Stochastic modeling of flexible biomolecules applied to NMR relaxation. I. Internal dynamics of cyclodextrins: γ-Cyclodextrin as a case study

Journal of Physical Chemistry B

Volumn 116, Issue 44, 2012, Pages 13159-13171

  Zerbetto, Mirco ^a   Kotsyubynskyy, Dmytro ^a   Kowalewski, Jozef ^b   Widmalm, Göran ^b   Polimeno, Antonino ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL APPROACH; COMPUTATIONAL PROTOCOLS; GLUCOPYRANOSE RING; HYDROXYMETHYL GROUPS; INTERNAL DYNAMICS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR PARAMETERS; NMR RELAXATION; OH GROUP; PARAMETRIZATIONS; QUALITATIVE ANALYSIS; STOCHASTIC EQUATIONS;

DYNAMICS; METHANOL; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STOCHASTIC SYSTEMS;

CYCLODEXTRINS;

CARBON; GAMMA CYCLODEXTRIN; GAMMA CYCLODEXTRIN DERIVATIVE; GAMMA-CYCLODEXTRIN;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

CARBON ISOTOPES; GAMMA-CYCLODEXTRINS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATION;

EID: 84868519375     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp306624d     Document Type: Article

References (46)

1. Cavanagh, J.; Fairbrother, W. J.; Palmer, A. G.; Skelton, N. J. Protein NMR Spectroscopy; Academic: San Diego, CA, 1996.
2. Landersjö, C.; Stenutz, R.; Widmalm, G. J. Am. Chem. Soc. 1997, 119, 8695
3. Kowalewski, J.; Mäler, L. Nuclear Spin Relaxation in Liquids; Taylor & Francis: New York, 2006.
4. Murali, N.; Krishnan, V. V. Conc. Magn. Reson. A 2003, 17A, 86
5. Tolman, J. R.; Ruan, K. Chem. Rev. 2006, 106, 1720
6. Meirovitch, E.; Shapiro, Y. E.; Polimeno, A.; Freed, J. H. J. Phys. Chem. A 2006, 110, 8366
7. Meirovitch, E.; Shapiro, Y. E.; Polimeno, A.; Freed, J. H. Prog. NMR Spectrosc. 2010, 56, 360
8. Zerbetto, M.; Polimeno, A.; Kotsyubynskyy, D.; Ghalebani, L.; Kowalewski, J.; Meirovitch, E.; Olsson, U.; Widmalm, G. J. Chem. Phys. 2009, 131, 234501
9. Zerbetto, M.; Buck, M.; Meirovitch, E.; Polimeno, A. J. Phys. Chem. B 2011, 115, 376
10. Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995
11. Shapiro, Y. E.; Polimeno, A.; Freed, J. H.; Meirovitch, E. J. Phys. Chem. B 2011, 115, 354
12. Meirovitch, E.; Zerbetto, M.; Polimeno, A.; Freed, J. H. J. Phys. Chem. B 2011, 115, 143
13. Meirovitch, E.; Shapiro, Y. E.; Zerbetto, M.; Polimeno, A. J. Phys. Chem. B 2012, 116, 886
14. Ghalebani, L.; Kotsyubynskyy, D.; Kowalewski, J. J. Magn. Reson. 2008, 195, 1
15. Kowalewski, J.; Widmalm, G. J. Phys. Chem. 1994, 98, 28
16. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546
17. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4559
18. Daragan, V. A.; Mayo, K. H. Prog. NMR Spectrosc. 1997, 31, 63
19. Bernatowicz, P.; Ruszczynska-Bartnik, K.; Ejchart, A.; Dodziuk, H.; Kaczorowska, E.; Ueda, H. J. Phys. Chem. B 2010, 114, 59
20. Bernatowicz, P.; Kowalewski, J.; Szymanski, S. J. Chem. Phys. 2006, 124, 024108
21. Behrends, R.; Kaatze, U. Chem. Phys. Chem. 2005, 6, 1133
22. Kaminski, K.; Wlodarczyk, P.; Adrjanowicz, K.; Kaminska, E.; Wojnarowska, Z.; Paluch, M. J. Phys. Chem. B 2010, 114, 11272
23. Zhang, Z.; Fleissner, M. R.; Tipikin, D. S.; Liang, Z.; Moscicki, J. K.; Earle, K. A.; Hubbell, W. L.; Freed, J. H. J. Phys. Chem. B 2010, 114, 5503
24. Polnaszek, C. F.; Freed, J. H. J. Phys. Chem. 1975, 21, 2283
25. Stenutz, R.; Carmichael, I.; Widmalm, G.; Serianni, A. S. J. Org. Chem. 2002, 67, 949
26. Bloomfield, V. A.; Dalton., W. G.; Van Holde, K. E. Biopolymers 1967, 5, 135
27. Bloomfield, V. A. Science 1968, 161, 1212
28. De La Torre, J. G.; Bloomfield, V. A. Rev. Biophys. 1981, 14, 81
29. De La Torre, J. G.; Huertas, M. L.; Carrasco, B. J. Magn. Reson. 2000, 147, 138
30. Barone, V.; Zerbetto, M.; Polimeno, A. J. Comput. Chem. 2009, 30, 2
31. Moro, G. Chem. Phys. 1987, 118, 181
32. Moro, G. J.; Freed, J. H. Large-Scale Eigenvalue Problems, Math Studies Series; Cullum, J.,; Willough, R.; Eds.; North Holland: Amsterdam, 1986; Vol. 127, p 143.
33. Chen, Y. Y.; Luo, S. Y.; Hung, S. C.; Chan, S. I.; Tzou, D. L. M. Carbohydr. Res. 2005, 340, 723
34. Abragam, A. The Principles of Nuclear Magnetism: Oxford University Press (Clarendon): Oxford, U.K., 1961.
35. Zerbetto, M.; Polimeno, A.; Meirovitch, E. J. Phys. Chem. B 2009, 113, 13613
36. Zerbetto, M.; Polimeno, A.; Meirovitch, E. Int. J. Quantum Chem. 2010, 110, 387
37. Moro, G. J.; Freed, J. H. J. Chem. Phys. 1981, 74, 3757
38. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten., K. J. Comput. Chem. 2005, 26, 1781
39. Kuttel, M.; Brady, J. W.; Naidoo, K. J. J. Comput. Chem. 2000, 23, 1236
40. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187
41. Schichman, S. A.; Amey, R. L. J. Phys. Chem. 1971, 75, 98
42. Henry, E. R.; Szabo, A. J. Chem. Phys. 1985, 82, 4753
43. Kowalewski, J.; Effemey, M.; Jokisaari, J. J. Magn. Reson. 2002, 157, 171
44. Ghalebani, L.; Bernatowicz, P.; Aski, S. N.; Kowalewski, J. Concepts Magn. Reson. A 2007, 30, 100
45. Behrends, R.; Cowman, M. K.; Eggers, F.; Eyring, E. M.; Kaatze, U.; Majewski, J.; Petrucci, S.; Richmann, K.-H.; Riech, M. J. Am. Chem. Soc. 1997, 119, 2182
46. Stenger, J.; Cowman, M.; Eggers, F.; Eyring, E. M.; Kaatze, U.; Petrucci, S. J. Phys. Chem. B 2000, 104, 4782