Structural properties of hydration shell around various conformations of simple polypeptides

Journal of Physical Chemistry B

Volumn 114, Issue 13, 2010, Pages 4536-4550

  Czapiewski, Dariusz ^a   Zielkiewicz, Jan ^a  

^a GDANSK UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL GEOMETRY; CONFORMATIONS; HYDROCARBONS; HYDROGEN; PEPTIDES; POLYPEPTIDES; SHELLS (STRUCTURES); SOLVATION; STRUCTURAL PROPERTIES; SURFACE STRUCTURE;

ALANINE PEPTIDE; AQUEOUS SOLUTIONS; BULK WATER; DYNAMIC PROPERTY; HARMONIC APPROXIMATION; HYDRATION SHELL; HYDROGEN BOND NETWORKS; LINEAR CONFORMATION; LOCAL ORDERING; LOCAL STRUCTURE; MEAN LIFETIME; METHYL GROUP; ORIENTATIONAL ORDERINGS; POLYALANINE; POLYGLYCINE; POLYPEPTIDE CHAIN; POLYPROLINE; RELATIVE STABILITIES; SECONDARY STRUCTURES; SELF-DIFFUSION COEFFICIENTS; SOLVATION LAYERS; SOLVATION SHELL; STRAIGHT LINES; STRUCTURAL ORDERING; SYSTEMATIC DEVIATION; THREE-TERM; WATER-WATER; WATER-WATER INTERACTIONS;

HYDROGEN BONDS;

EID: 77950554182     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9086199     Document Type: Article

References (69)

