Local order and mobility of water molecules around ambivalent helices

Journal of Physical Chemistry B

Volumn 115, Issue 42, 2011, Pages 12257-12265

  Bhattacharjee, Nicholus ^a   Biswas, Parbati ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; DYNAMICS; MOLECULAR DYNAMICS; PEPTIDES; WATER SUPPLY SYSTEMS;

BULK WATER; HELICAL CONFORMATION; HELICAL SEGMENTS; HYDRATION SHELL; LOCAL ORDER; LOCAL STRUCTURE; MOLECULAR DYNAMICS SIMULATIONS; ORDERED STRUCTURES; ORIENTATIONAL ORDERS; PROTEIN SURFACE; RESIDENCE TIME; SECONDARY STRUCTURES; SOLVATION SHELL; SOLVENT EFFECTS; STRUCTURE AND DYNAMICS; WATER DISTRIBUTIONS; WATER MODELS; WATER MOLECULE;

MOLECULES;

EID: 80054898636     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2066106     Document Type: Article

References (78)

1. Prabhu, N.; Sharp, K. Chem. Rev. 2006, 106, 1616
2. Ball, P. Chem. Rev. 2008, 108, 74
3. Levy, Y.; Onuchic, J. N. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 389
4. Nakasako, M.; Oka, T.; Mashumo, M.; Takahashi, H.; Shimada, I.; Yamaguchi, Y.; Kato, K.; Arata, Y. J. Mol. Biol. 2005, 351, 627
5. Nakasako, M.; Fujisawa, T.; Adachi, S.; Kudo, T.; Higuchi, S. Biochemistry 2001, 40, 3069
6. Bellissent-Funel, M. C., Ed.; Hydration Processes in Biology; IOS Press: Amsterdam, The Netherlands, 1999.
7. Bagchi, B. Chem. Rev. 2005, 105, 3197
8. Li, Z.; Lazaridis, T. Phys. Chem. Chem. Phys. 2007, 9, 573
9. Qvist, J.; Persson, E.; Mattea, C.; Halle, B. Faraday Discuss. 2009, 141, 131
10. Born, B.; Kim, S. J.; Ebbinghaus, S.; Gruebele, M.; Havenith, M. Faraday Discuss. 2009, 141, 161
11. Halle, B. Phil. Trans. R. Soc. London B 2004, 359, 1207
12. Purkiss, A.; Skoulakis, S.; Goodfellow, J. M. Phil. Trans. R. Soc. London A 2001, 359, 1515
13. Roberts, B. C.; Mancera, R. L. J. Chem. Inf. Model. 2008, 48, 397
14. Nakasako, M. J. Mol. Biol. 1999, 289, 547
15. Higo, J.; Nakasako, M. J. Comput. Chem. 2002, 23, 1323
16. Rashin, A. A.; Iofin, M.; Honig, B. Biochemistry 1986, 25, 3619
17. Meyer, E. Protein Sci. 1992, 1, 1543
18. Raymer, M. L.; Sanschagrin, P. C.; Punch, W. F.; Venkataraman, S.; Goodman, E. D.; Kuhn, L. A. J. Mol. Biol. 1997, 265, 445
19. Bottoms, C. A.; White, T. A.; Tanner, J. J. Proteins 2006, 64, 404
20. Nakasako, M.; Odaka, M.; Yohda, M.; Dohmae, N.; Takio, K.; Kamiya, N.; Endo, I. Biochemistry 1999, 38, 9887
21. Rodier, F.; Bahadur, R. P.; Chakrabarti, P.; Janin, J. Proteins 2005, 60, 36
22. Bhat, T. N.; Bentley, G. A.; Boulot, G.; Greene, M. I.; Tello, D.; Acqua, W. D.; Souchon, H.; Schwarz, F. P.; Mariuzza, R. A.; Poljak, R. J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1089
23. Nakasako, M.; Zikihara, K.; Matsuoka, D.; Katsura, H.; Tokutomi, S. J. Mol. Biol. 2008, 381, 718
24. Ferrand, M.; Dianoux, A. J.; Petry, W.; Zaccaï, G. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9668
25. Chen, S.-H.; Liu, L.; Fratini, E.; Baglioni, P.; Faraone, A.; Mamontov, E. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 9012
26. Graber, M.; Bousquet-Dubouch, M.-P.; Lamare, S.; Legoy, M.-D. Biochim. Biophys. Acta 2003, 1648, 24
27. Lind, P. A.; Daniel, R. M.; Monk, C.; Dunn, R. V. Biochim. Biophys. Acta 2004, 1702, 103
28. Chen, X.; Weber, I.; Harrison, R. W. J. Phys. Chem. B 2008, 112, 12073
29. Shou, J.-J.; Zeng, G.; Zhang, Y.-H.; Lu, G. Q. M. J. Phys. Chem. B 2009, 113, 9633
30. Huber, R.; Kukla, D.; Bode, W.; Schwager, P.; Bartels, K.; Deisenhofer, J.; Steigemann, W. J. Mol. Biol. 1974, 89, 73
