About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 185282, 15 pages
http://dx.doi.org/10.1155/2013/185282
Research Article

Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein

1Fish Health Management Division, Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, Odisha 751002, India
2Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, Bihar 800007, India

Received 30 March 2013; Revised 10 June 2013; Accepted 11 June 2013

Academic Editor: Claudio M. Soares

Copyright © 2013 Bikash Ranjan Sahoo et al. 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. S. Akira, S. Uematsu, and O. Takeuchi, “Pathogen recognition and innate immunity,” Cell, vol. 124, no. 4, pp. 783–801, 2006. View at Publisher · View at Google Scholar · View at Scopus
  2. S. de la Barrera, M. Alemán, and M. D. C. Sasiain, “Toll-like receptors in human infectious diseases,” Current Pharmaceutical Design, vol. 12, no. 32, pp. 4173–4184, 2006. View at Publisher · View at Google Scholar · View at Scopus
  3. T. Kawai and S. Akira, “The role of pattern-recognition receptors in innate immunity: update on toll-like receptors,” Nature Immunology, vol. 11, no. 5, pp. 373–384, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. R. Medzhitov, “Toll-like receptors and innate immunity,” Nature Reviews Immunology, vol. 1, no. 2, pp. 135–145, 2001. View at Scopus
  5. B. A. Beutler, “TLRs and innate immunity,” Blood, vol. 113, no. 7, pp. 1399–1407, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. U. Buwitt-Beckmann, H. Heine, K.-H. Wiesmüller et al., “TLR1- and TLR6-independent recognition of bacterial lipopeptides,” Journal of Biological Chemistry, vol. 281, no. 14, pp. 9049–9057, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. O. Takeuchi, S. Sato, T. Horiuchi et al., “Cutting edge: role of Toll-like receptor 1 in mediating immune response to microbial lipoproteins,” Journal of Immunology, vol. 169, no. 1, pp. 10–14, 2002. View at Scopus
  8. E. Lien, T. J. Sellati, A. Yoshimura et al., “Toll-like receptor 2 functions as a pattern recognition receptor for diverse bacterial products,” Journal of Biological Chemistry, vol. 274, no. 47, pp. 33419–33425, 1999. View at Publisher · View at Google Scholar · View at Scopus
  9. R. Medzhitov, P. Preston-Hurlburt, E. Kopp et al., “MyD88 is an adaptor protein in the hToll/IL-1 receptor family signaling pathways,” Molecular Cell, vol. 2, no. 2, pp. 253–258, 1998. View at Scopus
  10. R. Dziarski, “Recognition of bacterial peptidoglycan by the innate immune system,” Cellular and Molecular Life Sciences, vol. 60, no. 9, pp. 1793–1804, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. K. H. Schleifer and O. Kandler, “Peptidoglycan types of bacterial cell walls and their taxonomic implications,” Bacteriological Reviews, vol. 36, no. 4, pp. 407–477, 1972. View at Scopus
  12. R. Guan and R. A. Mariuzza, “Peptidoglycan recognition proteins of the innate immune system,” Trends in Microbiology, vol. 15, no. 3, pp. 127–134, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. D. Iwaki, H. Mitsuzawa, S. Murakami et al., “The extracellular toll-like receptor 2 domain directly binds peptidoglycan derived from Staphylococcus aureus,” Journal of Biological Chemistry, vol. 277, no. 27, pp. 24315–24320, 2002. View at Publisher · View at Google Scholar · View at Scopus
  14. H. Mitsuzawa, I. Wada, H. Sano et al., “Extracellular toll-like receptor 2 region containing Ser40-Ile64 but not Cys30-Ser39 is critical for the recognition of Staphylococcus aureus peptidoglycan,” Journal of Biological Chemistry, vol. 276, no. 44, pp. 41350–41356, 2001. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Schwandner, R. Dziarski, H. Wesche, M. Rothe, and C. J. Kirschning, “Peptidoglycan- and lipoteichoic acid-induced cell activation is mediated by Toll-like receptor 2,” Journal of Biological Chemistry, vol. 274, no. 25, pp. 17406–17409, 1999. View at Publisher · View at Google Scholar · View at Scopus
