Variation in quadrupole couplings of α deuterons in ubiquitin suggests the presence of Cα-Hα⋯O=C hydrogen bonds

Journal of the American Chemical Society

Volumn 132, Issue 22, 2010, Pages 7709-7719

  Sheppard, Devon ^a   Li, Da Wei ^b   Godoy Ruiz, Raquel ^a   Brüschweiler, Rafael ^b   Tugarinov, Vitali ^a  

^a Bldg 142   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AVERAGE VALUES; DATA SETS; HYDROGEN BONDINGS; INDIRECT MEASUREMENTS; INTERNAL DYNAMICS; INVERSE CUBE; MOLECULAR DYNAMICS SIMULATIONS; QUADRUPOLAR COUPLING; QUADRUPOLAR COUPLING CONSTANTS; QUADRUPOLE COUPLING; RELAXATION MEASUREMENTS; RELAXATION RATES; SENSITIVE PROBE; SOLID STATE NMR; SPIN SYSTEMS; THREE-DIMENSIONAL STRUCTURE; TIME-SCALES; UBIQUITIN;

COUPLINGS; DEUTERIUM; HYDROGEN; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR PHYSICS; PROTEINS; SPIN DYNAMICS;

HYDROGEN BONDS;

CARBON; DEUTERIUM; GLYCINE; HYDROGEN; OXYGEN; UBIQUITIN;

ARTICLE; CHEMICAL INTERACTION; CONTROLLED STUDY; CROSS COUPLING REACTION; HYDROGEN BOND; MOLECULAR DYNAMICS; NANOANALYSIS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN STRUCTURE; QUADRUPOLAR COUPLING CONSTANT ALPHA DEUTERON; REFERENCE VALUE; SIMULATION; SOLID STATE;

DEUTERIUM; HUMANS; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; UBIQUITIN;

EID: 77953097630     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja101691s     Document Type: Article

References (81)

