In Silico approach to inhibition of signaling pathways of toll-like receptors 2 and 4 by ST2L

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Basith, Shaherin ^a   Manavalan, Balachandran ^a   Govindaraj, Rajiv Gandhi ^a   Choi, Sangdun ^a  

^a Ajou University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; MEMBRANE PROTEIN ST2L; MYELOID DIFFERENTIATION FACTOR 88; PROTEIN MAL; REGULATOR PROTEIN; TOLL LIKE RECEPTOR 1; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR 6; UNCLASSIFIED DRUG; CARRIER PROTEIN; CELL SURFACE RECEPTOR; IL1RL1 PROTEIN, HUMAN; MAL PROTEIN, T CELL; MAL PROTEIN, T-CELL; MYELIN PROTEIN; PROTEOLIPID;

ARTICLE; COMPUTER MODEL; CRYSTAL STRUCTURE; MOLECULAR DOCKING; MOLECULAR MECHANICS; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SIMULATION; STRUCTURAL HOMOLOGY; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; HUMANS; MEMBRANE TRANSPORT PROTEINS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MYELIN PROTEINS; MYELOID DIFFERENTIATION FACTOR 88; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEOLIPIDS; RECEPTORS, CELL SURFACE; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; TOLL-LIKE RECEPTOR 2; TOLL-LIKE RECEPTOR 4; TOLL-LIKE RECEPTOR 6;

EID: 80052294520     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023989     Document Type: Article

References (62)

