Computational modelling of NF-κB activation by IL-1RI and its co-receptor TILRR, predicts a role for cytoskeletal sequestration of IκBαin inflammatory signalling

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Rhodes, David M ^a,b   Smith, Sarah A ^a   Holcombe, Mike ^b   Qwarnstrom, Eva E ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; I KAPPA B ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 1 RECEPTOR TYPE I; SPECTRIN; TOLL LIKE AND INTERLEUKIN 1 RECEPTOR REGULATOR; UNCLASSIFIED DRUG; I KAPPA B KINASE; INTERLEUKIN 1 RECEPTOR; INTERLEUKIN RECEPTOR; TILRR PROTEIN, HUMAN;

ARTICLE; COMPLEX FORMATION; COMPUTER MODEL; CONTROLLED STUDY; CYTOSKELETON; ENZYME ACTIVATION; ENZYME REGULATION; IN VITRO STUDY; INFLAMMATION; MOLECULAR DYNAMICS; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; PHYSIOLOGY;

CYTOSKELETON; GENE EXPRESSION REGULATION; HUMANS; I-KAPPA B KINASE; INFLAMMATION; MODELS, BIOLOGICAL; NF-KAPPA B; RECEPTORS, INTERLEUKIN; RECEPTORS, INTERLEUKIN-1; SIGNAL TRANSDUCTION;

EID: 84938352316     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0129888     Document Type: Article

References (31)

