Temperature-dependent mechanisms for the dynamics of protein-hydration waters: A Molecular dynamics simulation study

Journal of Physical Chemistry B

Volumn 113, Issue 28, 2009, Pages 9386-9392

  Vogel, M ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; AMINES; DIELECTRIC SPECTROSCOPY; HYDRATION; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; TEMPERATURE DISTRIBUTION;

COLLAGEN-LIKE PEPTIDES; DIFFUSIVE MOTIONS; DYNAMICAL HETEROGENEITIES; HYDRATION SHELL; HYDRATION WATER; HYDROGEN BOND NETWORKS; MODEL PEPTIDES; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SYMMETRY; PROTEIN HYDRATION; ROTATIONAL DYNAMICS; TEMPERATURE DEPENDENCE; TEMPERATURE DEPENDENT; WATER DYNAMICS; WATER MOTION;

DYNAMICS;

EID: 67650332907     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp901531a     Document Type: Article

References (60)

1. Kumar, P.; Franzese, G.; Stanley, H. E. J. Phys.: Condens. Matter 2008, 20, 244114.
2. Mishima, O.; Stanley, H. E. Nature 1998, 396, 329.
3. Angell, C. A. Science 2008, 319, 582.
4. Ito, K.; Moynihan, C. T.; Angell, C. A. Nature 1999, 398, 492.
5. Angell, C. A. Science 1995, 267, 1924.
6. Xu, L.; Kumar, P.; Buldyrev, S. V.; Chen, S.-H.; Poole, P. H.; Sciortino, F.; Stanley, H. E. Proc. Natl. Acad. Sci. 2005, 102, 16558.
7. Liu, L.; Chen, S.-H.; Faraone, A.; Yen, C.-W.; Mou, C.-Y. Phys. Rev. Lett. 2005, 95, 117802.
8. Chen, S.-H.; Liu, L.; Fratini, E.; Baglioni, P.; Faraone, A.; Mamontov, E. Proc. Natl. Acad. Sci. 2006, 103, 9012.
9. Bergman, R.; Swenson, J. Nature 2000, 403, 283.
10. Swenson, J.; Jansson, H.; Bergman, R. Phys. Rev. Lett. 2006, 96, 247802.
11. Pawlus, S.; Khodadadi, S.; Sokolov, A. P. Phys. Rev. Lett. 2008, 100, 108103.
12. Kumar, P.; Yan, Z.; Xu, L.; Mazza, M. G.; Buldyrev, S. V.; Chen, S.-H.; Sastry, S.; Stanley, H. E. Phys. Rev. Lett. 2006, 97, 177802.
13. Zanotti, J.-M.; Bellissent-Funel, M.-C.; Chen, S.-H. Europhys. Lett. 2005, 71, 91.
14. Capaccioli, S.; Ngai, K. L.; Shinyashiki, N. J. Phys. Chem. B 2007, 111, 8197.
15. Cerveny, S.; Schwartz, A.; Bergman, R.; Swenson, J. Phys. Rev. Lett. 2004, 93, 245702.
16. Rupley, J. A.; Careri, G. Adv. Protein Chem. 1991, 41, 37.
17. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Parak, F. G Proc. Natl. Acad. Sci. 2002, 99, 16047.
18. Fenimore, P. W.; Frauenfelder, H.; McMahon, B. H.; Young, R. D. Proc. Natl. Acad. Sci. 2004, 101, 14408.
19. Doster, W.; Settles, M. Biochim. Biophys. Act. 2005, 1749, 173.
20. Doster, W. Eur. Biophys. J. 2008, 37, 591.
21. Ngai, K. L.; Capaccioli, S.; Shinyashiki, N. J. Phys. Chem. B 2008, 112, 3826.
22. Khodadadi, S.; Pawlus, S.; Sokolov, A. P. J. Phys. Chem. B 2008, 112, 14273.
23. Bagchi, B. Chem. Rev. 2005, 105, 3197.
24. Rasmussen, B. F.; Stock, A. M.; Ringe, D.; Petsko, G. A. Nature 1992, 357, 423.
