Multiple-state ensemble structure determination from eNOE spectroscopy

Molecular Physics

Volumn 111, Issue 3, 2013, Pages 437-454

  Vögeli, Beat ^a   Güntert, Peter ^b,c   Riek, Roland ^a,d  

^a ETH ZURICH   (Switzerland)

^b FRANKFURT INSTITUTE FOR ADVANCED STUDIES   (Germany)

^c TOKYO METROPOLITAN UNIVERSITY   (Japan)

^d SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

Biological macromolecules; Correlated dynamics; Dynamics; NMR; NOE; Nuclear Overhauser effect; Proteins; Structure calculation; Structure ensemble

Indexed keywords

BIOLOGICAL MACROMOLECULE; CORRELATED DYNAMICS; NOE; NUCLEAR OVERHAUSER EFFECTS; STRUCTURE CALCULATION; STRUCTURE ENSEMBLES;

DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS; RELAXATION PROCESSES; X RAY DIFFRACTION;

NUCLEAR MAGNETIC RESONANCE;

EID: 84875851000     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268976.2012.728257     Document Type: Article

References (80)

1. K. Wuthrich, NMR of Proteins and Nucleic Acid (Wiley, New York, 1986).
2. D. Neuhaus and M.P. Williamson, The Nuclear Overhauser Effect in Structural and Conformational Analysis (Wiley, New York, 2000).
3. J. Cavanagh, W.J. Fairbrother, A.G. Palmer, M. Rance and N.J. Skleton, Protein NMR Spectroscopy. Principles and Practice (Academic Press, San Diego, 2007).
4. I. Solomon, Phys. Rev. 99, 559 (1955).
5. A. Kalk and H.J.C. Berendsen, J. Magn. Reson. 24, 343 (1976).
6. A. Kumar, G. Wagner, R.R. Ernst and K. Wuthrich, J. Am. Chem. Soc. 103, 3654 (1981).
7. J.W. Keepers and T.L. James, J. Magn. Reson. 57, 404 (1984).
8. E.T. Olejniczak, F.M. Poulsen and C.M. Dobson, J. Magn. Reson. 59, 518 (1984).
9. G.M. Clore and A.M. Gronenborn, J. Magn. Reson. 61, 158 (1985).
10. W. Massefski and P.H. Bolton, J. Magn. Reson. 65, 526 (1985).
11. E.T. Olejniczak, R.T. Gampe and S.W. Fesik, J. Magn. Reson. 67, 28 (1986).
12. J.F. Lefevre, A.N. Lane and O. Jardetzky, Biochemistry 26, 5076 (1987).
13. R. Boelens, T.M.G. Koning and R. Kaptein, J. Mol. Struct. 173, 299 (1988).
14. B.T. Farmer, S. Macura and L.R. Brown, J. Magn. Reson. 80, 1 (1988).
15. G.M. Clore and A.M. Gronenborn, J. Magn. Reson. 84, 398 (1989).
16. R. Boelens, T.M.G. Koning, G.A. Van der Marel, J.H. Van Boom and R. Kaptein, J. Magn. Reson. 82, 290 (1989).
17. A.K. Suri and R.M. Levy, J. Magn. Reson. B 106, 24 (1995).
18. S.J.F. Vincent, C. Zwahlen, P.H. Bolton, T.M. Logan and G. Bodenhausen, J. Am. Chem. Soc. 118, 3531 (1996).
19. B. Vogeli, T.F. Segawa, D. Leitz, A. Sobol, A. Choutko, D. Trzesniak, W. van Gunsteren and R. Riek, J. Am. Chem. Soc. 131, 17215 (2009).
20. B. Vogeli, M. Friedmann, D. Leitz, A. Sobol and R. Riek, J. Magn. Reson. 204, 290 (2010).
21. E.T. Olejniczak, C.M. Dobson, M. Karplus and R.M. Levy, J. Am. Chem. Soc. 106, 1923 (1984).
22. N. Tjandra and A. Bax, Science 278, 1111 (1997).
23. J. Iwahara and G.M. Clore, Nature 440, 1227 (2006).
24. G. Otting, J. Biomol. NMR 42, 1 (2008).
25. P. Guntert, Eur. Biophys. J. 38, 129 (2009).
26. R. Horst, G. Wider, J. Fiaux, E.B. Bertelson, A.L. Horwich and K. Wuthrich, Proc. Natl. Acad. Sci. USA 103, 15445 (2006).
27. T.S. Ulmer, B.E. Ramirez, F. Delaglio and A. Bax, J. Am. Chem. Soc. 125, 9179 (2003).
28. L. Yao, B. Vogeli, D.A. Torchia and A. Bax, J. Phys. Chem. B 112, 6045 (2008).
29. L. Yao, B. Vogeli, J. Ying and A. Bax, J. Am. Chem. Soc. 130, 16518 (2008).
30. P. Guntert, Prog. Nucl. Magn. Reson. Spectrosc. 43, 105 (2003).
31. R. Bruschweiler, M. Blackledge and R.R. Ernst, J. Biomol. NMR 1, 3 (1991).
32. A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. Kaptain, Proteins Struct. Func. Genet. 15, 385 (1993).
33. J. Kemmink, C.P.M. van Mierlo, R.M. Scheek and T.E. Creighton, J. Mol. Biol. 230, 312 (1993).
