Analysis of PKR-RNA interactions by sedimentation velocity

Methods in Enzymology

Volumn 488, Issue C, 2011, Pages 59-79

  Wong, C Jason ^a   Launer Felty, Katherine ^a   Cole, James L ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON; PROTEIN KINASE R; TAR;

ADENOVIRUS; ARTICLE; AUTOPHOSPHORYLATION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; INNATE IMMUNITY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN RNA BINDING; SEDIMENTATION RATE; STOICHIOMETRY; ULTRACENTRIFUGATION;

ADENOVIRIDAE;

EID: 78650944082     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381268-1.00003-3     Document Type: Chapter

References (58)

1. M.F. Bailey, B.E. Davidson, A.P. Minton, W.H. Sawyer, and G.J. Howlett The effect of self-association on the interaction of the Escherichia coli regulatory protein TyrR with DNA J. Mol. Biol. 263 1996 671 684
2. A. Balbo, H. Zhao, P.H. Brown, and P. Schuck Assembly, loading, and alignment of an analytical ultracentrifuge sample cell J. Vis. Exp. 33 2009 doi: 10.3791/1530
3. Y. Ben-Asouli, Y. Banai, Y. Pel-Or, A. Shir, and R. Kaempfer Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR Cell 108 2002 221 232
4. P.C. Bevilacqua, and T.R. Cech Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain of the RNA-activated protein kinase PKR Biochemistry 35 1996 9983 9994
5. P.C. Bevilacqua, C.S. George, C.E. Samuel, and T.R. Cech Binding of the protein kinase PKR to RNAs with secondary structure defects: Role of the tandem A-G mismatch and noncontinguous helices Biochemistry 37 1998 6303 6316
6. P.H. Brown, A. Balbo, and P. Schuck Characterizing proteinprotein interactions by sedimentation velocity analytical ultracentrifugation Curr. Protoc. Immunol. 2008 15, Chapter 18, Unit 18
7. J.R. Cann Interacting Macromolecules 1970 Academic Press New York
8. J. Carey Gel retardation Methods Enzymol. 208 1991 103 117
9. P.A. Clarke, and M.B. Mathews Interactions between the double-stranded RNA binding motif and RNA: Definition of the binding site for the interferon-induced protein kinase DAI (PKR) on adenovirus VA RNA RNA 1 1995 7 20
10. J.L. Cole Analysis of heterogeneous interactions Methods Enzymol. 384 2004 212 232
11. J.L. Cole Activation of PKR: An open and shut case? Trends Biochem. Sci. 32 2007 57 62
12. J.L. Cole, J.W. Lary, T.P. Moody, and T.M. Laue Analytical ultracentrifugation: Sedimentation velocity and sedimentation equilibrium Methods Cell Biol. 84 2008 143 179
13. H. Colfen, T.M. Laue, W. Wohlleben, K. Schilling, E. Karabudak, B.W. Langhorst, E. Brookes, B. Dubbs, D. Zollars, M. Rocco, and B. Demeler The open AUC project Eur. Biophys. J. 39 2009 347 359
14. J.J. Correia, and W.F. Stafford Extracting equilibrium constants from kinetically limited reacting systems Methods Enzymol. 455 2009 419 446
15. J. Dam, C.A. Velikovsky, R.A. Mariuzza, C. Urbanke, and P. Schuck Sedimentation velocity analysis of heterogeneous proteinprotein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s) Biophys. J. 89 2005 619 634 (Pubitemid 41098314)
16. A.C. Dar, T.E. Dever, and F. Sicheri Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR Cell 122 2005 887 900
17. M.A. Daugherty, and M.G. Fried D.J. Scott, Modern Analytical Ultracentrifugation: Techniques and Methods 2005 Royal Society of Chemistry Oxford 195 209
18. B. Demeler, E. Brookes, R. Wang, V. Schirf, and C.A. Kim Characterization of reversible associations by sedimentation velocity with UltraScan Macromol. Biosci. 10 2010 775 782
19. D.E. Draper, and P.H. von Hippel Measurement of macromolecular equilibrium binding constants by a sucrose gradient band sedimentation method. Application to proteinnucleic acid interactions Biochemistry 18 1979 753 760