31. Otting, G.; Liepinsh, E.; Wuthrich, K. Science 1991, 254, 974
32. Modig, K.; Liepinsh, E.; Otting, G.; Halle, B. J. Am. Chem. Soc. 2004, 126, 102
33. Bellissent-Funel, M.-C. J. Mol. Liq. 2000, 84, 39
34. Dellerue, S.; Bellissent-Funel, M.-C. Chem. Phys. 2000, 258, 315
35. Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. B 2002, 106, 12376
36. Denisov, V. P.; Halle, B. Faraday Discuss. 1996, 103, 227
37. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013
38. Grant, E. H.; Sheppard, R. J.; South, G. P. Dielectric behaviour of biological molecules in solution; Oxford University Press: Oxford, U.K., 1978.
39. Raschke, T. M. Curr. Opin. Struct. Biol. 2006, 16, 152
40. Kabsch, W.; Sander, C. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 1075
41. Rost, B. J. Struct. Biol. 2001, 134, 204
42. Kelly, J. W. Curr. Opin. Struct. Biol. 1998, 8, 101
43. Serpell, L. C. Biochim. Biophys. Acta 2000, 1502, 16
44. Bhattacharjee, N.; Biswas, P. BMC Bioinformat. 2010, 11, 519
45. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
46. Bhattacharjee, N.; Biswas, P. Biophys. Chem. 2011, 158, 73
47. Hobohm, U.; Sander, C. Protein Sci. 1994, 3, 522
48. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J., Jr.; E., F. M.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J. Mol. Biol. 1977, 112, 535
49. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577
50. Guo, J.; Chen, H.; Sun, Z.; Lin, Y. Proteins 2004, 54, 738
51. Hua, S.; Sun, Z. J. Mol. Biol. 2001, 308, 397
52. Kim, H.; Park, H. Protein Eng. 2003, 16, 553
53. Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. J. Mol. Biol. 1995, 247, 536
54. Wang, G.; Dunbrack, R. L., Jr. Bioinformatics 2003, 19, 1589
55. Matthews, B. W. J. Mol. Biol. 1968, 33, 491
56. Errington, J. R.; Debenedetti, P. G. Nature 2001, 409, 318
57. Case, D. A. AMBER 9; University of California: San Francisco, 2006.
58. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712
59. Best, R. B.; Hummer, G. J. Phys. Chem. B 2009, 113, 9004
60. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
61. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327
62. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684
63. Agarwal, M.; Kushwaha, H. R.; Chakravarty, C. J. Phys. Chem. B 2010, 114, 651
64. Park, S.; Saven, J. G. Proteins 2005, 60, 450
65. Bergman, D. L.; Lyubartsev, A. P.; Laaksonen, A. Phys. Rev. E 1999, 60, 4482
66. Handgraaf, J.-W.; Zerbetto, F. Proteins 2006, 64, 711
67. Lee, S. H.; Rasaiah, J. C. J. Phys. Chem. 1996, 100, 1420
68. Laage, D.; Hynes, J. T. J. Phys. Chem. B 2008, 112, 7697
69. Koneshan, S.; Rasaiah, J. C.; Lynden-Bell, R. M.; Lee, S. H. J. Phys. Chem. B 1998, 102, 4193
70. Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378
71. Makarov, V. A.; Andrews, B. K.; Smith, P. E.; Pettitt, B. M. Biophys. J. 2000, 79, 2966
72. Nandi, N.; Bagchi, B. J. Phys. Chem. B 1997, 101, 10954
73. Pal, S. K.; Zewail, A. H. Chem. Rev. 2004, 104, 2099
74. Nandi, N.; Bagchi, B. J. Phys. Chem. A 1998, 102, 8217
75. Bandyopadhyay, S.; Chakraborty, S.; Balasubramanian, S.; Pal, S.; Bagchi, B. J. Phys. Chem. B 2004, 108, 12608
76. Bandyopadhyay, S.; Chakraborty, S.; Balasubramanian, S.; Bagchi, B. J. Am. Chem. Soc. 2005, 127, 4071
77. Nilsson, L.; Halle, B. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13867
78. Li, T.; Hassanali, A. A.; Singer, S. J. J. Phys. Chem. B 2008, 112, 16121