Thickness of the hydration layer of a protein from molecular dynamics simulation

Journal of Physical Chemistry B

Volumn 112, Issue 27, 2008, Pages 8203-8209

  Sinha, Sudipta Kumar ^a   Chakraborty, Sudip ^a   Bandyopadhyay, Sanjoy ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ESTIMATION; HYDRATION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NANOFLUIDICS; QUANTUM CHEMISTRY; SOLUTIONS;

AQUEOUS SOLUTIONS; ATOMISTIC MOLECULAR-DYNAMICS; BIOLOGICAL WATER; BULK WATER; DYNAMICAL PROPERTIES; HYDRATION LAYERS; HYDRATION WATER; MOLECULAR DYNAMICS SIMULATION; NATURE OF WATER; PROTEIN HYDRATION; PROTEIN SURFACES; SLOW DYNAMICS; SUB DOMAINS; VILLIN HEADPIECE; WATER DYNAMICS; WATER MOLECULES; WATER PROPERTIES;

DYNAMICS;

EID: 49149126663     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8000724     Document Type: Article

References (77)

1. Protein-Solvent Interaction; Gregory, R. B., Ed.; Marcel Dekker: New York, 1995.
2. (a) Nandi, N.; Bagchi, B. J. Phys. Chem. B 1997, 101, 10954.
3. (b) Nandi, N.; Bagchi, B. J. Phys. Chem. 1996, 100, 13914.
4. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177.
5. Bagchi, B. Chem. Rev. 2005, 105, 3197.
6. (a) Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1763.
7. (b) Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. B 2002, 106, 12376:
8. Pal, S. K.; Zewail, A. H. Chem. Rev. 2004, 104, 2099.
9. (a) Bhattacharyya, K. Acc. Chem. Res. 2003, 36, 95.
10. (b) Guha, S.; Sahu, K.; Roy, D.; Mondal, S. K.; Roy, S.; Bhattacharyya, K. Biochemistry 2005, 44, 8940.
11. (a) Jordinades, X. J.; Lang, M. J.; Song, X.; Fleming, G. R. J. Phys. Chem. B 1999, 103, 7995.
12. (b) Fleming, G. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 15161.
13. Qiu, W.; Kao, Y.-T.; Zhang, L.; Yang, Y.; Wang, L.; Stites, W. E.; Zhong, D.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 13979.
14. Li, T.; Hassanali, A. A.; Kao, Y.-T.; Zhong, D.; Singer, S. J. J. Am. Chem. Soc. 2007, 129, 3376.
15. Otting, G.; Liepinsh, E.; Wüthrich, K. Science 1991, 254, 974.
16. Abbyad, P.; Shi, X.; Childs, W.; McAnaney, T. B.; Cohen, B. E.; Boxer, S. G. J. Phys. Chem. B 2007, 111, 8269.
17. (a) Sahu, K.; Mondal, S. K.; Ghosh, S.; Roy, D.; Sen, P.; Bhattacharyya, K. J. Phys. Chem. B 2006, 110, 1056.
18. (b) Samaddar, S.; Mandal, A. K.; Mondal, S. K.; Sahu, K.; Bhattacharyya, K.; Roy, S. J. Phys. Chem. B 2006, 110, 21210.
19. (a) Heugen, U.; Schwaab, G.; Bründermann, E.; Heyden, M.; Yu, X.; Leitner, D. M.; Havenith, M. Proc Natl. Acad. Sci. U.S.A. 2006, 103, 12301.
20. (b) Leitner, D. M.; Havenith, M.; Gruebele, M. Int. Rev. Phys. Chem. 2006, 25, 553.
21. Xu, J.; Plaxco, K. W.; Allen, S. J. J. Phys. Chem. B 2005, 110, 24255.
22. Zanotti, J. M.; Bellissent-Funel, M. C.; Parello, J. Biophys. J. 1999, 76, 2390.
23. Palmer, A. G., III Chem. Rev. 2004, 104, 3623.
24. (a) Russo, D.; Murarka, R. K.; Hura, G.; Verschell, E.; Copley, J. R. D.; Head-Gordon, T. J. Phys. Chem. B 2004, 108, 19885.
25. (b) Russo, D.; Murarka, R. K.; Copley, J. R. D.; Head-Gordon, T. J. Phys. Chem. B 2005, 109, 12966.
26. Oleinikova, A.; Sasisanker, P.; Weingartner, H. J. Phys. Chem. B 2004, 108, 8467.
27. Modig, K.; Liepinsh, E.; Otting, G.; Halle, B. J. Am. Chem. Soc. 2004, 126, 102.
28. (a) Rossky, P. J.; Karplus, M.; Rahman, A. Biopolymers 1979, 18, 825.
29. (b) Rossky, P. J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913.
30. Levitt, M.; Sharon, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7557.
31. Cheng, Y. K.; Rossky, P. J. Nature 1998, 392, 696.