  16. J. Asong, M. A. Wolfert, K. K. Maiti, D. Miller, and G.-J. Boons, “Binding and cellular activation studies reveal that toll-like receptor 2 can differentially recognize peptidoglycan from gram-positive and gram-negative bacteria,” Journal of Biological Chemistry, vol. 284, no. 13, pp. 8643–8653, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. I. C. Sutcliffe and N. Shaw, “Atypical lipoteichoic acids of gram-positive bacteria,” Journal of Bacteriology, vol. 173, no. 22, pp. 7065–7069, 1991. View at Scopus
  18. S. Deininger, S. Traub, D. Aichele et al., “Presentation of lipoteichoic acid potentiates its inflammatory activity,” Immunobiology, vol. 213, no. 6, pp. 519–529, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Von Aulock, S. Deininger, C. Draing, K. Gueinzius, O. Dehus, and C. Hermann, “Gender difference in cytokine secretion on immune stimulation with LPS and LTA,” Journal of Interferon and Cytokine Research, vol. 26, no. 12, pp. 887–892, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. I.-T. Lee, S.-W. Wang, C.-W. Lee et al., “Lipoteichoic acid induces HO-1 expression via the TLR2/MyD88/c-Src/NADPH oxidase pathway and Nrf2 in human tracheal smooth muscle cells,” Journal of Immunology, vol. 181, no. 7, pp. 5098–5110, 2008. View at Scopus
  21. B. N. Gantner, R. M. Simmons, S. J. Canavera, S. Akira, and D. M. Underhill, “Collaborative induction of inflammatory responses by dectin-1 and toll-like receptor 2,” Journal of Experimental Medicine, vol. 197, no. 9, pp. 1107–1117, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. G. D. Brown, J. Herre, D. L. Williams, J. A. Willment, A. S. J. Marshall, and S. Gordon, “Dectin-1 mediates the biological effects of β-glucans,” Journal of Experimental Medicine, vol. 197, no. 9, pp. 1119–1124, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. D. M. Underhill, A. Ozinsky, A. M. Hajjar et al., “The Toll-like receptor 2 is recruited to macrophage phagosomes and discriminates between pathogens,” Nature, vol. 401, no. 6755, pp. 811–815, 1999. View at Publisher · View at Google Scholar · View at Scopus
  24. A. Ozinsky, D. M. Underhill, J. D. Fontenot et al., “The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between Toll-like receptors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 25, pp. 13766–13771, 2000. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Sato, H. Sano, D. Iwaki et al., “Direct binding of toll-like receptor 2 to Zymosan, and Zymosan-induced NF-κB activation and TNF-α secretion are down-regulated by lung collectin surfactant protein A,” Journal of Immunology, vol. 171, no. 1, pp. 417–425, 2003. View at Scopus
  26. M. E. Frasnelli, D. Tarussio, V. Chobaz-Péclat, N. Busso, and A. So, “TLR2 modulates inflammation in zymosan-induced arthritis in mice,” Arthritis Research & Therapy, vol. 7, no. 2, pp. R370–379, 2005. View at Scopus
  27. C. Jault, L. Pichon, and J. Chluba, “Toll-like receptor gene family and TIR-domain adapters in Danio rerio,” Molecular Immunology, vol. 40, no. 11, pp. 759–771, 2004. View at Publisher · View at Google Scholar · View at Scopus
  28. A. H. Meijer, S. F. Gabby Krens, I. A. Medina Rodriguez et al., “Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish,” Molecular Immunology, vol. 40, no. 11, pp. 773–783, 2004. View at Publisher · View at Google Scholar · View at Scopus
  29. I. Hirono, M. Takami, M. Miyata et al., “Characterization of gene structure and expression of two toll-like receptors from Japanese flounder Paralichthys olivaceus,” Immunogenetics, vol. 56, no. 1, pp. 38–46, 2004. View at Publisher · View at Google Scholar · View at Scopus
