Energetics and dynamics of a cyclic oligosaccharide molecule in a confined protein pore environment. A molecular dynamics study

Journal of Physical Chemistry B

Volumn 107, Issue 29, 2003, Pages 7189-7201

  Shilov, Ignat Yu ^a   Kurnikova, Maria G ^a,b  

^a MARQUETTE UNIVERSITY   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; CONFORMATIONS; ELECTRON ENERGY LEVELS; HYDROGEN BONDS; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; MOLECULAR STRUCTURE; OLIGOMERS; PROTEINS; SOLUTIONS; VAN DER WAALS FORCES;

CYCLIC OLIGOSACCHARIDE; CYCLODEXTRIN; HEMOLYSIN; NONPOLAR SOLVATION; VAN DER WAALS INTERACTION;

POLYSACCHARIDES;

EID: 0042705190     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp034359w     Document Type: Article

References (90)

1. Toone, E. J.; Burkhalter, N. F.; Dimick, S. M. Carbohydr. Chem. Biol. 2000, 2, 863-914.
2. Toone, E. J. Curr. Opin. Struct. Biol. 1994, 4, 719-728.
3. Weis, W. I.; Drickamer, K. Annu. Rev. Biochem. 1996, 65, 441-473.
4. Dam, T. K.; Brewer, C. F. Chem. Rev. 2002, 102, 387-429.
5. Dwek, R. A. Chem. Rev. 1996, 96, 683-720.
6. Lis, H.; Sharon, N. Chem. Rev. 1998, 98, 637-674.
7. Lee, Y. C.; Lee, R. T. Acc. Chem. Res. 1995, 28, 321-327.
8. Sharon, N.; Ofek, I. Glycoconjugate J. 2000, 17, 659-664.
9. Nangia-Makker, P.; Conklin, J.; Hogan, V.; Raz, A. Trends Mol. Med. 2002, 8, 187-192.
10. Davis, A. P.; Wareham, R. S. Angew. Chem., Int. Ed. Engl. 1999, 38, 2979-2996.
11. Lemieux, R. U. Acc. Chem. Res. 1996, 29, 373-380.
12. Carver, J. P. Pure Appl. Chem. 1993, 65, 763-770.
13. Szejtli, J. Chem. Rev. 1998, 98, 1743-1754.
14. Rekharsky, M. V.; Inoue, Y. Chem. Rev. 1998, 98, 1875-1917.
15. Hedges, A. R. Chem. Rev. 1998, 98, 2035-2044.
16. Sorimachi, K.; Gal-Coeffet, M. F.; Williamson, G.; Archer, D. B.; Williamson, M. P. Structure (London) 1997, 5, 647-661.
17. Adachi, M.; Mikami, B.; Katsube, T.; Utsumi, S. J. Biol. Chem. 1998, 273, 19859-19865.
18. Sharff, A. J.; Rodseth, L. E.; Quiocho, F. A. Biochemistry 1993, 32, 10553-10559.
19. Kondo, S.; Ohtaki, A.; Tonozuka, T.; Sakano, Y.; Kamitori, S. J. Biochem. (Tokyo) 2001, 129, 423-428.
20. Yokota, T.; Tonozuka, T.; Shimura, Y.; Ichikawa, K.; Kamitori, S.; Sakano, Y. Biosci., Biotechnol., Biochem. 2001, 65, 619-626.
21. Gu, L.-Q.; Bayley, H. Biophys. J. 2000, 79, 1967-1975.
22. Gu, L.-Q.; Serra, M. D.; Vincent, J. B.; Vigh, G.; Cheley, S.; Braha, O.; Bayley, H. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3959-3964.
23. Gu, L.-Q.; Braha, O.; Conlan, S.; Cheley, S.; Bayley, H. Nature (London) 1999, 398, 686-690.
24. Gu, L.-Q.; Cheley, S.; Bayley, H. Science (Washington, D.C.) 2001, 291, 636-640.
25. Gu, L.-Q.; Cheley, S.; Bayley, H. J. Gen. Physiol. 2001, 118, 481-494.
26. Hansson, T.; Oostenbrink, C.; van Gunsteren, W. F. Curr. Opin. Struct. Biol. 2002, 12, 190-196.
27. Roux, B. Curr. Opin. Struct. Biol. 2002, 12, 182-189.
