Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy

Journal of the American Chemical Society

Volumn 133, Issue 4, 2011, Pages 909-919

  Esadze, Alexandre ^a   Li, Da Wei ^b   Wang, Tianzhi ^a   Brüschweiler, Rafael ^b   Iwahara, Junji ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO GROUP; BOND ROTATIONS; CORRELATION TIME; DYNAMIC BEHAVIORS; EXPERIMENTAL CORRELATION; EXPLICIT SOLVENTS; HETERONUCLEAR; HETERONUCLEAR CORRELATION; HYDROGEN BONDINGS; MODEL FREE; MOLECULAR DYNAMICS SIMULATIONS; NMR SPECTROSCOPY; ORDER PARAMETER; PROTEASOMAL DEGRADATION; RELAXATION DISPERSION; SIDE CHAINS; SIDE-CHAIN; SUBNANOSECOND LIFETIMES; SYMMETRY AXIS; THEORETICAL FRAMEWORK; TIME-SCALES; UBIQUITIN; UBIQUITINATION;

AMINO ACIDS; COMPUTER SIMULATION; EXPERIMENTS; HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS;

ROTATION;

AMINE; LYSINE; NITROGEN 15; PROTEASOME; UBIQUITIN;

ARTICLE; COMPUTER SIMULATION; CONCEPTUAL FRAMEWORK; CORRELATION ANALYSIS; DYNAMICS; HYDROGEN BOND; MOLECULAR DYNAMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; PH; PROTEIN DEGRADATION; PROTON NUCLEAR MAGNETIC RESONANCE;

AMINES; HUMANS; LYSINE; MOLECULAR DYNAMICS SIMULATION; MOVEMENT; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; UBIQUITIN;

EID: 79851490872     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jal07847d     Document Type: Article

References (86)

