Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins

Journal of the American Chemical Society

Volumn 128, Issue 30, 2006, Pages 9863-9872

  Parker, Laura L ^a   Houk, Andrew R ^a,b   Jensen, Jan H ^a,c  

^a E11 SSH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NUMERICAL METHODS; PROTONS; QUANTUM THEORY;

CHEMICAL SHIFTS; PROTEIN G; ROOT-MEAN-SQUARE DEVIATION (RMSD); UBIQUITIN;

PROTEINS;

AMIDE; HYDROGEN; UBIQUITIN;

AB INITIO CALCULATION; ARTICLE; COMPARATIVE STUDY; CORRELATION COEFFICIENT; HYDROGEN BOND; MODEL; PREDICTION; PROTEIN ANALYSIS; PROTEIN STABILITY; PROTEIN STRUCTURE; QUANTUM MECHANICS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 33746645192     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0617901     Document Type: Article

References (54)

1. Osapay, K.; Case, D. A. J. Am. Chem. Soc. 1991, 113, 9436.
2. Spera, S.; Bax, A. J. Am. Chem. Soc. 1991, 113, 5490.
3. Wishart, D. S.; Sykes, B. D.; Richards, F. M. J. Mol. Biol. 1991, 222, 311.
4. Dedios, A. C.; Pearson, J. G.; Oldfield, E. Science 1993, 260, 1491.
5. Williamson, M. P.; Asakura, T. J. Magn. Reson. Series B 1993, 101, 63.
6. Szilagyi, L. Prog. Nucl. Magn. Reson. Spectrosc. 1995, 27, 325.
7. deDios, A. C. Prog. Nucl. Magn. Reson. Spectrosc. 1996, 29, 229.
8. Gronwald, W.; Boyko, R. F.; Sonnichsen, F. D.; Wishart, D. S.; Sykes, B. D. J. Biomol. NMR 1997, 10, 165.
9. Sitkoff, D.; Case, D. A. J. Am. Chem. Soc. 1997, 119, 12262.
10. Wishart, D. S.; Watson, M. S.; Boyko, R. F.; Sykes, B. D. J. Biomol. NMR 1997, 10, 329.
11. Ando, I.; Kameda, T.; Asakawa, N.; Kuroki, S.; Kurosu, H. J. Mol. Struct. 1998, 441, 213.
12. Cornilescu, G.; Delaglio, F.; Bax, A. J. Biomol. NMR 1999, 13, 289.
13. Iwadate, M.; Asakura, T.; Williamson, M. P. J. Biomol. NMR 1999, 13, 199.
14. Xu, X. P.; Case, D. A. J. Biomol. NMR 2001, 21, 321.
15. Meiler, J. J. Biomol. NMR 2003, 26, 25.
16. Neal, S.; Nip, A. M.; Zhang, H. Y.; Wishart, D. S. J. Biomol. NMR 2003, 26, 215.
17. Wang, Y. J. J. Biomol. NMR 2004, 30, 233.
18. Meiler, J.; Baker, D. Proc. Nat'l. Acad. Sci., U.S.A. 2003, 100, 15404.
19. Wishart, D. S.; Case, D. A. Use of chemical shifts in macromolecular structure determination. In Methods Enzymol. 2001, 138, 1.
20. Sitkoff, D.; Case, D. A. Prog. Nucl. Magn. Reson. Spectrosc. 1998, 32, 165.
21. Wagner, G.; Pardi, A.; Wüthrich, K. J. Am. Chem. Soc. 1983, 105, 5948.
22. Cordier, F.; Grzesiek, S. J. Am. Chem. Soc. 1999, 121, 1601.
23. Barfield, M. J. Am. Chem. Soc. 2002, 124, 4158.
24. Jensen, P. R.; Axelsen, J. B.; Lerche, M. H.; Poulsen, F. M. J. Biomol. NMR 2004, 28, 31.
25. Chesnut, D. B. The Ab Initio Computation of Nuclear Magn. Reson. Chemical Shielding. In Reviews in Computational Chemistry, Boyd, D. B.; Ed.; 1996; Vol. 8; p 245.
