Y. B. Liu, R. Brousseau, and J. L. Schwartz, “Helix 4 of the Bacillus thuringiensis Cry1Aa toxin lines the lumen of the ion channel,” The Journal of Biological Chemistry, vol. 274, no. 45, pp. 31996–32000, 1999. View at Publisher · View at Google Scholar · View at Scopus
  36. A. Z. Ge, N. I. Shivarova, and D. H. Dean, “Location of the Bombyx mori specificity domain on a Bacillus thuringiensisδ-endotoxin protein,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 11, pp. 4037–4041, 1989. View at Scopus
  37. W. Ahmad and D. J. Ellar, “Directed mutagenesis of selected regions of a Bacillus thuringiensis entomocidal protein,” FEMS Microbiology Letters, vol. 68, no. 1-2, pp. 97–104, 1990. View at Scopus
  38. D. Wu and A. I. Aronson, “Localized mutagenesis defines regions of the Bacillus thuringiensisδ endotoxin involved in toxicity and specificity,” The Journal of Biological Chemistry, vol. 267, no. 4, pp. 2311–2317, 1992.
  39. F. S. Walters, S. L. Slatin, C. A. Kulesza, and L. H. English, “Ion channel activity of N-terminal fragments from CryIA(c) δ-endotoxin,” Biochemical and Biophysical Research Communications, vol. 196, no. 2, pp. 921–926, 1993. View at Publisher · View at Google Scholar · View at Scopus
  40. D. H. Dean, F. Rajamohan, M. K. Lee et al., “Probing the mechanism of action of Bacillus thuringiensis insecticidal proteins by site-directed mutagenesis—a minireview,” Gene, vol. 179, no. 1, pp. 111–117, 1996. View at Publisher · View at Google Scholar · View at Scopus
  41. E. Gazit, N. Burshtein, D. J. Ellar, T. Sawyer, and Y. Shai, “Bacillus thuringiensis cytolytic toxin associates specifically with its synthetic helices A and C in the membrane bound state. Implications for the assembly of oligomeric transmembrane pores,” Biochemistry, vol. 36, no. 49, pp. 15546–15554, 1997. View at Publisher · View at Google Scholar · View at Scopus
  42. J. L. Schwartz, L. Potvin, X. J. Chen, R. Brousseau, R. Laprade, and D. H. Dean, “Single-site mutations in the conserved alternating-arginine region affect ionic channels formed by CryIAa, a Bacillus thuringiensis toxin,” Applied and Environmental Microbiology, vol. 63, no. 10, pp. 3978–3984, 1997. View at Scopus
  43. C. R. Pigott and D. J. Ellar, “Role of receptors in Bacillus thuringiensis crystal toxin activity,” Microbiology and Molecular Biology Reviews, vol. 71, no. 2, pp. 255–281, 2007. View at Publisher · View at Google Scholar · View at Scopus
  44. I. Gómez, L. Pardo-López, C. Munoz-Garay et al., “Role of receptor interaction in the mode of action of insecticidal Cry and Cyt toxins produced by Bacillus thuringiensis,” Peptides, vol. 28, no. 1, pp. 169–173, 2007. View at Publisher · View at Google Scholar
  45. G. P. Smith and D. J. Ellar, “Mutagenesis of two surface-exposed loops of the Bacillus thuringiensis CrylC δ-endotoxin affects insecticidal specificity,” Biochemical Journal, vol. 302, no. 2, pp. 611–616, 1994. View at Scopus
  46. X. J. Chen, M. K. Lee, and D. H. Dean, “Site-directed mutations in a highly conserved region of Bacillus thuringiensisδ-endotoxin affect inhibition of short circuit current across Bombyx mori midgets,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 19, pp. 9041–9045, 1993. View at Publisher · View at Google Scholar