1. Akira S, Uematsu S, Takeuchi O, (2006) Pathogen recognition and innate immunity. Cell 124: 783-801.
2. Krishnan J, Selvarajoo K, Tsuchiya M, Lee G, Choi S, (2007) Toll-like receptor signal transduction. Exp Mol Med 39: 421-438.
3. Govindaraj RG, Manavalan B, Lee G, Choi S, (2010) Molecular modeling-based evaluation of hTLR10 and identification of potential ligands in Toll-like receptor signaling. PLoS One 5: e12713.
4. Kawai T, Akira S, (2010) The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat Immunol 11: 373-384.
5. O'Neill LA, Fitzgerald KA, Bowie AG, (2003) The Toll-IL-1 receptor adaptor family grows to five members. Trends Immunol 24: 286-290.
6. Zhu J, Brownlie R, Liu Q, Babiuk LA, Potter A, et al. (2009) Characterization of bovine Toll-like receptor 8: ligand specificity, signaling essential sites and dimerization. Mol Immunol 46: 978-990.
7. Medzhitov R, Preston-Hurlburt P, Kopp E, Stadlen A, Chen C, et al. (1998) MyD88 is an adaptor protein in the hToll/IL-1 receptor family signaling pathways. Mol Cell 2: 253-258.
8. Basith S, Manavalan B, Lee G, Kim SG, Choi S, (2011) Toll-like receptor modulators: a patent review (2006-2010). Expert Opin Ther Pat 21: 927-944.
9. Palsson-McDermott EM, O'Neill LA, (2007) Building an immune system from nine domains. Biochem Soc Trans 35: 1437-1444.
10. Carpenter S, O'Neill LA, (2009) Recent insights into the structure of Toll-like receptors and post-translational modifications of their associated signalling proteins. Biochem J 422: 1-10.
11. Manavalan B, Basith S, Choi S, (2011) Similar structures but different roles - an updated perspective on TLR structures. Front Physio 2: 41.
12. Krishnan J, Lee G, Choi S, (2009) Drugs targeting Toll-like receptors. Arch Pharm Res 32: 1485-1502.
13. Tominaga S, (1989) A putative protein of a growth specific cDNA from BALB/c-3T3 cells is highly similar to the extracellular portion of mouse interleukin 1 receptor. FEBS Lett 258: 301-304.
14. Klemenz R, Hoffmann S, Werenskiold AK, (1989) Serum- and oncoprotein-mediated induction of a gene with sequence similarity to the gene encoding carcinoembryonic antigen. Proc Natl Acad Sci U S A 86: 5708-5712.
15. Bergers G, Reikerstorfer A, Braselmann S, Graninger P, Busslinger M, (1994) Alternative promoter usage of the Fos-responsive gene Fit-1 generates mRNA isoforms coding for either secreted or membrane-bound proteins related to the IL-1 receptor. EMBO J 13: 1176-1188.
16. Xu D, Chan WL, Leung BP, Huang F, Wheeler R, et al. (1998) Selective expression of a stable cell surface molecule on type 2 but not type 1 helper T cells. J Exp Med 187: 787-794.
17. Lohning M, Stroehmann A, Coyle AJ, Grogan JL, Lin S, et al. (1998) T1/ST2 is preferentially expressed on murine Th2 cells, independent of interleukin 4, interleukin 5, and interleukin 10, and important for Th2 effector function. Proc Natl Acad Sci U S A 95: 6930-6935.
18. Coyle AJ, Lloyd C, Tian J, Nguyen T, Erikkson C, et al. (1999) Crucial role of the interleukin 1 receptor family member T1/ST2 in T helper cell type 2-mediated lung mucosal immune responses. J Exp Med 190: 895-902.
19. Brint EK, Fitzgerald KA, Smith P, Coyle AJ, Gutierrez-Ramos JC, et al. (2002) Characterization of signaling pathways activated by the interleukin 1 (IL-1) receptor homologue T1/ST2. A role for Jun N-terminal kinase in IL-4 induction. J Biol Chem 277: 49205-49211.
20. Brint EK, Xu D, Liu H, Dunne A, McKenzie AN, et al. (2004) ST2 is an inhibitor of interleukin 1 receptor and Toll-like receptor 4 signaling and maintains endotoxin tolerance. Nat Immunol 5: 373-379.
21. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 36: D13-21.
22. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Chapter 5: Unit 5 6.
23. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP, (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14: 617-623.
24. Wallner B, Fang H, Elofsson A, (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 53 (Suppl 6): 534-541.
25. McGuffin LJ, (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics 24: 586-587.
26. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM, (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9: 403.
27. Manavalan B, Basith S, Choi YM, Lee G, Choi S, (2010) Structure-function relationship of cytoplasmic and nuclear IkappaB proteins: an in silico analysis. PLoS One 5: e15782.
28. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G, (2004) Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins 57: 678-683.
29. Ponder JW, Case DA, (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85.
30. Tovchigrechko A, Vakser IA, (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34: W310-314.
31. Chen R, Li L, Weng Z, (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52: 80-87.
32. Nunez Miguel R, Wong J, Westoll JF, Brooks HJ, O'Neill LA, et al. (2007) A dimer of the Toll-like receptor 4 cytoplasmic domain provides a specific scaffold for the recruitment of signalling adaptor proteins. PLoS One 2: e788.