32. Hua, L.; Huang, X.; Zhou, R.; Berne, B. J. J. Phys. Chem. B 2006, 110, 3704.
33. (a) Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378.
34. (b) Merzel, F.; Smith, J. C. J. Chem. Inf. Model. 2005, 45, 1593.
35. Smolin, N.; Winter, R. J. Phys. Chem. B 2004, 108, 15928.
36. (a) Rocchi, C.; Bizzarri, A. R.; Cannistraro, S. Phys. Rev. E 1998, 57, 3315.
37. (b) Bizzarri, A. R.; Cannistraro, S. J. Phys. Chem. B 2002, 106, 6617.
38. Marchi, M.; Sterpone, F.; Ceccarelli, M. J. Am. Chem. Soc. 2002, 124, 6787.
39. Pizzitutti, F.; Marchi, M.; Sterpone, F.; Rossky, P. J. J. Phys. Chem. B 2007, 111, 7584.
40. (a) Tarek, M.; Tobias, D. J. Biophys. J. 2000, 79, 3244.
41. (b) Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
42. (a) Makarov, V.; Andrews, K. A.; Pettitt, B. M. Biopolymers 1998, 45, 469.
43. (b) Makarov, V.; Pettitt, B. M.; Feig, M. Acc Chem. Res. 2002, 35, 376.
44. Xu, H.; Berne, B. J. J. Phys. Chem. B 2001, 105, 11929.
45. Bandyopadhyay, S.; Chakraborty, S.; Balasubramanian, S.; Pal, S.; Bagchi, B. J. Phys. Chem. B 2004, 108, 12608.
46. Bandyopadhyay, S.; Chakraborty, S.; Bagchi, B. J. Am. Chem. Soc. 2005, 127, 16660.
47. (a) Chakraborty, S.; Bandyopadhyay, S. J. Phys. Chem. B 2007, 111, 7626.
48. (b) Chakraborty, S.; Sinha, S. K.; Bandyopadhyay, S. J. Phys. Chem. B 2007, 111, 13626.
49. (a) Bandyopadhyay, S.; Chakraborty, S.; Balasubramanian, S.; Bagchi, B. J. Am. Chem. Soc. 2005, 127, 4071.
50. (b) Bandyopadhyay, S.; Chakraborty, S.; Bagchi, B. J. Phys. Chem. B 2006, 110, 20629.
51. Golosov, A. A.; Karplus, M. J. Phys. Chem. B 2007, 111, 1482.
52. Ebbinghaus, S.; Kim, S. J.; Heyden, M.; Yu, X.; Heugen, U.; Gruebele, M.; Leitner, D. M.; Havenith, M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 20749.
53. (a) McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nat. Struct. Biol. 1997, 4, 180.
54. (b) McKnight, C. J.; Doering, D. S.; Matsudaira, P. T.; Kim, P. S. J. Mol. Biol. 1996, 260, 126.
55. (a) Doering, D. S.; Matsudaira, P. Biochemistry 1996, 35, 12677.
56. (b) Pope, B.; Way, M.; Matsudaira, P. T.; Weeds, A. FEBS Lett. 1994, 338, 58.
57. Tuckerman, M. E.; Yarne, D. A.; Samuelson, S. O.; Hughs, A. L.; Martyna, G. J. Comput. Phys. Commun. 2000, 128, 333.
58. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
59. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
60. Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 87, 1117.
61. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
62. (a) Procacci, P.; Darden, T.; Marchi, M. J. Phys. Chem. 1996, 100, 10464.
63. (b) Procacci, P.; Marchi, M.; Martyna, G. J. J. Chem. Phys. 1998, 108, 8799.
64. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon; Oxford, 1987.
65. Chanda, J.; Bandyopadhyay, S. J. Phys. Chem. B 2006, 110, 23482.
66. (a) Stillinger, F. H. Science 1980, 209, 451.
67. (b) Stillinger, F. H. Adv. Chem. Phys. 1975, 57, 1.
68. Rapaport, D. C. Mol. Phys. 1983, 50, 1151.
69. Luzar, A.; Chandler, D. J. Chem. Phys. 1993, 98, 8160.
70. (a) Walrafen, G. E.; Chu, Y. C. J. Phys. Chem. 1995, 99, 11225.
71. (b) Walrafen, G. E.; Chu, Y. C.; Piermarini, G. J. J. Phys. Chem. 1996, 100, 10363.
72. Marti, J.; Padro, J. A.; Guardia, E. J. Chem. Phys. 1996, 105, 639.
73. Brubach, J. B.; Mermet, A.; Filabozzi, A.; Gerschel, A.; Roy, P. J. Chem. Phys. 2005, 122, 184509.
74. Pal, S.; Balasubramanian, S.; Bagchi, B. Phys. Rev. E 2003, 67, 061502.
75. Choudhury, N.; Pettitt, B. M. J. Phys. Chem. B 2005, 109, 6422.
76. Li, J. J. Chem. Phys. 1996, 105, 6733.
77. Crupi, V.; Dianoux, A. J.; Majolino, D.; Migliardo, P.; Venuti, V. Phys. Chem. Chem. Phys. 2002, 4, 2768.