1. Prabhu, N.; Sharp, K. Chem. Rev. 2006, 106, 1616
2. Ball Chem. Rev. 2008, 108, 74
3. Levy, Y.; Onuchic, J. N. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 389
4. Wang, C.; Liu, L.-P.; Deber, C. M. Phys. Chem. Chem. Phys. 1999, 1, 1539
5. Krittanai, C.; Johnson, W. C. Proteins: Struct. Funct. Genet. 2000, 39, 132
6. Kohtani, M.; Jones, T. C.; Schneider, J. E.; Jarrold, M. F. J. Am. Chem. Soc. 2004, 126, 7420
7. Sorin, E. J.; Rhee, Y. M.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2006, 356, 248
8. Levy, Y.; Jortner, J.; Becker, O. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 2188
9. Nguyen, H. G.; Marchut, A. J.; Hall, C. K. Protein Sci. 2004, 13, 2909
10. Raschke, T. M. Curr. Op. Str. Biol. 2006, 16, 152
11. V. Helms, V. ChemPhysChem 2007, 8, 23
12. Bagchi, B. Chem. Rev. 2005, 105, 3197
13. Daggett, V. Chem. Rev. 2006, 106, 1898
14. Johnson, M. E.; Malardier-Jugroot, C.; Murarka, R. K.; Head-Gordon, T. J. Phys. Chem. B 2009, 113, 4082
15. Schlitter, J. Chem. Phys. Lett. 1993, 215, 617
16. Schäfer, H.; Mark, A. E.; van Gunsteren, W. F. J. J. Chem. Phys. 2000, 113, 7809
17. Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115, 6289
18. Harano, Y.; Kinoshita, M. J. Chem. Phys. 2006, 125 024910
19. Harano, Y.; Kinoshita, M. Biophys. J. 2005, 89, 2701
20. Lin, S.-T.; Blanco, M.; Goddard, W. A. J. Chem. Phys. 2003, 119, 11792
21. Lin, S.-T.; Maiti K.; Goddard, W. A. J. Phys. Chem. B 2005, 109, 8663
22. Jana, B.; Pal, S.; Maiti K.; Lin, S.-T.; Hynes, J. T.; Bagchi, B. J. Phys. Chem. B 2006, 110, 19611
23. Kuffel, A.; Zielkiewicz, J. J. Phys. Chem. B 2008, 112, 15503
24. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman A. AMBER 10; University of California: San Francisco, 2008.
25. Wernet, Ph.; Nordlund, D.; Bergmann, U.; Cavalleri, M.; Odelius, M.; Ogasawara, H.; Näslund, L. A.; Hirsch, T. K.; Ojamäe, L.; Glatzel; Pettersson, L. G. M.; Nilsson, A. Science 2004, 304, 995
26. Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: New York, 1987.
27. Green, H. S. The Molecular Theory of Fluids; North-Holland: Amsterdam, 1952; Chapter III.
28. Nettleton, N. E.; Green, M. S. J. Chem. Phys. 1958, 29, 1365
29. Raveché, H. J. J. Chem. Phys. 1971, 55, 2242
30. Baranyai, A.; Evans, D. J. Phys. Rev. A 1989, 40, 3817
31. Baranyai, A.; Evans, D. J. Phys. Rev. A 1990, 42, 849
32. Wallace, D. C. J. Chem. Phys. 1987, 87, 2282
33. Wallace, D. C. Phys. Rev. A 1989, 39, 4843
34. Lazaridis, T.; Paulaitis, M. E. J. Phys. Chem. 1992, 96, 3847
35. Lazaridis, T.; Paulaitis, M. E. J. Phys. Chem. 1992, 97, 5789
36. Laird, B. B.; Haymet, A. D. J. J. Chem. Phys. 1992, 97, 2153
37. Lazaridis, T.; Karplus, M. J. Chem. Phys. 1996, 105, 4294
38. Zielkiewicz, J. J. Chem. Phys. 2005, 123, 104501;
39. J. Chem. Phys. 2006, 124, 109901.
40. Zielkiewicz, J. J. Phys. Chem. B 2008, 112, 7810
41. Truskett, T. M.; Torquato, S.; Debenedetti G. Phys. Rev. E. 2000, 62, 993
42. Esposito, R.; Saija, F.; Saitta, A. M.; Giaquinta V. Phys. Rev. E. 2006, 73 040502
43. Chau-L.; Hardwick, A. J. Mol. Phys. 1998, 93, 511
44. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in Fortran 77. The Art of Scientific Computing, 2nd ed.; Cambridge University Press: Cambridge, U.K., 2001.
45. Henchman, R. H. J. Chem. Phys. 2003, 119, 400
46. Henchman, R. H. J. Chem. Phys. 2007, 126 064504
47. Zielkiewicz, J. J. Chem. Phys. 2008, 128, 196101
48. Errington, J. R.; Debenedetti G. Nature 2001, 409, 318
49. Luzar, A.; Chandler, D. Nature 1996, 397, 55
50. Luzar, A.; Chandler, D. Phys. Rev. Lett. 1996, 76, 928
51. Rezus, Y. L. A.; Bakker, H. J. Phys. Rev. Lett. 2007, 99, 148301
52. Laage, B.; Hynes, J. T. Science 2006, 311, 832
53. Laage, B.; Hynes, J. T. J. Phys. Chem. B 2008, 112, 14230
54. See Supplementary Information.
55. Laage, B.; Stirnemann, G.; Hynes, J. T. J. Phys. Chem. B 2009, 113, 2428
56. Jana, B.; Pal, S.; Bagchi, B. J. Phys. Chem. B 2008, 112, 9112
57. Halle, B. Philos. Trans. R. Soc. Lond. B 2004, 359, 1207
58. Idrissi, A.; Sokolic, F.; Perera, A. J. Chem. Phys. 2000, 112, 9479
59. Idrissi, A.; Damay J. Non-Cryst. Solids 2006, 352, 4486
60. Mezei, M.; Fleming J.; Srinivasan, R.; Rose, G. D. Proteins 2004, 55, 502
61. Löpez-Llano, J.; Campos, L. A.; Sancho, J. Proteins 2006, 64, 769
62. Shi, Zh.; Chen, K.; Liu, Zh.; Sosnick, T. R.; Kallenbach, N. R. Proteins 2006, 63, 312
63. Chen, K.; Liu, Zh.; Kallenbach, N. R. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15352
64. Fleming J.; Fitzkee, N. C.; Mezei, M.; Srinivasan, R.; Rose, G. D. Protein Sci. 2005, 14, 111
65. Kentsis, A.; Mezei, M.; Osman, R. Proteins 2005, 61, 769
66. Shi, Zh.; Olson, C. A.; Rose, G. D.; Baldwin, R. L.; Kallenbach, N. R. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9190
67. Yang, S.; Cho, M. J. Phys. Chem. B 2007, 111, 605
68. Young, W. S.; Brooks, C. L., III. J. Mol. Biol. 1996, 259, 560
69. Tran, H. T.; Mao, A.; Pappu, R. V. J. Am. Chem. Soc. 2008, 130, 7380