26. Rablen, P. R.; Pearlman, S. A.; Finkbiner, J. J. Phys. Chem. A 1999, 103, 7357.
27. Porubcan, M. A.; Neves, D. E.; Rausch, S. K.; Markley, J. L. Biochemistry 1978, 17, 4640.
28. Harris, R. K.; Becker, E. D.; Cabral de Menezes, S. M.; Goodfellow, R.; Granger, P. Pure Appl. Chem. 2002, 73, 1795.
29. Molina, P. A.; Jensen, J. H. J. Phys. Chem. B 2003, 107, 6226.
30. PQS version 2.4, P. Q. S.; Fayetteville, Arkansas, http://www.pqs-chem. com; sales@pqs-chem.com.
31. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomert, J. A. J. Comput. Chem. 1993, 14, 1347.
32. Derrick, J. P.; Wigley, D. B. J. Mol. Biol. 1994, 243, 906.
33. Alexeev, D.; Barlow, P. N.; Bury, S. M.; Charrier, J. D.; Cooper, A.; Hadfield, D.; Jamieson, C.; Kelly, S. M.; Layfield, R.; Mayer, R. J.; McSparron, H.; Price, N. C.; Ramage, R.; Sawyer, L.; Starkmann, B. A.; Uhrin, D.; Wilken, J.; Young, D. W. Chembiochem 2003, 4, 894.
34. Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A. Nucleic Acids Res. 2004, 32, W665.
35. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995.
36. Li, H.; Jensen, J. H. J. Comput. Chem. 2004, 25, 1449.
37. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 107, 3210.
38. Klamt, A.; Schuurmann, G. J. Chem. Soc.-Perkin Trans. 2 1993, 799.
39. Orban, J.; Alexander, P.; Bryan, P. Biochemistry 1992, 31, 3604.
40. Weber, P. L.; Brown, S. C.; Mueller, L. Biochemistry 1987, 26, 7282.
41. Vijaykumar, S.; Bugg, C. E.; Cook, W. J. J. Mol. Biol. 1987, 194, 531.
42. Case, D. A. J. Biomol. NMR 1995, 6, 341.
43. Wieczorek, R.; Dannenberg, J. J. J. Am. Chem. Soc. 2005, 127, 17216.
44. Koch, O.; Bocola, M.; Klebe, G. Proteins-Struct. Funct. Bioinform. 2005, 61, 310.
45. Salvador, P.; Kobko, N.; Wieczorek, R.; Dannenberg, J. J. J. Am. Chem. Soc. 2004, 126, 14190.
46. Viswanathan, R.; Asensio, A.; Dannenberg, J. J. J. Phys. Chem. A 2004, 108, 9205.
47. Kobko, N.; Dannenberg, J. J. J. Phys. Chem. A 2003, 107, 6688.
48. Ireta, J.; Neugebauer, J.; Scheffler, M.; Rojo, A.; Galvan, M. J. Phys. Chem. B 2003, 107, 1432.
49. Lin, J. Q.; Luo, S. W.; Wu, Y. D. J. Comput. Chem. 2002, 23, 1551.
50. Miller, J. S.; Kennedy, R. J.; Kemp, D. S. J. Am. Chem. Soc. 2002, 124, 945.
51. Topol, I. A.; Burt, S. K.; Deretey, E.; Tang, T. H.; Perczel, A.; Rashin, A.; Csizmadia, I. G. J. Am. Chem. Soc. 2001, 123, 6054.
52. Kobko, N.; Paraskevas, L.; del Rio, E.; Dannenberg, J. J. J. Am. Chem. Soc. 2001, 123, 4348.
53. Jaravine, V. A.; Alexandrescu, A. T.; Grzesiek, S. Protein Sci. 2001, 10, 943.
54. Guo, H.; Gresh, N.; Roques, B. P.; Salahub, D. R. J. Phys. Chem. B 2000, 104, 9746.