25. Zanotti, J.-M.; Bellissent-Funel, M. C.; Kolesnikov, A. I. Eur. Phys. J. Spec. Top. 2007, 141, 227.
26. Vogel, M. Phys. Rev. Lett. 2008, 101, 225701.
27. Bohmer, R.; Diezemann, G.; Hinze, G.; Rössler, E. Prog. Nucl. Magn. Reson. Spectrosc. 2001, 39, 191.
28. Vogel, M.; Rössler, E. J. Chem. Phys. 2001, 114, 5802.
29. Jana, B.; Pal, S.; Bagchi, B. J. Phvs. Chem. B 2008, 112, 9112.
30. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
31. Tarek, M.; Tobias, D. J. Eur. Biophys. J. 2008, 37, 701.
32. Tobias, D. J.; Sengupta, N.; Tarek, M. Faraday Discuss. 2009, 141, 99.
33. Tournier, A. L.; Smith, J. C. Phys. Rev. Lett. 2003, 91, 208106.
34. Tournier, A. L.; Xu, J.; Smith, J. C. Biophys. J. 2003, 85, 1871.
35. Smith, J. C.; Merzel, F.; Bondar, A.-N.; Tournier, A.; Fischer, S. Phil. Trans. R. Soc. London B 2004, 359, 1181.
36. Kurkal-Siebert, V.; Agarwal, R.; Smith, J. C. Phys. Rev. Lett. 2008, 100, 138102.
37. Oleinikova, A.; Brovchenko, I.; Smolin, N.; Krukau, A.; Geiger, A.; Winter, R. Phys. Rev. Lett. 2005, 95, 247802.
38. Lagi, M.; Chu, X.; Kim, C.; Mallamace, F.; Baglioni, P.; Chen, S.-H. J. Phys. Chem. B 2008, 112, 1571.
39. Li, B.; Alonso, D. O. V.; Bennion, B. J.; Daggett, V. J. Am. Chem. Soc. 2001, 123, 11991.
40. Schreiner, E.; Nicolini, C.; Ludolph, B.; Ravindra, R.; Otte, N.; Kohlmeyer, A.; Rousseau, R.; Winter, R.; Marx, D. Phys. Rev. Lett. 2004, 92, 148101.
41. Baer, M.; Schreiner, E.; Kohlmeyer, A.; Rousseau, R.; Marx, D. J. Phys. Chem. B 2006, 110, 3576.
42. The letter O is used as single-letter code of hydroxyproline.
43. Mooney, S. D.; Huang, C. C.; Kollman, P. A.; Klein, T. E. Biopolymers 2001, 58, 347.
44. Mooney, S. D.; Kollman, P. A.; Klein, T. E. Biopolymers 2002, 64, 63.
45. Bronco, S.; Cappelli, C.; Monti, S. J. Phys. Chem. B 2004, 108, 10101.
46. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306.
47. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.
48. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 manual and user guide; Hochschulverlag an der ETH Zürich: Zurich, 1996.
49. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dotrecht, 1986.
50. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
51. Myamato, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952.
52. Essman, U.; Perela, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
53. Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182.
54. Nosé, S. Mol. Phys. 1984, 52, 255.
55. Hoover, W. G. Phys. Rev. A 1985, 31, 1695.
56. Mark, P.; Nilsson, L. J. Phys. Chem. A 2001, 105, 9954.
57. van der Spoel, D.; van Maaren, P. J.; Berendsen, H. J. C. J. Chem. Phys. 1998, 108, 10220.
58. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Sci. 1988, 110, 1657.
59. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
60. Kumar, P.; Franzese, G.; Stanley, H. E. Phys. Rev. Lett. 2008, 100, 105701.