Structural and dynamics aspects of ASC speck assembly

Structure

Volumn 22, Issue 12, 2014, Pages 1722-1734

  Sahillioglu, Ali Can ^a   Sumbul, Fidan ^a   Ozoren, Nesrin ^a   Haliloglu, Turkan ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSKELETON PROTEIN; INFLAMMASOME; INTERLEUKIN 1BETA CONVERTING ENZYME; PYCARD PROTEIN, HUMAN;

CHEMICAL STRUCTURE; HEK293 CELL LINE; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION;

CASPASE 1; CYTOSKELETAL PROTEINS; HEK293 CELLS; HUMANS; INFLAMMASOMES; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION;

EID: 84914132282     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.09.011     Document Type: Article

References (53)

1. I. Bahar, and A.J. Rader Coarse-grained normal mode analysis in structural biology Curr. Opin. Struct. Biol. 15 2005 586 592
2. I. Bahar, A.R. Atilgan, M.C. Demirel, and B. Erman Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability Phys. Rev. Lett. 80 1998 2733
3. B. Balci-Peynircioglu, A.L. Waite, P. Schaner, Z.E. Taskiran, N. Richards, D. Orhan, S. Gucer, S. Ozen, D. Gumucio, and E. Yilmaz Expression of ASC in renal tissues of familial mediterranean fever patients with amyloidosis: postulating a role for ASC in AA type amyloid deposition Exp. Biol. Med. (Maywood) 233 2008 1324 1333
4. P. Berens CircStat: a MATLAB toolbox for circular statistics J. Stat. Softw. 31 2009 1 21
5. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
6. P. Broz, K. Newton, M. Lamkanfi, S. Mariathasan, V.M. Dixit, and D.M. Monack Redundant roles for inflammasome receptors NLRP3 and NLRC4 in host defense against Salmonella J. Exp. Med. 207 2010 1745 1755
7. P. Broz, J. von Moltke, J.W. Jones, R.E. Vance, and D.M. Monack Differential requirement for Caspase-1 autoproteolysis in pathogen-induced cell death and cytokine processing Cell Host Microbe 8 2010 471 483
8. X. Cai, J. Chen, H. Xu, S. Liu, Q.X. Jiang, R. Halfmann, and Z.J. Chen Prion-like polymerization underlies signal transduction in antiviral immune defense and inflammasome activation Cell 156 2014 1207 1222
9. D.A. Case, T.A. Darden, T. Cheatham Iii, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, and K.M. Merz AMBER 11 142 2010 University of California San Francisco
10. J. Cheng, A.L. Waite, E.R. Tkaczyk, K. Ke, N. Richards, A.J. Hunt, and D.L. Gumucio Kinetic properties of ASC protein aggregation in epithelial cells J. Cell. Physiol. 222 2010 738 747
11. E. de Alba Structure and interdomain dynamics of apoptosis-associated speck-like protein containing a CARD (ASC) J. Biol. Chem. 284 2009 32932 32941
12. A. Ertekin, R. Nussinov, and T. Haliloglu Association of putative concave protein-binding sites with the fluctuation behavior of residues Protein Sci. 15 2006 2265 2277
13. T. Fernandes-Alnemri, J. Wu, J.W. Yu, P. Datta, B. Miller, W. Jankowski, S. Rosenberg, J. Zhang, and E.S. Alnemri The pyroptosome: a supramolecular assembly of ASC dimers mediating inflammatory cell death via caspase-1 activation Cell Death Differ. 14 2007 1590 1604
14. O. Gross, C.J. Thomas, G. Guarda, and J. Tschopp The inflammasome: an integrated view Immunol. Rev. 243 2011 136 151
15. T. Haliloglu, and B. Erman Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding Phys. Rev. Lett. 102 2009 088103
16. T. Haliloglu, I. Bahar, and B. Erman Gaussian dynamics of folded proteins Phys. Rev. Lett. 79 1997 3090
17. T. Haliloglu, E. Seyrek, and B. Erman Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model Phys. Rev. Lett. 100 2008 228102-228102
18. B.A. Hall, S.L. Kaye, A. Pang, R. Perera, and P.C. Biggin Characterization of protein conformational states by normal-mode frequencies J. Am. Chem. Soc. 129 2007 11394 11401
19. V. Hornung, and E. Latz Critical functions of priming and lysosomal damage for NLRP3 activation Eur. J. Immunol. 40 2010 620 623
20. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28
21. J.A. Johnston, C.L. Ward, and R.R. Kopito Aggresomes: a cellular response to misfolded proteins J. Cell Biol. 143 1998 1883 1898
22. J.W. Jones, N. Kayagaki, P. Broz, T. Henry, K. Newton, K. O'Rourke, S. Chan, J. Dong, Y. Qu, and M. Roose-Girma Absent in melanoma 2 is required for innate immune recognition of Francisella tularensis Proc. Natl. Acad. Sci. USA 107 2010 9771 9776
23. K. Kersse, J. Verspurten, T. Vanden Berghe, and P. Vandenabeele The death-fold superfamily of homotypic interaction motifs Trends Biochem. Sci. 36 2011 541 552
24. M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz, T. Pupko, and N. Ben-Tal ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Nucleic Acids Res. 33 2005 W299 W302
25. E. Latz, T.S. Xiao, and A. Stutz Activation and regulation of the inflammasomes Nat. Rev. Immunol. 13 2013 397 411