1. Abragam, A. Principles of Nuclear Magnetism; Clarendon Press: Oxford, U.K., 1961.
2. Sheppard, D. and Tugarinov, V. J. Magn. Reson. 2010, 203, 316-322
3. Soda, G. and Chiba, T. J. Chem. Phys. 1969, 50, 439-446
4. Hunt, M. J. and Mackay, A. L. J. Magn. Reson. 1976, 22, 295-301
5. LiWang, A. C. and Bax, A. J. Magn. Reson. 1997, 127, 54-64
6. Muller, C., Schajor, W., Zimmermann, H., and Haeberlen, U. J. Magn. Reson. 1984, 56, 235-346
7. Muhandiram, D. R., Yamazaki, T., Sykes, B. D., and Kay, L. E. J. Am. Chem. Soc. 1995, 117, 11536-11544
8. Millet, O., Muhandiram, D. R., Skrynnikov, N. R., and Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6439-6448
9. Skrynnikov, N. R., Millet, O., and Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6449-6460
10. Millet, O., Mittermaier, A., Baker, D., and Kay, L. E. J. Mol. Biol. 2003, 329, 551-563
11. Tugarinov, V., Ollerenshaw, J. E., and Kay, L. E. J. Am. Chem. Soc. 2005, 127, 8214-8225
12. Tugarinov, V. and Kay, L. E. J. Am. Chem. Soc. 2006, 128, 12484-12489
13. Yang, D., Mittermaier, A., Mok, Y. K., and Kay, L. E. J. Mol. Biol. 1998, 276, 939-954
14. Pervushin, K., Wider, G., and Wüthrich, K. J. Am. Chem. Soc. 1997, 119, 3842-3843
15. Sheppard, D., Li, D. W., Brüschweiler, R., and Tugarinov, V. J. Am. Chem. Soc. 2009, 131, 15853-15865
16. Mittermaier, A. and Kay, L. E. J. Am. Chem. Soc. 1999, 121, 10608-10613
17. Sutor, D. J. Nature 1962, 195, 68-69
18. Taylor, R. and Kennard, O. J. Am. Chem. Soc. 1982, 104, 5063-5070
19. Cordier, F., Barfield, M., and Grzesiek, S. J. Am. Chem. Soc. 2003, 125, 15750-15751
20. Lundström, P., Teilum, K., Carstensen, T., Bezsonova, I., Wiesner, S., Hansen, D. F., Religa, T. L., Akke, M., and Kay, L. E. J. Biomol. NMR 2007, 38, 199-212
21. Meiboom, S. and Gill, D. Rev. Sci. Instrum. 1958, 29, 688
22. Carr, H. Y. and Purcell, E. M. Phys. Rev. 1954, 94, 630-638
23. Bax, A. and Ikura, M. J. Biomol. NMR 1991, 1, 99-104
24. Shaka, A. J., Keeler, J., Frenkiel, T., and Freeman, R. J. Magn. Reson. 1983, 52, 335-338
25. McCoy, M. A. and Mueller, L. J. Magn. Reson. 1992, 98, 674-679
26. McCoy, M. A. and Mueller, L. J. Am. Chem. Soc. 1992, 114, 2108-2112
27. Patt, S. L. J. Magn. Reson. 1992, 96, 94-102
28. Boyd, J. and Soffe, N. J. Magn. Reson. 1989, 85, 406-413
29. Kay, L. E., Ikura, M., Tschudin, R., and Bax, A. J. Magn. Reson. 1990, 89, 496-514
30. Emsley, L. and Bodenhausen, G. Chem. Phys. Lett. 1987, 165, 469-476
31. Palmer, A. G., Cavanagh, J., Wright, P. E., and Rance, M. J. Magn. Reson. 1991, 93, 151-170
32. Kay, L. E., Keifer, P., and Saarinen, T. J. Am. Chem. Soc. 1992, 114, 10663-10665
33. Schleucher, J., Sattler, M., and Griesinger, C. Angew. Chem., Int. Ed. 1993, 32, 1489-1491
34. Marion, D., Ikura, M., Tschudin, R., and Bax, A. J. Magn. Reson. 1989, 85, 393-399
35. Tjandra, N. and Bax, A. J. Magn. Reson. 1997, 124, 512-515
36. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. J. Biomol. NMR 1995, 6, 277-293
37. Kamith, U. and Shriver, J. W. J. Biol. Chem. 1989, 264, 5586-5592
38. Lipari, G. and Szabo, A. J. Am. Chem. Soc. 1982, 104, 4559-4570
39. Lipari, G. and Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546-4559
40. Palmer, A. G. I., Hochstrasser, R. A., Millar, D. P., Rance, M., and Wright, P. E. J. Am. Chem. Soc. 1993, 115, 6333-6345
41. Woessner, D. E. J. Chem. Phys. 1962, 37, 647-654
42. Vijay-Kumar, S., Bugg, C. E., and Cook, W. J. J. Mol. Biol. 1987, 194, 531-544
43. Jeffrey, G. Accurate molecular structures, their determination and importance; Oxford University Press: Oxford, U.K., 1992.
