Influence of decreased solvent permittivity on the structure and magnesium(II)-binding properties of the catalytic domain 5 of a group II intron ribozyme

Inorganica Chimica Acta

Volumn 362, Issue 3, 2009, Pages 771-776

  Furler, Maya ^a   Knobloch, Bernd ^a   Sigel, Roland K O ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Dielectric constant; Metal ion binding; NMR; RNA; Solvent permittivity

Indexed keywords

BINDING ENERGY; BINDING SITES; METAL IONS; METALS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PERMITTIVITY; RNA; SOLVENTS;

BINDING PROPERTIES; CATALYTIC DOMAINS; CATALYTIC TRIAD; METAL ION BINDING; METAL-ION BINDING PROPERTIES; METAL-ION COORDINATION; ONE-AND TWO-DIMENSIONAL NMR; RNA STRUCTURES;

MAGNESIUM COMPOUNDS;

EID: 58849101858     PISSN: 00201693     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ica.2008.03.095     Document Type: Article

References (74)

1. Lehmann K., and Schmidt U. Crit. Rev. Biochem. Mol. Biol. 38 (2003) 249
2. Fedorova O., and Zingler N. Biol. Chem. 388 (2007) 665
3. Nilsen T.W. Encycl. Biol. Chem. 4 (2004) 88
4. Michel F., and Ferat J.L. Annu. Rev. Biochem. 64 (1995) 435
5. Qin P.Z., and Pyle A.M. Biochemistry 36 (1997) 4718
6. Sigel R.K.O., Vaidya A., and Pyle A.M. Nat. Struct. Biol. 7 (2000) 1111
7. Sigel R.K.O. Eur. J. Inorg. Chem. 12 (2005) 2281
8. Shiman R., and Draper D.E. J. Mol. Biol. 302 (2000) 79
9. Draper D.E., Grilley D., and Soto A.M. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 221
10. Pyle A.M. Met. Ions Biol. Syst. 32 (1996) 479
11. Sigel R.K.O., and Pyle A.M. Chem. Rev. 107 (2007) 97
12. Freisinger E., and Sigel R.K.O. Coord. Chem. Rev. 251 (2007) 1834
13. Gordon P.M., Sontheimer E.J., and Piccirilli J.A. Biochemistry 39 (2000) 12939
14. Fedor M.J. Curr. Opin. Struct. Biol. 12 (2002) 289
15. Hougland J.L., Kravchuk A.V., Herschlag D., and Piccirilli J.A. Plos Biol. 3 (2005) 1536
16. Cate J.H., Hanna R.L., and Doudna J.A. Nat. Struct. Biol. 4 (1997) 553
17. Shan S.-O., Yoshida A., Sun S., Piccirilli J.A., and Herschlag D. Proc. Natl. Acad. Sci. USA 96 (1999) 12299
18. Knobloch B., Sigel R.K.O., Lippert B., and Sigel H. Angew. Chem., Int. Ed. 43 (2004) 3793
19. Pyle A.M. J. Biol. Inorg. Chem. 7 (2002) 679
20. Lippert B. Prog. Inorg. Chem. 54 (2005) 385
21. Sigel R.K.O., and Lippert B. Chem. Commun. (1999) 2167
22. Sigel R.K.O., Freisinger E., and Lippert B. J. Biol. Inorg. Chem. 5 (2000) 287
23. Sigel R.K.O., Freisinger E., and Lippert B. Chem. Commun. (1998) 219
24. Lüth M.S., Willermann M., and Lippert B. Chem. Commun. (2001) 2058
25. Brüning W., Sigel R.K.O., Freisinger E., and Lippert B. Angew. Chem., Int. Ed. 40 (2001) 3397
26. Roitzsch M., and Lippert B. J. Am. Chem. Soc. 126 (2004) 2421
27. Sigel R.K.O., Thompson S.M., Freisinger E., and Lippert B. Chem. Eur. J. 7 (2001) 1968
28. Brüning W., Freisinger E., Sabat M., Sigel R.K.O., and Lippert B. Chem. Eur. J. 8 (2002) 4681
29. Noah J.W., and Lambowitz A.M. Biochemistry 42 (2003) 12466
30. Su L.H.J., Brenowitz M., and Pyle A.M. J. Mol. Biol. 334 (2003) 639
31. Sigel R.K.O., Sashital D.G., Abramovitz D.L., Palmer III A.G., Butcher S.E., and Pyle A.M. Nat. Struct. Mol. Biol. 11 (2004) 187
