A thorough dynamic interpretation of residual dipolar couplings in ubiquitin

Journal of Biomolecular NMR

Volumn 34, Issue 2, 2006, Pages 101-115

  Lakomek, Nils A ^a   Carlomagno, Teresa ^a   Becker, Stefan ^a   Griesinger, Christian ^a   Meiler, Jens ^b  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b VANDERBILT UNIVERSITY   (United States)

Author keywords

Dynamical averaging; Model free approach; Nuclear magnetic resonance (NMR); Residual dipolar couplings (rdcs); Ubiquitin

Indexed keywords

CARBON 13; CETYLPYRIDINIUM SALT; ETHYLENE GLYCOL; HEXANOL; MACROGOL; NITROGEN 15; POLYACRYLAMIDE GEL; UBIQUITIN;

ACCURACY; ANALYTICAL ERROR; ANISOTROPY; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; HUMAN; MATHEMATICAL COMPUTING; MOTION; NOISE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLARIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; QUALITY CONTROL; TIME;

HUMANS; MODELS, CHEMICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; UBIQUITIN;

EID: 33645469988     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-005-5686-0     Document Type: Article

References (60)

1. M. Akke A.G. Palmer 1996 J. Am. Chem. Soc. 118 911-912 10.1021/ja953503r
2. L.G. Barrientos C. Dolan A.M. Gronenborn 2000 J. Biomol. NMR 16 329-337 10.1023/A:1008356618658
3. R. Beal Q. Deveraux G. Xia M. Rechsteiner C. Pickart 1996 Proc. Natl. Acad. Sci. U.S.A 93 861-866 10.1073/pnas.93.2.861 1996PNAS...93..861B
4. P. Bernado M. Blackledge 2004a J. Am. Chem. Soc. 126 4907-4920
5. P. Bernado M. Blackledge 2004b J. Am. Chem. Soc. 126 7760-7761
6. C.W. Bertoncini Y.S. Jung C.O. Fernandez W. Hoyer C. Griesinger T.M. Jovin M. Zweckstetter 2005 Proc. Natl. Acad. Sci. U.S.A 102 1430-1435 10.1073/pnas.0407146102 2005PNAS..102.1430B
7. T. Bremi R. Brueschweiler 1997 J. Am. Chem. Soc. 119 6672-6673
8. T. Bremi R. Brueschweiler R.R. Ernst 1997 J. Am. Chem. Soc. 119 4272-4284 Brueschweiler R. R.R. Ernst
9. K.B. Briggman J.R. Tolman 2003 J. Am. Chem. Soc. 125 10164-10165 10.1021/ ja035904+
10. B. Brutscher R. Brueschweiler R.R. Ernst 1997 Biochemistry 36 13043-13053 10.1021/bi971538t
11. T.J. Burch A.L. Haas 1994 Biochemistry 33 7300-7308 10.1021/bi00189a035
12. S.-L. Chang N. Tjandra 2005 J. Magn. Res. 174 43-53 10.1016/ j.jmr.2005.01.008 2005JMagR.174...43C
13. J.J. Chou S. Gaemers B. Howder J.M. Louis A. Bax 2001 J. Biomol. NMR 21 377-382
14. G.M. Clore C.D. Schwieters 2004 J. Am. Chem. Soc. 126 2923-2938 10.1021/ ja0386804
15. G. Cornilescu J.L. Marquardt M. Ottiger A. Bax 1998 J. Am. Chem. Soc. 120 6836-6837 10.1021/ja9812610
16. E. Alba de J.L. Baber N. Tjandra 1999 J. Am. Chem. Soc. 121 4282-4283
17. F. Delaglio S. Grzesiek G.W. Vuister G. Zhu J. Pfeifer A. Bax 1995 J. Biomol. NMR 6 277-293 10.1007/BF00197809
18. J. Dittmer G. Bodenhausen 2004 J. Am. Chem. Soc. 126 1314-1315 10.1021/ ja0386243
19. D. Fushman D. Cowburn 1998 J. Am. Chem. Soc. 120 7109-7110
20. A.L. Haas T.J. Siepmann 1997 FASEB J. 11 1257-1268
21. E.C. Johnson G.A. Lazar J.R. Desjarlais T.M. Handel 1999 Structure Fold Des. 7 967-976
22. L.E. Kay D.A. Torchia A. Bax 1989 Biochemistry 28 8972-8979
23. R. Kitahara S. Yokoyama K. Akasaka 2005 J. Mol. Biol. 347 277-285 10.1016/j.jmb.2005.01.052
24. B.W. Koenig J.-S. Hu M. Ottiger S. Bose R.W. Hendler A. Bax 1999 J. Am. Chem. Soc. 121 1385-1386 10.1021/ja9837856
25. K.D. Kopple K.K. Bhandary G. Kartha Y.S. Wang K.N. Parameswaran 1986 J. Am. Chem. Soc. 108 4637-4642 10.1021/ja00275a060