  30. H. Oshiumi, T. Tsujita, K. Shida, M. Matsumoto, K. Ikeo, and T. Seya, “Prediction of the prototype of the human Toll-like receptor gene family from the pufferfish, Fugu rubripes, genome,” Immunogenetics, vol. 54, no. 11, pp. 791–800, 2003. View at Scopus
  31. P. Baoprasertkul, E. Peatman, J. Abernathy, and Z. Liu, “Structural characterisation and expression analysis of Toll-like receptor 2 gene from catfish,” Fish and Shellfish Immunology, vol. 22, no. 4, pp. 418–426, 2007. View at Publisher · View at Google Scholar · View at Scopus
  32. Y.-W. Li, X.-C. Luo, X.-M. Dan et al., “Orange-spotted grouper (Epinephelus coioides) TLR2, MyD88 and IL-1β involved in anti-Cryptocaryon irritans response,” Fish and Shellfish Immunology, vol. 30, no. 6, pp. 1230–1240, 2011. View at Publisher · View at Google Scholar · View at Scopus
  33. Y. C. Wei, T. S. Pan, M. X. Chang et al., “Cloning and expression of Toll-like receptors 1 and 2 from a teleost fish, the orange-spotted grouper Epinephelus coioides,” Veterinary Immunology and Immunopathology, vol. 141, no. 3-4, pp. 173–182, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. C. M. S. Ribeiro, T. Hermsen, A. J. Taverne-Thiele, H. F. J. Savelkoul, and G. F. Wiegertjes, “Evolution of recognition of ligands from gram-positive bacteria: similarities and differences in the TLR2-mediated response between mammalian vertebrates and teleost fish,” Journal of Immunology, vol. 184, no. 5, pp. 2355–2368, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Samanta, B. Swain, M. Basu et al., “Molecular characterization of toll-like receptor 2 (TLR2), analysis of its inductive expression and associated down-stream signaling molecules following ligands exposure and bacterial infection in the Indian major carp, rohu (Labeo rohita),” Fish and Shellfish Immunology, vol. 32, no. 3, pp. 411–425, 2012. View at Publisher · View at Google Scholar · View at Scopus
  36. M. Basu, B. Swain, B. R. Sahoo, N. K. Maiti, and M. Samanta, “Induction of toll-like receptor (TLR) 2, and MyD88-dependent TLR- signaling in response to ligand stimulation and bacterial infections in the Indian major carp, mrigal (Cirrhinus mrigala),” Molecular Biology Reports, vol. 39, no. 5, pp. 6015–6028, 2012. View at Publisher · View at Google Scholar · View at Scopus
  37. J. P. Clewley and C. Arnold, “MEGALIGN. The multiple alignment module of LASERGENE,” Methods in Molecular Biology, vol. 70, pp. 119–129, 1997. View at Scopus
  38. J. Shi, T. L. Blundell, and K. Mizuguchi, “FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties,” Journal of Molecular Biology, vol. 310, no. 1, pp. 243–257, 2001. View at Publisher · View at Google Scholar · View at Scopus
  39. K. Mizuguchi, C. M. Deane, T. L. Blundell, M. S. Johnson, and J. P. Overington, “JOY: protein sequence-structure representation and analysis,” Bioinformatics, vol. 14, no. 7, pp. 617–623, 1998. View at Publisher · View at Google Scholar · View at Scopus
  40. A. Sali and T. L. Blundell, “Comparative protein modelling by satisfaction of spatial restraints,” Journal of Molecular Biology, vol. 234, no. 3, pp. 779–815, 1993. View at Publisher · View at Google Scholar · View at Scopus
  41. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, “GROMACS: fast, flexible, and free,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1701–1718, 2005. View at Publisher · View at Google Scholar · View at Scopus
  42. G. Vriend, “WHAT IF: a molecular modeling and drug design program,” Journal of Molecular Graphics, vol. 8, no. 1, pp. 52–56, 1990. View at Scopus