20. R. Giebeler S.E. Harding, A.J. Rowe, J.C. Horton, Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992 Royal Society of Chemistry Cambridge 16 25
21. G.A. Gilbert, and R.C. Jenkins Sedimentation and electrophoresis of interacting substances. II. Asymptotic boundary shape for two substances interacting reversibly Proc. R. Soc. A 253 1959 420 437
22. T.C. Goodman, L. Nagel, W. Rappold, G. Klotz, and D. Riesner Viroid replication: Equilibrium association constant and comparative activity measurements for the viroid-polymerase interaction Nucleic Acids Res. 12 1984 6231 6246
23. L.A. Heinicke, C.J. Wong, J. Lary, S.R. Nallagatla, A. Diegelman-Parente, X. Zheng, J.L. Cole, and P.C. Bevilacqua RNA dimerization promotes PKR dimerization and activation J. Mol. Biol. 390 2009 319 338
24. L.M. Hellman, and M.G. Fried Electrophoretic mobility shift assay (EMSA) for detecting proteinnucleic acid interactions Nat. Protoc. 2 2007 1849 1861
25. D.E. Jensen, and P.H. von Hippel A boundary sedimentation velocity method for determining nonspecific nucleic acidprotein interaction binding parameters Anal. Biochem. 80 1977 267 281
26. S.R. Kar, J.S. Kingsbury, M.S. Lewis, T.M. Laue, and P. Schuck Analysis of transport experiments using pseudo-absorbance data Anal. Biochem. 285 2000 135 142
27. J.O. Langland, J.M. Cameron, M.C. Heck, J.K. Jancovich, and B.L. Jacobs Inhibition of PKR by RNA and DNA viruses Virus Res. 119 2006 100 110
28. K.W. Lanks, and R.K. Eng Detection of nucleic acidprotein complexes by equilibrium ultracentrifugation Res. Commun. Chem. Pathol. Pharmacol. 15 1976 377 380
29. T.M. Laue, B.D. Shah, T.M. Ridgeway, and S.L. Pelletier S. Harding, A. Rowe, J. Horton, Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992 Royal Society of Chemistry Cambridge 90 125
30. T.M. Laue, D.F. Senear, S. Eaton, and J.B. Ross 5-hydroxytryptophan as a new intrinsic probe for investigating proteinDNA interactions by analytical ultracentrifugation. Study of the effect of DNA on self-assembly of the bacteriophage lambda cI repressor Biochemistry 32 1993 2469 2472
31. K. Launer-Felty, C.J. Wong, A.M. Wahid, G.L. Conn, and J.L. Cole Magnesium-dependent interaction of PKR with adenovirus VAI RNA J. Mol. Biol. 2010 638 644
32. P.A. Lemaire, E. Anderson, J. Lary, and J.L. Cole Mechanism of PKR activation by dsRNA J. Mol. Biol. 381 2008 351 360
33. N. Leulliot, S. Quevillon-Cheruel, M. Graille, H. van Tilbeurgh, T.C. Leeper, K.S. Godin, T.E. Edwards, S.T. Sigurdsson, N. Rozenkrants, R.J. Nagel, M. Ares, and G. Varani A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III EMBO J. 23 2004 2468 2477
34. M.S. Lewis, R.I. Shrager, and S.-J. Kim T.M. Shuster, T.M. Laue, Modern Analytical Ultracentrifugation 1994 Birkhauser Boston 94 115
35. Y. Liu, M. Lei, and C.E. Samuel Chimeric double-stranded RNA-specific adenosine deaminase ADAR1 proteins reveal functional selectivity of double-stranded RNA binding domains from ADAR1 and protein kinase PKR Proc. Natl. Acad. Sci. USA 97 2000 12541 12546
36. T.M. Lohman, C.G. Wensley, J. Cina, R.R. Burgess, and M.T. Record Jr. Use of difference boundary sedimentation velocity to investigate nonspecific proteinnucleic acid interactions Biochemistry 19 1980 3516 3522
37. L. Manche, S.R. Green, C. Schmedt, and M.B. Mathews Interactions between double-stranded RNA regulators and the protein kinase DAI Mol. Cell. Biol. 12 1992 5238 5248
38. S.A. McKenna, D.A. Lindhout, I. Kim, C.W. Liu, V.M. Gelev, G. Wagner, and J.D. Puglisi Molecular framework for the activation of RNA-dependent protein kinase J. Biol. Chem. 282 2007 11474 11486