34. A.M.J.J. Bonvin, R. Boelens and R. Kaptain, J. Biomol. NMR 4, 143 (1994).
35. D.F. Mierke, R.M. Scheek and H. Kessler, Biopolymers 34, 559 (1994).
36. J. Fennen, A.E. Torda and W.F. van Gunsteren, J. Biomol. NMR 6, 163 (1995).
37. A.M.J.J. Bonvin and A.T. Brunger, J. Mol. Biol. 250, 80 (1995).
38. A.M.J.J. Bonvin and A.T. Brunger, J. Biomol. NMR 7, 72 (1996).
39. P. Bernado and M.J. Blackledge, Am. Chem. Soc. 126, 4907 (2004).
40. G.M. Clore and C.D. Schwieters, J. Am. Chem. Soc. 126, 2923 (2004).
41. G.M. Clore and C.D. Schwieters, Biochemistry 43, 10 678 (2004).
42. K. Lindorff-Larsen, R.B. Best, M.A. DePristo, C.M. Dobson and M. Vendruscolo, Nature 433, 128 (2005).
43. G. Bouvignies, P. Bernado, S. Meier, K. Cho, S. Grzesiek, R. Bruschweiler and M. Blackledge, Proc. Natl. Acad. Sci. USA 102, 13885 (2005).
44. G.M. Clore and C.D. Schwieters, J. Mol. Biol. 355, 879 (2006).
45. B. Vogeli, L. Yao and A. Bax, J. Biomol. NMR 41, 17 (2008).
46. B.T. Farmer, J. Magn. Reson. 93, 635 (1991).
47. S.M. Pascal, D.R. Muhandiram, T. Yamazaki, J.D. Forman-Kay and L.E. Kay, J. Magn. Reson. Ser. B 103, 197 (1994).
48. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer and A. Bax, J. Biomol. NMR 6, 277 (1995).
49. B.A. Johnson and R.A. Blevins, J. Biomol. NMR 4, 603 (1994).
50. D. Neri, G. Otting and K. Wuthrich, Tetrahedron 46, 3287 (1990).
51. L.E. Kay, D.A. Torchia and A. Bax, Biochemistry 28, 8972 (1989).
52. J.B. Hall and D. Fushman, J. Biomol. NMR 27, 261 (2003).
53. B. Vogeli, J.F. Ying, A. Grishaev and A. Bax, J. Am. Chem. Soc. 129, 9377 (2007).
54. A.C. Wang and A. Bax, J. Am. Chem. Soc. 118, 2483 (1996).
55. B.Vogeli andL.Yao,J.Am. Chem. Soc. 131, 3668 (2009).
56. J. Orts, B. Vogeli and R. Riek, J. Chem. Theory Comput. (2012), doi: 10.1021/ct3002249.
57. R. Bruschweiler, B. Roux, M. Blackledge, C. Griesinger, M. Karplus and R.R. Ernst, J. Am. Chem. Soc. 114, 2289 (1992).
58. C.B. Post, J. Mo. Biol. 224, 1087 (1992).
59. D. Leitz, B. Vogeli, J. Greenwald and R. Riek, J. Phys. Chem. B 115, 7648 (2011).
60. K. Wuthrich, M. Billeter and W. Braun, J. Mol. Biol. 169, 949 (1983).
61. T.M.G. Koning, R. Boelens and R. Kaptein, J. Magn. Reson. 90, 111 (1990).
62. C.M. Fletcher, D.N.M. Jones, R. Diamond and D. Neuhaus, J. Biomol. NMR 8, 292 (1996).
63. P. Guntert, W. Braun and K. Wuthrich, J. Mol. Biol. 217, 517 (1991).
64. P. Guntert, C. Mumenthaler and K. Wuthrich, J. Mol. Biol. 273, 283 (1997).
65. K. Houben and R. Boelens, J. Biomol. NMR 29, 151 (2004).
66. C. Fares, N.A. Lakomek, K.F.A. Walter, B.T.C. Frank, J. Meiler, S. Becker and C. Griesinger, J. Biomol. NMR 45, 23 (2009).
67. A.T. Brunger, G.M. Clore, A.M. Gronenborn, R. Saffrich and M. Nilges, Science 261, 328 (1993).
68. J.P. Derrick and D.B. Wigley, J. Mol. Biol. 243, 906 (1994).
69. E. Miclet, J. Boisbouvier and A. Bax, J. Biomol. NMR 31, 201 (2005).
70. L.Y. Lian, J.P. Derrick, M.J. Sutcliffe, J.C. Yang and G.C.K. Roberts, J. Mol. Biol. 228, 1219 (1992).
71. J.J. Chou, D.A. Case and A. Bax, J. Am. Chem. Soc. 125, 8959 (2003).
72. J.S. Hu, S. Grzesiek and A. Bax, J. Am. Chem. Soc. 119, 1803 (1997).
73. C. Perez, F. Lohr, H. Ruterjans and J.M. Schmidt, J. Am. Chem. Soc. 119, 7081 (2001).
74. B. Vogeli and R. Riek, J. Biomol. NMR 46, 135 (2010).
75. A. Bax and D.G. Davies, J. Magn. Reson. 65, 355 (1985).
76. A.J. Shaka, P.B. Barker and R. Freeman, J. Magn. Reson. 194, 547 (1985).
77. R. Tycko, A. Pines and J. Guckenheimer, J. Chem. Phys. 83, 2775 (1985).
78. T. Fujiwara and K. Nagayama, J. Magn. Reson. 77, 53 (1988).
79. J.M. Bohlen and G. Bodenhausen, J. Magn. Reson. Ser. A 102, 293 (1993).
80. D. Marion, M. Ikura, R. Tschudin and A. Bax, J. Magn. Reson. 85, 393 (1989).