1. Baltimore D. NF-κB is 25. Nat Immunol. 2011; 12(8):683-685. doi: 10.1038/ni.2072 PMID: 21772275
2. Ben-Neriah Y, Karin M. Inflammation meets cancer, with NF-κB as the matchmaker. Nature Immunol. 2011; 12 (8) 715-723. doi: 10.1038/ni.2060 PMID: 21772280
3. Perkins ND. The diverse and complex roles of NF-kappa B subunits in cancer. Nat. Rev. Cancer. 2012; 12(2), 121-132. doi: 10.1038/nrc3204 PMID: 22257950
4. Kanarek N, Ben-Neriah Y. Regulation of NF-κB by ubiquitination and degradation of the IκBs. Immunological Reviews. 2012; 246: 77-94. doi: 10.1111/j.1600-065X.2012.01098.x PMID: 22435548
5. O'Neill LAJ, Golenbock D, Bowie AG. The history of Toll-like receptors- redefining innate immunity. Nat. Rev.Immunol. 2013; 13:453-460. doi: 10.1038/nri3446 PMID: 23681101
6. Gay NJ, Symmons MF, Gangloff M, Bryant CE. Assembly and localization of Toll-like receptor signalling complexes. Nat. Immunol. 2014; 14: 546-558. doi: 10.1038/nri3713 PMID: 25060580
7. Tanaka T, Grusby MJ, Kaisho T. PDLIM2-mediated termination of transcription factor NF-κB activation by intracellular sequestration and degradation of the p65 subunit. Nature Immunol. 2007; 8(6) 584-591. PMID: 17468759
8. Legrand-Poels S, Kustermans G, Bex F, Kremmer E, Kufer TA, Piette J. Modulation of Nod2-dependent NFkappaB signaling by the actin cytoskeleton. J Cell Sci 2007; 120 (7) 1299-1310. PMID: 17356065
9. Mammoto A, Mammoto T, Ingber DE. Mechanosensitive mechanisms in transcriptional regulation. J. Cell Sci. 2012; 125: 1-13. doi: 10.1242/jcs.105999 PMID: 22294611
10. Bowe RA, Cox OT, Ayllon V, Tresse E, Healy NC, Edmunds SJ, et al. PDLIM2 regulates transcription factor activity in epithelial-to-mesenchymal transition via the COP9 signalosome. Mol Biol Cell. 2014; 25: 184-195. doi: 10.1091/mbc.E13-06-0306 PMID: 24196835
11. Pogson M, Holcombe M, Smallwood R, Qwarnstrom E. Introducing Spatial Information into Predictive NF-kappa B Modelling-An Agent-Based Approach PlosOne 2008; 3(6):e2367, doi: 10.1371/ journal.phone.0002367 PMID: 18523553
12. Sriswasdi S, Harper S, Hsin-Yao T, Gallagher PG, Speicher DW. Probing large conformational rearrangements in wild-type and mutant spectrin using structural mass spectrometry. Proc. Natl. Acad. Sci. U S A. 2009; 111(5): 1801-1806.
13. Zhang X, Shephard F, Kim HB, Palmer IR, McHarg S, Fowler GJ, et al. TILRR, a novel IL-1RI co-receptor, potentiates MyD88 recruitment to control Ras-dependent amplification of NF-kappa B. J Biol. Chem. 2010; 285(10):7222-7232. doi: 10.1074/jbc.M109.073429 PMID: 19940113
14. Zhang X, Pino GM, Shephard F, Kiss-Toth E, Qwarnstrom EE. Distinct Control of MyD88 Adapter-dependent and Akt Kinase-regulated Responses by the Interleukin (IL)-1RI Co-receptor, TILRR. J Biol. Chem. 2012; 287(15):12348-12352. doi: 10.1074/jbc.C111.321711 PMID: 22262840
15. Greenough C, Worth D, Chin S, Holcombe M, Coakley S. The exploitation of parallel high performance systems in the FLAME agent-based simulation framework. RAL Technical Reports RAL-TR-2008-022.
16. Richmond P, Walker D, Coakley S, Romano D. High performance cellular level agent-based simulation with FLAME for the GPU. Brief Bioinform. 2010; 11: 334-347. doi: 10.1093/bib/bbp073 PMID: 20123941
17. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403 (6767):335-338. PMID: 10659856
18. Pogson M, Smallwood R, Qwarnstrom E, Holcombe M. Formal agent-based modelling of intracellular chemical interactions. Biosystems. 2006; 85(1):37-45. PMID: 16581178
19. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008; 9: 40. doi: 10.1186/1471-2105-9-40 PMID: 18215316
20. Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 200; 22(2): 195-201.
21. Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 2006; 34: 310-314.
22. Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, et al. Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci. 2006; 31(2): 76-78. PMID: 16406633
23. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins. 2008; 57: 702-710.
24. Yang L, Ross K, Qwarnstrom EE. RelA control of I kappa B alpha phosphorylation-A positive feedback loop for high affinity NF-kappa B complexes. J. Biol. Chem. 2003; 278(33):30881-30888. PMID: 12663663
25. Lamboy JA, Kim H, Lee KS, Ha T, Komives EA. Visualization of the nanospring dynamics of the IκBαankyrin like repeat domain in real time. Proc. Natl. Acad. Sci. 2011; 108 (25) 10178-101183. doi: 10.1073/pnas.1102226108 PMID: 21628581
26. Ke X, Guisheng Z, Xiaowei Z. Actin, Spectrin and associated proteins form a periodic cytoskeletal structure in axons. Science. 2013; 339 (6118) 452-456. doi: 10.1126/science.1232251 PMID: 23239625
27. Zheng L, Beeker DM, Bartles JR. Characterisation and regulation of an additional actin-filament binding site in large isoforms of the stereocilia actin-bundling protein epsin. J. Cell Science. 2014; 127: 1306-1317. doi: 10.1242/jcs.143255 PMID: 24424026
28. Carlotti F, Chapman R, Dower SK, Qwarnstrom EE. Activation of nuclear factor kappa B in single living cells - Dependence of nuclear translocation and anti-apoptotic function on EGFPRELA concentration. J. Biol. Chem. 1999; 274(53):37941-37949. PMID: 10608861
29. Carlotti F, Dower SK, Qwarnstrom EE. Dynamic Shuttling of Nuclear Factor κB between the Nucleus and Cytoplasm as a Consequence of Inhibitor Dissociation. J. Biol. Chem. 2000; 275(52):41028-41034. PMID: 11024020
30. Di Z, Herpers B, Fredriksson L, Yan K, Van de Water B, Verbeek FJ, et al. Automated Analysis of NF-kappa B Nuclear Translocation Kinetics in High-Throughput Screening. Plos One. 2012; 7(12): e52337. doi: 10.1371/ journal.phone.0052337 PMID: 23300644
31. Davis CN, Mann E, Behrens MM, Gaidarova S, Rebek M, Rebek J Jr, et al. MyD88-dependent and - independent signaling by IL-1 in neurons probed by bifunctional toll/IL-1 receptor domain/BB-loop mimetics. Proc. Natl. Acad. Sci. USA. 2006; 103(8):2953-2958. PMID: 16477040