Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides

Journal of Chemical Physics

Volumn 126, Issue 21, 2007, Pages

  Murarka, Rajesh K ^a,c   Head Gordon, Teresa ^a,b  

^a University of California at Berkeley   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c Department of Molecular Biology and Genetics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDRATION DYNAMICS; HYDROPHILIC PROTEIN BACKBONE;

CONCENTRATION (PROCESS); HYDRATION; HYDROPHILICITY; HYDROPHOBICITY; NEUTRON SCATTERING; PEPTIDES;

MOLECULAR DYNAMICS;

PEPTIDE; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; HYDROPHOBICITY;

HYDROPHOBICITY; MODELS, CHEMICAL; PEPTIDES; WATER;

EID: 34249985015     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2737050     Document Type: Article

References (69)

1. G. Careri and M. Peyrard, Cell Mol. Biol. (Paris) 47, 745 (2001).
2. A. R. Bizzarri and S. J. Cannistraro, J. Phys. Chem. B 106, 6617 (2002).
3. R. M. Daniel, R. V. Dunn, J. L. Finney, and J. C. Smith, Annu. Rev. Biophys. Biomol. Struct. 32, 69 (2003).
4. B. Halle, Philos. Trans. R. Soc. London, Ser. B 359, 1207 (2004).
5. B. Bagchi, Chem. Rev. (Washington, D.C.) 105, 3197 (2005).
6. V. P. Denisov and B. Halle, Faraday Discuss. 103, 227 (1996).
7. B. Halle and V. P. Denisov, Methods Enzymol. 338, 178 (2001).
8. K. Modig, E. Liepinsh, G. Otting, and B. Halle, J. Am. Chem. Soc. 126, 102 (2004).
9. E. H. Grant, R. J. Sheppard, and P. G. South, Dielectric Behavior of Biological Molecules in Solutions (Clarendon, Oxford, 1978).
10. E. Dachwitz, F. Parak, and M. Stockhauser, Ber. Bunsenges. Phys. Chem. 93, 1454 (1989).
11. R. Pethig, Annu. Rev. Phys. Chem. 43, 177 (1992).
12. A. Knocks and H. Weingartner, J. Phys. Chem. B 105, 3635 (2001).
13. A. Oleinikova, P. Sasisanker, and H. Weingartner, J. Phys. Chem. B 108, 8467 (2004).
14. G. Otting, Prog. Nucl. Magn. Reson. Spectrosc. 31, 259 (1997).
15. K. Venu, L. A. Svensson, and B. Halle, Biophys. J. 77, 1074 (1999).
16. X. J. Jordanides, S. Lang, and G. R. Fleming, J. Phys. Chem. B 103, 7995 (1999).
17. K. Bhattacharyya and B. Bagchi, J. Phys. Chem. A 104, 10603 (2000).
18. S. K. Pal, D. Mandal, S. Sen, and K. Bhattacharyya, J. Phys. Chem. B 105, 1438 (2001).
19. H. Shirota and E. W. J. Castner, J. Am. Chem. Soc. 123, 12877 (2001).
20. L. Frauchiger, H. Shirota, K. E. Ulrich, and E. W. J. Castner, J. Phys. Chem. B 106, 7463 (2002).
21. S. K. Pal, J. Peon, B. Bagchi, and A. H. Zewail, J. Phys. Chem. B 106, 12376 (2002).
22. K. Bhattacharyya, Acc. Chem. Res. 36, 95 (2003).
23. S. K. Pal and A. H. Zewail, Chem. Rev. (Washington, D.C.) 104, 2099 (2004).
24. U. Wanderlingh, R. Giordano, and J. Teixeira, J. Mol. Struct. 296, 271 (1993).
25. M. Diehl, W. Doster, W. Petry, and H. Schober, Biophys. J. 73, 2726 (1997).
26. J. M. Zanotti, M. C. Bellissent-Funel, and J. Parello, Biophys. J. 76, 2390 (1999).
27. L. Almasy, P. Banki, M. C. Bellissent-Funel, M. Bokor, L. Cser, G. Jancso, K. Tompa, and J. M. Zanotti, Appl. Phys. A: Mater. Sci. Process. 74, S516 (2002).
28. F. Gabel, D. Bicout, U. Lehnert, M. Tehei, M. Weik, and G. Zaccai, Q. Rev. Biophys. 35, 327 (2002).