44. Ottiger, M. and Bax, A. J. Am. Chem. Soc. 1998, 120, 12334-12341
45. Tjandra, N. and Bax, A. J. Am. Chem. Soc. 1997, 119, 9576-9577
46. Engelke, J. and Rüterjans, H. J. Biomol. NMR 1995, 5, 173-182
47. Engelke, J. and Rüterjans, H. In Biological Magnetic Resonance: Structure Computation and Dynamics in Protein NMR; Krishna, N. R. and Berliner, L. J., Eds.; Kluwer Academic Publishers: New York, 1999; Vol. 17.
48. Grzesiek, S. and Bax, A. J. Am. Chem. Soc. 1994, 116, 10196-10201
49. Bevington, P. R. and Robinson, D. K. Data Reduction and Error Analysis for the Physical Sciences; WCB/McGraw-Hill: New York, 1992.
50. Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. J. J. Comput. Chem. 2005, 26, 1668-1688
51. Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. Proteins 2006, 65, 712-725
52. Prompers, J. J. and Brüschweiler, R. J. Am. Chem. Soc. 2002, 124, 4522-4534
53. Wooten, J. B., Savitsky, G. B., Jacobus, J., Beyerlein, A. L., and Emsley, J. W. J. Chem. Phys. 1979, 70, 438-442
54. Schramm, S. and Oldfield, E. Biochemistry 1983, 22, 2908-2913
55. Tjandra, N., Feller, S. E., Pastor, R. W., and Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566
56. Lee, L. K., Rance, M., Chazin, W. J., and Palmer, A. G. J. Biomol. NMR 1997, 9, 287-298
57. Showalter, S. A. and Brüschweiler, R. J. Chem. Theory Comput. 2007, 3, 961-975
58. Trbovic, N., Kim, B., Friesner, R. A., and Palmer, A. G. I. Proteins 2008, 71, 684-694
59. Koller, A. N., Schwalbe, H., and Gohlke, H. Biophys. J. 2008, 95, L04-L06
60. Bui, J. M., Gsponer, J., Vendruscolo, M., and Dobson, C. M. Biophys. J. 2009, 97, 2513-2520
61. Brüschweiler, R. J. Am. Chem. Soc. 1992, 114, 5341-5344
62. Henry, E. R. and Szabo, A. J. Chem. Phys. 1985, 82, 4753-4761
63. Vasos, P. R., Hall, J. B., Kummerle, R., and Fushman, D. J. Biomol. NMR 2006, 36, 27-36
64. Yamazaki, T., Muhandiram, R., and Kay, L. E. J. Am. Chem. Soc. 1994, 116, 8266-8278
65. Kay, L. E., Torchia, D. A., and Bax, A. Biochemistry 1989, 28, 8972-8979
66. Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., and Gronenborn, A. M. J. Am. Chem. Soc. 1990, 112, 4989-4991
67. Boyd, J., Mal, T. K., Soffe, N., and Campbell, I. D. J. Magn. Reson. 1997, 124, 61-71
68. Sanctuary, B. C. and Selwyn, L. J. Chem. Phys. 1981, 74, 906-912
69. Ramage, R., Green, J., Muir, T. W., Ogunjobi, O. M., Love, S., and Shaw, K. Biochem. J. 1994, 299, 151-158
70. Alexeev, D., Bury, S. M., Turner, M. A., Ogunjobi, O. M., Muir, T. W., Ramage, R., and Sawyer, L. Biochem. J. 1994, 299, 159-163
71. Cornilescu, G., Marquardt, J., Ottiger, M., and Bax, A. J. Am. Chem. Soc. 1998, 120, 6836-6837
72. Steiner, T. Chem. Commun. 1997, 727-734
73. Derewenda, Z. S., Lee, L., and Derewenda, U. J. Mol. Biol. 1995, 252, 248-62
74. Wahl, M. C. and Sundaralingham, M. Trends Biochem. Sci. 1997, 22, 97-102
75. Vargas, R., Garza, J., Dixon, D. A., and Hay, B. P. J. Am. Chem. Soc. 2000, 122, 4750-4755
76. Addlagatta, A., Krzywda, S., Czapinska, H., Otlewski, J., and Jaskolski, M. Acta Crystallogr. 2001, D57, 649-663
77. Esposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A., and Mazzarella, L. J. Mol. Biol. 2000, 297, 713-732
78. Koradi, R., Billeter, M., and Wüthrich, K. J. Mol. Graphics 1996, 14, 51-55
79. Lindorff-Larsen, K., Best, R. B., Depristo, M. A., Dobson, C. M., and Vendruscolo, M. Nature 2005, 433, 128-132
80. Bella, J. and Berman, H. M. J. Mol. Biol. 1996, 264, 734-742
81. Burnett, L. H. and Muller, B. H. J. Chem. Phys. 1971, 55, 5829-5831