32. Seetharam M., Eldho N.V., Padgett R.A., and Dayie K.T. RNA 12 (2006) 235
33. Erat M.C., Zerbe O., Fox T., and Sigel R.K.O. ChemBioChem 8 (2007) 306
34. Erat M.C., and Sigel R.K.O. Inorg. Chem 46 (2007) 11224
35. Gordon P.M., Fong R., and Piccirilli J.A. Chem. Biol. 14 (2007) 607
36. Rees D.C. J. Mol. Biol. 141 (1980) 323
37. Moore G.R. FEBS Lett. 161 (1983) 171
38. Rogers N.K., Moore G.R., and Sternberg M.J.E. J. Mol. Biol. 182 (1985) 613
39. Demchuk E., and Wade R.C. J. Phys. Chem. 100 (1996) 17373
40. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G.L. Acta Crystallogr., Sect. D 54 (1998) 905
41. Iversen G., Kharkats Y.I., and Ulstrup J. Mol. Phys. 94 (1998) 297
42. Sham Y.Y., Muegge I., and Warshel A. Biophys. J. 74 (1998) 1744
43. Richard J.P., and Amyes T.L. Bioorg. Chem. 32 (2004) 354
44. Sigel H., Martin R.B., Tribolet R., Haring U.K., and Malini-Balakrishnan R. Eur. J. Biochem. 152 (1985) 187
45. Jin R., and Breslauer K.J. Proc. Natl. Acad. Sci. USA 85 (1988) 8939
46. Barawkar D.A., and Ganesh K.N. Nucleic Acids Res. 23 (1995) 159
47. Zimmerly S., Guo H., Eskes R., Yang J., Perlman P.S., and Lambowitz A.M. Cell 83 (1995) 529
48. Petrov A.S., Lamm G., and Pack G.R. J. Phys. Chem. B 106 (2002) 3294
49. Young M.A., Jayaram B., and Beveridge D.L. J. Phys. Chem. B 102 (1998) 7666
50. Okamoto A., Tainaka K., and Saito I. Bioconjugate Chem. 16 (2005) 1105
51. Deubel D.V. J. Am. Chem. Soc. 126 (2004) 5999
52. Liang G.G., Corfu N.A., and Sigel H. Z. Naturforsch. B 44 (1989) 538
53. Sigel H., and McCormick D.B. Accounts Chem. Res. 3 (1970) 201
54. Sigel H. Pure Appl. Chem. 61 (1989) 923
55. Tribolet R., Malini-Balakrishnan R., and Sigel H. J. Chem. Soc., Dalton Trans., Inorg. Chem. (1985) 2291
56. Liang G.G., and Sigel H. Inorg. Chem. 29 (1990) 3631
57. Sigel H., and Tribolet R. J. Inorg. Biochem. 40 (1990) 163
58. Sigel H., and Kapinos L.E. Coord. Chem. Rev. 200-202 (2000) 563
59. Bianchi E.M., Griesser R., and Sigel H. Helv. Chim. Acta 88 (2005) 406
60. Åkerlöf G., and Short O.A. J. Am. Chem. Soc. 58 (1936) 1241
61. Critchfield F.E., Gibson J.A., and Hall J.L. J. Am. Chem. Soc. 75 (1953) 1991
62. Swisher J., Duarte C.M., Su L.J., and Pyle A.M. EMBO J. 20 (2001) 2051
63. Gallo S., Furler M., and Sigel R.K.O. CHIMIA 59 (2005) 812
64. Cavaluzzi M.J., and Borer P.N. Nucleic Acids Res. 32 (2004) e13
65. Davanloo P., Rosenberg A.H., Dunn J.J., and Studier F.W. Proc. Natl. Acad. Sci. USA A81 (1984) 2035
66. Grodberg J., and Dunn J.J. J. Bacteriol. 170 (1988) 1245
67. T.G. Goddard, D.G. Kneller, SPARKY 3: NMR Assignment and Integration Software, University of California, San Francisco, 1977.
68. Konforti B.B., Abramovitz D.L., Duarte C.M., Karpeisky A., Beigelman L., and Pyle A.M. Mol. Cell 1 (1998) 433
69. Zhang L., and Doudna J.A. Science 295 (2002) 2084
70. Gordon P.M., and Piccirilli J.A. Nat. Struct. Biol. 8 (2001) 893
71. Davis J.H., Foster T.R., Tonelli M., and Butcher S.E. RNA 13 (2007) 76
72. Heus H.A., and Pardi A. Science 253 (1991) 191
73. Rüdisser S., and Tinoco Jr. I. J. Mol. Biol. 295 (2000) 1211
74. Koradi R., Billeter M., and Wüthrich K. J. Mol. Graphics 14 (1996) 29 and 51-55