29. C. Mattos, Trends Biochem. Sci. 27, 203 (2002).
30. D. Russo, P. Baglioni, E. Peroni, and J. Teixeira, J. Chem. Phys. 292, 235 (2003).
31. M. R. Harpham, B. M. Ladanyi, N. E. Levinger, and K. W. Herwig, J. Chem. Phys. 121, 7855 (2004).
32. C. Rocchi, A. R. Bizzarri, and S. Cannistraro, Phys. Rev. E 57, 3315 (1998).
33. V. A. Makarov, M. Feig, B. K. Andrews, and B. M. Pettitt, Biophys. J. 75, 150 (1998).
34. M. Tarek and D. J. Tobias, Biophys. J. 79, 3244 (2000).
35. H. Xu and B. J. Berne, J. Phys. Chem. B 105, 11929 (2001).
36. M. Marchi, P. Sterpone, and M. Ceccarelli, J. Am. Chem. Soc. 124, 6787 (2002).
37. M. Tarek and D. J. Tobias, Phys. Rev. Lett. 88, 8101 (2002).
38. S. Balasubramanian, S. Pal, and B. Bagchi, Phys. Rev. Lett. 89, 115505 (2002).
39. F. Merzel and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 99, 5378 (2002).
40. A. L. Tournier, J. C. Xu, and J. C. Smith, Biophys. J. 85, 1871 (2003).
41. S. Bandyopadhyay, S. Chakraborty, B. Bagchi, J. Am. Chem. Soc. 127, 16660 (2005).
42. S. Bandyopadhyay and B. Bagchi, J. Chem. Phys. 125, 084912 (2006).
43. A. A. Golosov and M. Karplus, J. Phys. Chem. B 111, 1482 (2007).
44. D. Russo, G. Hura, and T. Head-Gordon, Biophys. J. 86, 1852 (2004).
45. D. Russo, R. K. Murarka, G. Hura, E. R. Verschell, J. R. D. Copley, and T. Head-Gordon, J. Phys. Chem. B 108, 19885 (2004).
46. G. Hura, J. M. Sorenson, R. M. Glaeser, and T. Head-Gordon, Perspect. Drug Discovery Des. 17, 97 (1997).
47. A. Pertsemlidis, A. K. Soper, J. M. Sorenson, and T. Head-Gordon, Proc. Natl. Acad. Sci. U.S.A. 96, 481 (1999).
48. J. M. Sorenson, G. Hura, A. K. Soper, A. Pertsemlidis, and T. Head-Gordon, J. Phys. Chem. B 103, 5413 (1999).
49. D. Russo, R. K. Murarka, J. R. D. Copley, and T. Head-Gordon, J. Phys. Chem. B 109, 12966 (2005).
50. C. Malardier-Jogroot and T. Head-Gordon, Phys. Chem. Chem. Phys. 9, 1962 (2007).
51. R. K. Murarka and T. Head-Gordon, Proc. Natl. Acad. Sci. U.S.A. (submitted).
52. P. A. Egelstaff, An Introduction to the Liquid State (Clarendon, Oxford, 1992).
53. V. F. Sears, Can. J. Phys. 44, 1299 (1966).
54. F. Sciortino, P. Gallo, P. Tartaglia, and S. H. Chen, Phys. Rev. E 54, 6331 (1996).
55. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
56. H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, G. Hura, T. Head-Gordon, J. Chem. Phys. 120, 9665 (2004).
57. H. C. Andersen, J. Chem. Phys. 72, 2384 (1980).
58. S. Nose, Mol. Phys. 52, 255 (1984).
59. W. G. Hoover, Phys. Rev. A 31, 1695 (1985).
60. G. J. Martyna, M. E. Tuckerman, and M. L. Klein, J. Chem. Phys. 97, 2635 (1992).
61. H. C. Andersen, J. Comput. Phys. 52, 24 (1983).
62. V. Kraeutler, W. F. van Gunsteren, and P. H. Huenenberger, J. Comput. Chem. 22, 501 (2001).
63. M. Bee, Quasi-elastic Neutron Scattering (Adam Hilger, Philadelphia, 1988).
64. M. Bee, J. Phys. IV 10, 1 (2000).
65. S. H. Chen, P. Gallo, and F. Sciortino, Phys. Rev. E 56, 4231 (1997).
66. M. D. Ediger, Annu. Rev. Phys. Chem. 51, 99 (2000).
67. P. G. Debenedetti and F. H. Stillinger, Nature (London) 410, 259 (2001).
68. W. Gotze and L. Sjogren, Rep. Prog. Phys. 55, 241 (1992).
69. P. Gallo, M. Rovere, and E. Spohr, Phys. Rev. Lett. 85, 4320 (2000).