1. Liepinsh, E.; Otting, G. Magn. Reson. Med. 1996, 35, 35-42.
2. Segawa, T.; Kateb, F.; Duma, L.; Bodenhausen, G.; Pelupessy, P. Chem Bio Chem 2008, 9, 9-42.
3. Iwahara, J.; Jung, Y. S.; Clore, G. M. J. Am. Chem. Soc. 2007, 129, 129-80.
4. Poon, D. K.; Schubert, M.; Au, J.; Okon, M.; Withers, S. G.; Mcintosh, L. P. J. Am. Chem. Soc. 2006, 128, 128-9.
5. Takayama, Y.; Castañeda, C. A.; Chimenti, M.; García-Moreno, B.; Iwahara. T. J. Am. Chem. Soc. 2008, 130, 130-5.
6. Englander, S. W.; Downer, N. W.; Teitelbaum, H. Annu. Rev. Biochem. 1972, 41, 41-24.
7. Bodenhausen, G.; Ruben, D. J. Chem. Phys. Lett. 1980, 69, 69-189.
8. Bax, A.; Griffey, R. H.; Hawkins, B. L. J. Magn. Reson. 1983, 55, 55-315.
9. Müller, L. J. Am. Chem. Soc. 1979, 101, 101-4484.
10. Ollerenshaw, J. E.; Tugarinov, V.; Kay, L. E. Magn. Reson. Chem. 2003, 41, 41-852.
11. Tugarinov, V.; Hwang, P. M.; Ollerenshaw, J. E.; Kay, L. E. J. Am. Chem. Soc. 2003, 125, 125-8.
12. Blaum, B. S.; Deakin, J. A.; Johansson, C. M.; Herbert, A. P.; Barlow, P. N.; Lyon, M.; Uhrin, D. J. Am. Chem. Soc. 2010, 132, 132-81.
13. Takayama, Y.; Sahu, D.; Iwahara, J. J. Magn. Reson. 2008, 194, 194-6.
14. Tomlinson, J. H.; Ullah, S.; Hansen, P. E.; Williamson, M. P. J. Am. Chem. Soc. 2009, 131, 131-84.
15. Abragam, A The Principle of Nuclear Magnetism; Carendon Press: Oxford, 1961; pp 264-353.
16. Sheppard, D.; Sprangers, R.; Tugarinov, V. Prog. Nucl. Magn. Reson. Spectrosc. 2010, 56, 56-45.
17. Sarkar, S. K.; Hiyama, Y.; Niu, C. H.; Young, P. E.; Gerig, J. T.; Torchia, D. A. Biochemistry 1987, 26, 26-800.
18. Lehmann, M. S.; Koetzle, T. F.; Hamilton, W. C. J. Am. Chem. Soc. 1971, 94, 94-2660.
19. Wei, A.; Raymond, M. K.; Roberts, J. D. J. Am. Chem. Soc. 1997, 119, 2915-2920.
20. Burke, T. E. J. Mam. Reson. 1970, 2, 2-140.
21. Kay, L. E.; Torchia, D. A. J. Magn. Reson. 1991, 95, 95-547.
22. Lipari, G.; Szabo, A J. Am. Chem. Soc. 1982, 104, 104-4559.
23. Showalter, S. A.; Johnson, E.; Rance, M.; Brüschweiler, R. J. Am. Chem. Soc. 2007, 129, 129-14147.
24. Brüschweiler, R.; Liao, X.; Wright, P. E. Science 1995, 268, 268-9.
25. Fushman, D.; Cowburn, D. J. Biomol. NMR 1999, 13, 13-47.
26. Lee, L. K.; Rance, M.; Chazin, W. J.; Palmer, A. G., III. J. Biomol. NMR 1997, 9, 9-98.
27. Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A J. Am. Chem. Soc. 1995, 117, 117-12566.
28. Woessner, D. E. J. Chem. Phys. 1962, 37, 37-654.
29. Kay, L. E.; Bull, T. E.; Nicholson, L. K.; Griesinger, C.; Schwalbe, H.; Bax, A.; Torchia, D. A J. Magn. Reson. 1992, 100, 100-558.
30. Palmer, A. G.; Wright, P. E.; Rance, M. Chem. Phys. Lett. 1991, 185, 41-46.
31. Hansen, D. F.; Vallurupalli, P.; Kay, L. E. J. Phys. Chem. B 2008, 112, 5898-904.
32. Baldwin, A. J.; Hansen, D. F.; Vallurupalli, P.; Kay, L. E. J. Am. Chem. Soc. 2009, 131, 131-48.
33. Carr, H. Y.; Purcell, E. M. Phys. Rev. 1954, 94, 94-638.
34. Meiboom, S.; Gill, D. Rev. Sci. Instrum. 1958, 29, 29-691.
35. Ferrage, F.; Cowburn, D.; Ghose, R. J. Am. Chem. Soc. 2009, 131, 131-9.
36. Ferrage, F.; Piserchio, A.; Cowburn, D.; Ghose, R. J. Magn. Reson. 2008, 192, 192-13.
37. Kumar, A.; Grace, R. C. R.; Madhu, P. K. Prog. Nucl. Magn. Reson. Spectrosc. 2000, 37, 37-319.
38. Grzesiek, S.; Bax, A. J. Am. Chem. Soc. 1993, 115, 115-12594.
39. Idiyatullin, D.; Daragan, V. A.; Mayo, K. H. J. Magn. Reson. 2001, 153, 153-143.
40. Li, Y. C.; Montelione, G. T. J. Magn. Reson., Ser. B 1994, 105, 105-51.
41. Skelton, N. J.; Palmer, A. G.; Akke, M.; Kordel, J.; Rance, M.; Chazin, W. J. J. Magn. Reson., Ser. B 1993, 102, 102-264.
42. Skrynnikov, N. R.; Ernst, R. R. J. Magn. Reson. 1999, 137, 137-80.
43. Cavanagh, J.; Fairbrother, W. J.; Palmer, A. G., III; Rance, M.; Skelton, N. J. Protein NMR Sprectroscopy: Principles and Practice, 2nd ed.; Elsevier Academic Press: Burlington, 2007.