  43. V. B. Chen, W. B. Arendall III, J. J. Headd et al., “MolProbity: all-atom structure validation for macromolecular crystallography,” Acta Crystallographica Section D, vol. 66, no. 1, pp. 12–21, 2010. View at Publisher · View at Google Scholar · View at Scopus
  44. B. Wallner, H. Fang, and A. Elofsson, “Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller,” Proteins, vol. 53, no. 6, pp. 534–541, 2003. View at Publisher · View at Google Scholar · View at Scopus
  45. L. J. Mcguffin, “The ModFOLD server for the quality assessment of protein structural models,” Bioinformatics, vol. 24, no. 4, pp. 586–587, 2008. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Pawlowski, M. J. Gajda, R. Matlak, and J. M. Bujnicki, “MetaMQAP: a meta-server for the quality assessment of protein models,” BMC Bioinformatics, vol. 9, article 403, 2008. View at Publisher · View at Google Scholar · View at Scopus
  47. B. Huang, “Metapocket: a meta approach to improve protein ligand binding site prediction,” OMICS A Journal of Integrative Biology, vol. 13, no. 4, pp. 325–330, 2009. View at Publisher · View at Google Scholar · View at Scopus
  48. A. T. R. Laurie and R. M. Jackson, “Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites,” Bioinformatics, vol. 21, no. 9, pp. 1908–1916, 2005. View at Publisher · View at Google Scholar · View at Scopus
  49. R. Huey, G. M. Morris, A. J. Olson, and D. S. Goodsell, “A semiempirical free energy force field with charge-based desolvation,” Journal of Computational Chemistry, vol. 28, no. 6, pp. 1145–1152, 2007. View at Publisher · View at Google Scholar · View at Scopus
  50. M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, “A fast flexible docking method using an incremental construction algorithm,” Journal of Molecular Biology, vol. 261, no. 3, pp. 470–489, 1996. View at Publisher · View at Google Scholar · View at Scopus
  51. G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor, “Development and validation of a genetic algorithm for flexible docking,” Journal of Molecular Biology, vol. 267, no. 3, pp. 727–748, 1997. View at Publisher · View at Google Scholar · View at Scopus
  52. B. R. Sahoo, M. Basu, B. Swain, et al., “Structural insights of rohu TLR3, its binding site analysis with fish reovirus dsRNA, poly I:C and zebrafish TRIF,” International Journal of Biological Macromolecules, vol. 51, no. 4, pp. 531–543, 2012.
  53. Y. Li, C. L. Efferson, R. Ramesh, G. E. Peoples, P. Hwu, and C. G. Ioannides, “A peptidoglycan monomer with the glutamine to serine change and basic peptides bind in silico to TLR-2 (403–455),” Cancer Immunology, Immunotherapy, vol. 60, no. 4, pp. 515–524, 2011. View at Publisher · View at Google Scholar · View at Scopus
  54. S. J. de Vries, M. van Dijk, and A. M. J. J. Bonvin, “The HADDOCK web server for data-driven biomolecular docking,” Nature Protocols, vol. 5, no. 5, pp. 883–897, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. R. Chen, L. Li, and Z. Weng, “ZDOCK: an initial-stage protein-docking algorithm,” Proteins, vol. 52, no. 1, pp. 80–87, 2003. View at Publisher · View at Google Scholar · View at Scopus
  56. S. Basith, B. Manavalan, R. G. Govindaraj, and S. Choi, “In silico approach to inhibition of signaling pathways of toll-like receptors 2 and 4 by ST2L,” PLoS ONE, vol. 6, no. 8, Article ID e23989, 2011. View at Publisher · View at Google Scholar · View at Scopus
  57. M. S. Jin, S. E. Kim, J. Y. Heo et al., “Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide,” Cell, vol. 130, no. 6, pp. 1071–1082, 2007. View at Publisher · View at Google Scholar · View at Scopus
  58. J. Y. Kang, X. Nan, M. S. Jin et al., “Recognition of lipopeptide patterns by toll-like receptor 2-toll-like receptor 6 heterodimer,” Immunity, vol. 31, no. 6, pp. 873–884, 2009. View at Publisher · View at Google Scholar · View at Scopus