39. S.A. McKenna, D.A. Lindhout, T. Shimoike, C.E. Aitken, and J.D. Puglisi Viral dsRNA inhibitors prevent self-association and autophosphorylation of PKR J. Mol. Biol. 372 2007 103 113
40. M.A. Minks, D.K. West, S. Benvin, and C. Baglioni Structural requirements of double-stranded RNA for the activation of 2'5'-Oligo(A) polymerase and protein kinase of interferon-treated HeLa cells J. Biol. Chem. 254 1979 10180 10183
41. R. Nagel, and M. Ares Jr. Substrate recognition by a eukaryotic RNase III: The double-stranded RNA-binding domain of Rnt1p selectively binds RNA containing a 5'-AGNN-3' tetraloop RNA 6 2000 1142 1156
42. S. Nanduri, B.W. Carpick, Y. Yang, B.R. Williams, and J. Qin Structure of the double-stranded RNA binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation EMBO J. 17 1998 5458 5465
43. J.S. Philo Improved methods for fitting sedimentation coefficient distributions derived by time-derivative techniques Anal. Biochem. 354 2006 238 246
44. A. Revzin, and R.P. Woychik Quantitation of the interaction of Escherichia coli RNA polymerase holoenzyme with double-helical DNA using a thermodynamically rigorous centrifugation method Biochemistry 20 1981 250 256
45. C. Schmedt, S.R. Green, L. Manche, D.R. Taylor, Y. Ma, and M.B. Mathews Functional characterization of the RNA-binding domain and motif of the double-stranded RNA-dependent protein kinase DAI (PKR) J. Mol. Biol. 249 1995 29 44
46. P. Schuck A model for sedimentation in inhomogeneous media. I. Dynamic density gradients from sedimenting co-solutes Biophys. Chem. 108 2004 187 200
47. P. Schuck Some statistical properties of differencing schemes for baseline correction of sedimentation velocity data Anal. Biochem. 401 2010 280 287
48. R.J. Spanggord, and P.A. Beal Selective binding by the RNA binding domain of PKR revealed by affinity cleavage Biochemistry 40 2001 4272 4280
49. W.F. Stafford Boundary analysis in sedimentation transport experiments: A procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile Anal. Biochem. 203 1992 295 301
50. W.F. Stafford III Proteinprotein and ligandprotein interactions studied by analytical ultracentrifugation Methods Mol. Biol. 490 2009 83 113
51. W.F. Stafford, and P.J. Sherwood Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants Biophys. Chem. 108 2004 231 243
52. B. Tian, P.C. Bevilacqua, A. Diegelman-Parente, and M.B. Mathews The double-stranded RNA binding motif: Interference and much more Nat. Rev. Mol. Cell Biol. 5 2004 1013 1023
53. A.M. Toth, P. Zhang, S. Das, C.X. George, and C.E. Samuel Interferon action and the double-stranded RNA-dependent enzymes ADAR1 adenosine deaminase and PKR protein kinase Prog. Nucleic Acid Res. Mol. Biol. 81 2006 369 434
54. J.W. Ucci, and J.L. Cole Global analysis of non-specific proteinnucleic interactions by sedimentation equilibrium Biophys. Chem. 108 2004 127 140
55. J.W. Ucci, Y. Kobayashi, G. Choi, A.T. Alexandrescu, and J.L. Cole Mechanism of interaction of the double-stranded RNA (dsRNA) binding domain of protein kinase R with short dsRNA sequences Biochemistry 46 2007 55 65
56. J. VanOudenhove, E. Anderson, S. Krueger, and J.L. Cole Analysis of PKR structure by small-angle scattering J. Mol. Biol. 387 2009 910 920
57. K. Wojtuszewski, M.E. Hawkins, J.L. Cole, and I.J. Mukerji HU Binding to DNA: Evidence for multiple complex formation and DNA bending Biochemistry 40 2001 2588 2598
58. I. Wong, and T.M. Lohman A double-filter method for nitrocellulose-filter binding: Application to proteinnucleic acid interactions Proc. Natl. Acad. Sci. USA 90 1993 5428 5432