26. N.A. Lakomek C. Farés S. Becker T. Carlomagno J. Meiler C. Griesinger 2005 Angew. Chem. Int. Ed. 44 7776-7778 10.1002/anie.200502573
27. S.F. Lienin T. Bremi B. Brutscher R. Brueschweiler R.R. Ernst 1998 J. Am. Chem. Soc. 120 9870-9879 10.1021/ja9810179
28. K. Lindorff-Larsen R.B. Best M.A. Depristo C.M. Dobson M. Vendruscolo 2005 Nature 433 128-132 10.1038/nature03199 2005Natur.433..128L
29. G. Lipari A. Szabo 1982a J. Am. Chem. Soc. 104 4546-4559
30. G. Lipari A. Szabo 1982b J. Am. Chem. Soc. 104 4559-4570
31. J.A. Losonczi J.H. Prestegard 1998 J. Biomol. NMR 12 447-451 10.1023/ A:1008302110884
32. F. Massi M.J. Grey A.G. Palmer 2005 Protein Sci. 14 735-742 10.1110/ ps.041139505
33. J. Meiler W. Peti C. Griesinger 2000 J. Biomol. NMR 17 283-294 10.1023/ A:1008362931964
34. J. Meiler W. Peti J. Prompers C. Griesinger R. Brueschweiler 2001 J. Am. Chem. Soc. 123 6098-6107 10.1021/ja010002z
35. J. Meiler W. Peti C. Griesinger 2003 J. Am. Chem. Soc. 125 8072-8073 10.1021/ja029816l
36. J.L. Mills T. Szyperski 2002 J. Biomol. NMR 23 63-67 10.1023/ A:1015397305148
37. T. Miura W. Klaus B. Gsell C. Miyamoto H. Senn 1999 J. Mol. Biol. 290 213-228 10.1006/jmbi.1999.2859
38. A.J. Nederveen A.M.J.J. Bonvin 2005 J. Chem. Theory Comput. 1 363-374 10.1021/ct0498829
39. M. Ottiger F. Delaglio A. Bax 1998 J. Magn. Res. 131 373-378 10.1006/ jmre.1998.1361
40. A.G. Palmer 3rd 2004 Chem. Rev. 104 3623-3640 10.1021/cr030413t
41. W. Peti J. Meiler R. Brueschweiler C. Griesinger 2002 J. Am. Chem. Soc. 124 5822-5833 10.1021/ja011883c
42. R. Ramage J. Green T.W. Muir O.M. Ogunjobi S. Love K. Shaw 1994 Biochem. J. 299 151-158
43. M. Ruckert G. Otting 2000 J. Am. Chem. Soc. 122 7793-7797 10.1021/ ja001068h
44. H.J. Sass G. Musco S.J. Stahl P.T. Wingfield S. Grzesiek 2000 J. Biomol. NMR 18 303-309 10.1023/A:1026703605147
45. D.M. Schneider M.J. Dellwo A.J. Wand 1992 Biochemistry 31 3645-3652
46. T. Sivaraman C.B. Arrington A.D. Robertson 2001 Nat. Struct. Biol. 8 331-333 10.1038/86208
47. N. Tjandra S.E. Feller R.W. Pastor A. Bax 1995 J. Am. Chem. Soc. 117 12562-12566
48. J.R. Tolman 2001 Curr. Opin. Struct. Biol. 11 532-539 10.1016/ S0959-440X(00)00245-1 532-539 10.1016/S0959-440X(00)00245-1
49. J.R. Tolman 2002 J. Am. Chem. Soc. 124 12020-12030 10.1021/ja0261123
50. J.R. Tolman J.M. Flanagan M.A. Kennedy J.H. Prestegard 1995 Proc. Natl. Acad. Sci. U.S.A 92 9279-9283 1995PNAS...92.9279T
51. J.R. Tolman J.H. Prestegard 1996a J. Magn. Reson. B 112 245-252
52. J.R. Tolman J.H. Prestegard 1996b J. Magn. Reson. B 112 269-274
53. J.R. Tolman J.M. Flanagan M.A. Kennedy J.H. Prestegard 1997 Nat. Struct. Biol. 4 292-297 10.1038/nsb0497-292
54. J.R. Tolman H.M. Al-Hashimi L.E. Kay J.H. Prestegard 2001 J. Am. Chem. Soc. 123 1416-1424 10.1021/ja002500y
55. R. Tycko F.J. Blanco Y. Ishii 2000 J. Am. Chem. Soc. 122 9340-9341 10.1021/ja002133q
56. S. Vijay Kumar C.E. Bugg W.J. Cook 1987 J. Mol. Biol. 194 531-544
57. K.D. Wilkinson E. Laleli-Sahin J. Urbauer C.N. Larsen G.H. Shih A.L. Haas S.T. Walsh A.J. Wand 1999 J. Mol. Biol. 291 1067-1077
58. J. Wist D. Frueh J.R. Tolman G. Bodenhausen 2004 J. Biomol. NMR 28 263-272 10.1023/B:JNMR.0000013699.48099.38
59. M. Zweckstetter A. Bax 2001 J. Biomol. NMR 20 365-377 10.1023/ A:1011263920003
60. M. Zweckstetter A. Bax 2002 J. Biomol. NMR 23 127-137 10.1023/ A:1016316415261