44. Andre, I.; Linse, S.; Mulder, F. A J. Am. Chem. Soc. 2007, 129, 129-13.
45. Hwang, T. L.; van Zijl, P. C.; Mori, S. J. Biomol. NMR 1998, 11, 11-6.
46. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 6-293.
47. Johnson, B. A.; Blevins, R. A. J. Biomol. NMR 1994, 4, 4-614.
48. Case, D. A.; Cheatham, T. E., III.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 26-88.
49. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 65-25.
50. Li, D. W.; Brüschweiler, R. J. Am. Chem. Soc. 2009, 131, 131-7.
51. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 23-341.
52. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 91-6271.
53. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 98-10092.
54. Vijay-Kumar, S.; Bugg, C. E.; Cook. W. J. J. Mol. Biol. 1987, 194, 194-44.
55. Prompers, J. J.; Bruschweiler, R. J. Am. Chem. Soc. 2002, 124, 124-34.
56. Loria, J. P.; Rance, M.; Palmer, A. G. J. Am. Chem. Soc. 1999, 121, 121-2332.
57. Brüschweiler, R.; Wright, P. E. J. Am. Chem. Soc. 1994, 116, 116-8427.
58. Ming, D.; Brüschweiler, R. J. Biomol. NMR 2004, 29, 29-8.
59. Batchelder, L. S.; Sullivan, C. E.; Jelinski, L. W.; Torchia, D. A. Proc. Natl. Acad. Sci. U. S. A. 1982, 79, 79-9.
60. Ishima, R.; Petkova, A. P.; Louis, J. M.; Torchia, D. A. J. Am. Chem. Soc. 2001, 123, 123-71.
61. Muhandiram, D. R.; Yamazaki, T.; Sykes, B. D.; Kay, L. E. J. Am. Chem. Soc. 1995, 117, 117-11544.
62. Nicholson, L. K.; Kay, L. E.; Baldisseri, D. M.; Arango, J.; Young, P. E.; Bax, A.; Torchia, D. A. Biochemistry 1992, 31, 31-63.
63. Xue, Y.; Pavlova, M. S.; Ryabov, Y. E.; Reif, B.; Skrynnikov, N. R. J. Am. Chem. Soc. 2007, 129, 129-38.
64. Zhang, X.; Sui, X.; Yang, D. J. Am. Chem. Soc. 2006, 128, 128-81.
65. Showalter, S. A.; Bruschweiler, R. J. Chem. Theory Comput. 2007, 3, 3-975.
66. Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; van Gunsteren, W. F. J. Biomol. NMR 2004, 30, 30-422.
67. Trbovic, N.; Kim, B.; Friesner, R. A.; Palmer, A G., III. Proteins 2008, 71, 71-94.
68. Sheppard, D.; Li, D. W.; Godoy-Ruiz, R.; Brüschweiler, R.; Tugarinov, V. J. Am. Chem. Soc. 2010, 132, 132-19.
69. Trbovic, N.; Cho, J. H.; Abel, R.; Friesner, R. A.; Rance, M.; Palmer, A. G., III. J. Am. Chem. Soc. 2009, 131, 131-22.
70. Gale, G. M.; Gallot, G.; Hache, F.; Lascoux, N.; Bratos, S.; Leicknam, J. C. Phys. Rev. Lett. 1999, 82, 82-1071.
71. Keutsch, F. N.; Saykally, R. J. Proc. Natl. Acad. Sci. U. SA. 2001, 98, 98-40.
72. Lawrence, C. P.; Skinner, J. L. Chem. Phys. Lett. 2003, 369, 369-477.
73. Halle, B. Philos. Trans. R Soc., B 2004, 359, 359-23.
74. Grzesiek, S.; Cordier, F.; Jaravine, V.; Barfield, M. Prog. Nucl. Magn. Reson. Svectrosc. 2004, 45, 45-300.
75. Bandyopadhyay, S.; Chakraborty, S.; Bagchi, B. J. Am. Chem. Soc. 2005, 127, 127-7.
76. Hershko, A.; Ciechanover, A. Annu. Rev. Biochem. 1992, 61, 61-807.
77. Hershko, A. Curr. Opin. Cell Biol. 1997, 9, 9-99.
78. Bhoj, V. G.; Chen, Z. J. Nature 2009, 458, 458-7.
79. Fushman, D.; Walker, O. J. Mol. Biol. 2010, 395, 395-14.
80. Peng, J.; Schwartz, D.; Elias, J. E.; Thoreen, C. C.; Cheng, D.; Marsischky, G.; Roelofs, J.; Finley, D.; Gygi, S. P. Nat. Biotechnol. 2003, 21, 21-6.
81. Radivojac, P.; Vacic, V.; Haynes, C.; Cocklin, R. R.; Mohan, A.; Heyen, J. W.; Goebl, M. G.; Iakoucheva, L. M. Proteins 2010, 78, 78-380.
82. Voet, D.; Voet, J. G. Biochemistry, 3rd ed.; Wiley: Hoboken, 2004.
83. Shaka, A. J.; Keeler, J.; Freeman, R. J. Magn. Reson. 1983, 53, 53-340.
84. Kupče, E.; Boyd, J.; Campbell, I. D. J. Magn. Reson., Ser. B 1995, 106, 106-303.
85. Kay, L. E.; Xu, G. Y.; Yamazaki, T. J. Magn. Reson., Ser. A 1994, 109, 109-133.
86. Hansen, D. F.; Kay, L. E. J. Biomol. NMR 2007, 37, 37-55.