26. J.C. Leemans, S.L. Cassel, and F.S. Sutterwala Sensing damage by the NLRP3 inflammasome Immunol. Rev. 243 2011 152 162
27. E. Liepinsh, R. Barbals, E. Dahl, A. Sharipo, E. Staub, and G. Otting The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition J. Mol. Biol. 332 2003 1155 1163
28. S.C. Lin, Y.C. Lo, and H. Wu Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling Nature 465 2010 885 890
29. A. Lu, V.G. Magupalli, J. Ruan, Q. Yin, M.K. Atianand, M.R. Vos, G.F. Schröder, K.A. Fitzgerald, H. Wu, and E.H. Egelman Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes Cell 156 2014 1193 1206
30. I. Luque, and E. Freire Structural stability of binding sites: consequences for binding affinity and allosteric effects Proteins Suppl 4 2000 63 71
31. J. Masumoto, S. Taniguchi, K. Ayukawa, H. Sarvotham, T. Kishino, N. Niikawa, E. Hidaka, T. Katsuyama, T. Higuchi, and J. Sagara ASC, a novel 22-kDa protein, aggregates during apoptosis of human promyelocytic leukemia HL-60 cells J. Biol. Chem. 274 1999 33835 33838
32. J. Masumoto, S. Taniguchi, and J. Sagara Pyrin N-terminal homology domain- and caspase recruitment domain-dependent oligomerization of ASC Biochem. Biophys. Res. Commun. 280 2001 652 655
33. K. Matsushita, M. Takeoka, J. Sagara, N. Itano, Y. Kurose, A. Nakamura, and S. Taniguchi A splice variant of ASC regulates IL-1beta release and aggregates differently from intact ASC Mediators Inflamm. 2009 2009 287387
34. E.A. Miao, J.V. Rajan, and A. Aderem Caspase-1-induced pyroptotic cell death Immunol. Rev. 243 2011 206 214
35. M. Moriya, S. Taniguchi, P. Wu, E. Liepinsh, G. Otting, and J. Sagara Role of charged and hydrophobic residues in the oligomerization of the PYRIN domain of ASC Biochemistry 44 2005 575 583
36. R. Muñoz-Planillo, P. Kuffa, G. Martínez-Colón, B.L. Smith, T.M. Rajendiran, and G. Núñez K efflux is the common trigger of NLRP3 inflammasome activation by bacterial toxins and particulate matter Immunity 38 2013 1142 1153
37. A. Natarajan, R. Ghose, and J.M. Hill Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling J. Biol. Chem. 281 2006 31863 31875
38. P. Ozbek, S. Soner, B. Erman, and T. Haliloglu DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues Nucleic Acids Res. 38 2010 W417 W423
39. P. Ozbek, S. Soner, and T. Haliloglu Hot spots in a network of functional sites PLoS ONE 8 2013 e74320
40. H.H. Park, E. Logette, S. Raunser, S. Cuenin, T. Walz, J. Tschopp, and H. Wu Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex Cell 128 2007 533 546
41. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
42. M. Proell, M. Gerlic, P.D. Mace, J.C. Reed, and S.J. Riedl The CARD plays a critical role in ASC foci formation and inflammasome signalling Biochem. J. 449 2013 613 621
43. H. Qin, S.M. Srinivasula, G. Wu, T. Fernandes-Alnemri, E.S. Alnemri, and Y. Shi Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1 Nature 399 1999 549 557
44. N. Richards, P. Schaner, A. Diaz, J. Stuckey, E. Shelden, A. Wadhwa, and D.L. Gumucio Interaction between pyrin and the apoptotic speck protein (ASC) modulates ASC-induced apoptosis J. Biol. Chem. 276 2001 39320 39329
45. K. Schroder, and J. Tschopp The inflammasomes Cell 140 2010 821 832
46. C.S. Shi, K. Shenderov, N.N. Huang, J. Kabat, M. Abu-Asab, K.A. Fitzgerald, A. Sher, and J.H. Kehrl Activation of autophagy by inflammatory signals limits IL-1β production by targeting ubiquitinated inflammasomes for destruction Nat. Immunol. 13 2012 255 263
47. T. Srimathi, S.L. Robbins, R.L. Dubas, H. Chang, H. Cheng, H. Roder, and Y.C. Park Mapping of POP1-binding site on pyrin domain of ASC J. Biol. Chem. 283 2008 15390 15398
48. L.S. Swapna, R.M. Bhaskara, J. Sharma, and N. Srinivasan Roles of residues in the interface of transient protein-protein complexes before complexation Sci Rep 2 2012
49. P.R. Vajjhala, R.E. Mirams, and J.M. Hill Multiple binding sites on the pyrin domain of ASC protein allow self-association and interaction with NLRP3 protein J. Biol. Chem. 287 2012 41732 41743
50. P.R. Vajjhala, S. Kaiser, S.J. Smith, Q.R. Ong, S.L. Soh, K.J. Stacey, and J.M. Hill Identification of Multifaceted Binding Modes for Pyrin and ASC Pyrin Domains Gives Insights into Pyrin Inflammasome Assembly J Biol Chem 2014 jbc. M114. 553305
51. T. Wang, X. Zhang, and J.J. Li The role of NF-kappaB in the regulation of cell stress responses Int. Immunopharmacol. 2 2002 1509 1520
52. L. Wang, J.K. Yang, V. Kabaleeswaran, A.J. Rice, A.C. Cruz, A.Y. Park, Q. Yin, E. Damko, S.B. Jang, and S. Raunser The Fas-FADD death domain complex structure reveals the basis of DISC assembly and disease mutations Nat. Struct. Mol. Biol. 17 2010 1324 1329
53. R. Zhou, A.S. Yazdi, P. Menu, and J. Tschopp A role for mitochondria in NLRP3 inflammasome activation Nature 469 2011 221 225