33. Motshwene PG, Moncrieffe MC, Grossmann JG, Kao C, Ayaluru M, et al. (2009) An oligomeric signaling platform formed by the Toll-like receptor signal transducers MyD88 and IRAK-4. J Biol Chem 284: 25404-25411.
34. Ohnishi H, Tochio H, Kato Z, Orii KE, Li A, et al. (2009) Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling. Proc Natl Acad Sci U S A 106: 10260-10265.
35. Dunne A, Ejdeback M, Ludidi PL, O'Neill LA, Gay NJ, (2003) Structural complementarity of Toll/interleukin-1 receptor domains in Toll-like receptors and the adaptors Mal and MyD88. J Biol Chem 278: 41443-41451.
36. Monie TP, Moncrieffe MC, Gay NJ, (2009) Structure and regulation of cytoplasmic adapter proteins involved in innate immune signaling. Immunol Rev 227: 161-175.
37. Jiang Z, Georgel P, Li C, Choe J, Crozat K, et al. (2006) Details of Toll-like receptor:adapter interaction revealed by germ-line mutagenesis. Proc Natl Acad Sci U S A 103: 10961-10966.
38. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
39. Maiti R, Van Domselaar GH, Zhang H, Wishart DS, (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 32: W590-594.
40. Cole C, Barber JD, Barton GJ, (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36: W197-201.
41. Xu Y, Tao X, Shen B, Horng T, Medzhitov R, et al. (2000) Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Nature 408: 111-115.
42. Gay NJ, Gangloff M, Weber AN, (2006) Toll-like receptors as molecular switches. Nat Rev Immunol 6: 693-698.
43. Nyman T, Stenmark P, Flodin S, Johansson I, Hammarstrom M, et al. (2008) The crystal structure of the human toll-like receptor 10 cytoplasmic domain reveals a putative signaling dimer. J Biol Chem 283: 11861-11865.
44. Ronni T, Agarwal V, Haykinson M, Haberland ME, Cheng G, et al. (2003) Common interaction surfaces of the toll-like receptor 4 cytoplasmic domain stimulate multiple nuclear targets. Mol Cell Biol 23: 2543-2555.
45. Brown V, Brown RA, Ozinsky A, Hesselberth JR, Fields S, (2006) Binding specificity of Toll-like receptor cytoplasmic domains. Eur J Immunol 36: 742-753.
46. Horng T, Barton GM, Medzhitov R, (2001) TIRAP: an adapter molecule in the Toll signaling pathway. Nat Immunol 2: 835-841.
47. Piao W, Song C, Chen H, Wahl LM, Fitzgerald KA, et al. (2008) Tyrosine phosphorylation of MyD88 adapter-like (Mal) is critical for signal transduction and blocked in endotoxin tolerance. J Biol Chem 283: 3109-3119.
48. von Bernuth H, Picard C, Jin Z, Pankla R, Xiao H, et al. (2008) Pyogenic bacterial infections in humans with MyD88 deficiency. Science 321: 691-696.
49. Akira S, Takeda K, Kaisho T, (2001) Toll-like receptors: critical proteins linking innate and acquired immunity. Nat Immunol 2: 675-680.
50. Tao X, Xu Y, Zheng Y, Beg AA, Tong L, (2002) An extensively associated dimer in the structure of the C713S mutant of the TIR domain of human TLR2. Biochem Biophys Res Commun 299: 216-221.
51. Gautam JK, Ashish, Comeau LD, Krueger JK, Smith MF Jr, (2006) Structural and functional evidence for the role of the TLR2 DD loop in TLR1/TLR2 heterodimerization and signaling. J Biol Chem 281: 30132-30142.
52. Kenny EF, Talbot S, Gong M, Golenbock DT, Bryant CE, et al. (2009) MyD88 adaptor-like is not essential for TLR2 signaling and inhibits signaling by TLR3. J Immunol 183: 3642-3651.
53. Khan JA, Brint EK, O'Neill LA, Tong L, (2004) Crystal structure of the Toll/interleukin-1 receptor domain of human IL-1RAPL. J Biol Chem 279: 31664-31670.
54. Chan SL, Low LY, Hsu S, Li S, Liu T, et al. (2009) Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain. J Biol Chem 284: 21386-21392.
55. Chan SL, Mukasa T, Santelli E, Low LY, Pascual J, (2010) The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants. Protein Sci 19: 155-161.
56. Poltorak A, He X, Smirnova I, Liu MY, Van Huffel C, et al. (1998) Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science 282: 2085-2088.
57. Slack JL, Schooley K, Bonnert TP, Mitcham JL, Qwarnstrom EE, et al. (2000) Identification of two major sites in the type I interleukin-1 receptor cytoplasmic region responsible for coupling to pro-inflammatory signaling pathways. J Biol Chem 275: 4670-4678.
58. Gong J, Wei T, Stark RW, Jamitzky F, Heckl WM, et al. (2010) Inhibition of Toll-like receptors TLR4 and 7 signaling pathways by SIGIRR: a computational approach. J Struct Biol 169: 323-330.
59. Lin SC, Lo YC, Wu H, (2010) Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling. Nature 465: 885-890.
60. Gay NJ, Gangloff M, O'Neill LA, (2011) What the Myddosome structure tells us about the initiation of innate immunity. Trends Immunol 32: 104-109.
61. Li C, Zienkiewicz J, Hawiger J, (2005) Interactive sites in the MyD88 Toll/interleukin (IL) 1 receptor domain responsible for coupling to the IL1beta signaling pathway. J Biol Chem 280: 26152-26159.
62. Liew FY, Xu D, Brint EK, O'Neill LA, (2005) Negative regulation of toll-like receptor-mediated immune responses. Nat Rev Immunol 5: 446-458.