28. Tieleman, D. P.; Biggin, P. C.; Smith, G. R.; Sansom, M. S. P. Q. Rev. Biophys. 2001, 34, 473-561.
29. Duan, Y.; Kollman, P. A. Science (Washington, D.C.) 1998, 282, 740-744.
30. Daggett, V. Curr. Opin. Struct. Biol. 2000, 10, 160-164.
31. Zacharias, M.; Straatsma, T. P.; McCammon, J. A.; Quiocho, F. A. Biochemistry 1993, 32, 7428-7434.
32. Imberty, A.; Perez, S. Glycobiology 1994, 4, 351-366.
33. Åqvist, J.; Mowbray, S. L. J. Biol. Chem. 1995, 270, 9978-9981.
34. Liang, G.; Schmidt, R. K.; Yu, H. A.; Cumming, D. A.; Brady, J. W. J. Phys. Chem. 1996, 100, 2528-2534.
35. Cheong, Y.; Shim, G.; Kang, D.; Kim, Y. J. Mol. Struct. 1999, 475, 219-232.
36. Pathiaseril, A.; Woods, R. J. J. Am. Chem. Soc. 2000, 122, 331-338.
37. Bernardi, A.; Galgano, M.; Belvisi, L.; Colombo, G. J. Comput.-Aided Mol. Des. 2001, 15, 117-128.
38. Bryce, R. A.; Hillier, I. H.; Naismith, J. H. Biophys. J. 2001, 81, 1373-1381.
39. Lipkowitz, K. B. Chem. Rev. 1998, 98, 1829-1873.
40. Prabhakaran, M. Biochem. Biophys. Res. Commun. 1991, 178, 191-197.
41. Lipkowitz, K. B. J. Org. Chem. 1991, 56, 6357-6367.
42. Kozar, T.; Venanzi, C. A. THEOCHEM 1997, 395-396, 451-468.
43. Wertz, D. A.; Shi, C. X.; Venanzi, C. A. J. Comput. Chem. 1992, 13, 41-56.
44. Koehler, J. E. H.; Saenger, W.; Van Gunsteren, W. F. Eur. Biophys. J. 1988, 16, 153-168.
45. Linert, W.; Margl, P.; Renz, F. Chem. Phys. 1992, 161, 327-338.
46. Barbiric, D. J.; de Rossi, R. H.; Castro, E. A. THEOCHEM 2001, 537, 235-243.
47. Fronza, G.; Mele, A.; Redenti, E.; Ventura, P. J. Org. Chem. 1996, 61, 909-914.
48. Ivanov, P. M.; Salvatierra, D.; Jaime, C. J. Org. Chem. 1996, 61, 7012-7017.
49. Dodziuk, H.; Lukin, O.; Nowinski, K. S. THEOCHEM 2000, 503, 221-230.
50. Salvatierra, D.; Sanchez-Ruiz, X.; Garduno, R.; Cervello, E.; Jaime, C.; Virgili, A.; Sanchez-Ferrando, F. Tetrahedron 2000, 56, 3035-3041.
51. Yeh, I.-C.; Hummer, G. J. Am. Chem. Soc. 2002, 124, 6563-6568.
52. Lichtenthaler, F. W.; Immel, S. Liebigs Ann. 1996, 27-37.
53. Gouaux, E. J. Struct. Biol. 1998, 121, 110-122.
54. Song, L.; Hobaugh, M. R.; Shustak, C.; Cheley, S.; Bayley, H.; Goauax, J. E. Science (Washington, D.C.) 1996, 274, 1859-1866.
55. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E. I.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1-42.
56. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
57. Glennon, T. M.; Zheng, Y.-J.; LeGrand, S. M.; Shutzberg, B. A.; Merz, K. M., Jr. J. Comput. Chem. 1994, 15, 1019-1040.
58. Mamonov, A.; Coalson, R. D.; Nitzan, A.; Kurnikova, M. G. Biophys. J. 2003, 84, 3646-3661.
59. Wu, Y.; He, K.; Ludtke, S. J.; Huang, H. W. Biophys. J. 1995, 68, 2361-2369.
60. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
61. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
62. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
63. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
64. McQuarrie, D. A. Statistical mechanics; Harper & Row Publishers: New York, 1976.
65. Allen, M. P.; Tildesley, D. J. Computer simulation of liquids; Oxford University Press: Oxford, England, 1987; p 450.
66. Leach, A. R. Molecular modelling: principles and applications, 2nd ed.; Prentice Hall: Harlow, England, and Reading, MA, 2001.
67. Gilson, M. K.; Honig, B. Proteins: Struct., Funct., Genet. 1988, 4, 7-18.
68. Kurnikova, M. G.; Coalson, R. D.; Graf, P.; Nitzan, A. Biophys. J. 1999, 76, 642-656.
69. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379-400.
70. Le Grand, S. M.; Merz, Jr.; Kenneth, M. J. Comput. Chem. 1993, 14, 349-352.
71. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
72. Paduano, L.; Sartorio, R.; Vitagliano, V.; Costantino, L. J. Solution Chem. 1990, 19, 31-39.
73. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L. Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. I. Acc. Chem. Res. 2000, 33, 889-897.
74. Jayaram, B.; McConnell, K.; Dixit, S. B.; Das, A.; Beveridge, D. L. J. Comput. Chem. 2002, 23, 1-14.
75. Noskov, S. Y.; Lim, C. Biophys. J. 2001, 81, 737-750.
76. Sigurskjold, B. W.; Christensen, T.; Payre, N.; Cottaz, S.; Dirguez, H.; Svensson, B. Biochemistry 1998, 37, 10446-10452.
77. Thomson, J.; Liu, Y.; Sturtevant, J. M.; Quiocho, F. A. Biophys. Chem. 1998, 70, 101-108.
78. Kuhn, B.; Kollman, P. A. J. Med. Chem. 2000, 43, 3786-3791.
79. Reyes, C. M.; Kollman, P. A. J. Mol. Biol. 2000, 297, 1145-1158.
80. Åqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Acc. Chem. Res. 2002, 35, 358-365.
81. Blokzijl, W.; Engberts, J. B. F. N. Angew. Chem., Int. Ed. Engl. 1993, 32, 1545-1579.
82. Gallicchio, E.; Kubo, M. M.; Levy, R. M. J. Am. Chem. Soc. 1998, 120, 4526-4527.
83. Saenger, W.; Jacob, J.; Gessler, K.; Steiner, T.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T. Chem. Rev. 1998, 98, 1787-1802.
84. Quiocho, F. A. Pure Appl. Chem. 1989, 61, 1293-1306.
85. Skrynnikov, N. R.; Goto, N. K.; Yang, D.; Choy, W. Y.; Tolman, J. R.; Mueller, G. A.; Kay, L. E. J. Mol. Biol. 2000, 295, 1265-1273.
86. Betzel, C.; Saenger, W.; Hingerty, B. E.; Brown, G. M. J. Am. Chem. Soc. 1984, 106, 7545-7557.
87. Hille, B. Ionic channels of excitable membranes, 3rd ed.; Sinauer: Sunderland, MA, 2001.
88. Sayle, R. A.; Milner-White, E. J. Trends Biochem. Sci. 1995, 20, 374-376.
89. Klug, C. S.; Su, W.; Feix, J. B. Biochemistry 1997, 36, 13027-13033.
90. The limited dynamics of the protein backbone in the beta-barrel has been demonstrated in the experiment, e.g., ref 89, and indirectly, in the theoretical study of ion current through the porin protein in which modeling by the all-atom MD simulation and by Brownian dynamics simulation of ions in the rigid protein gave very similar distributions of ions inside the channel indicating that the dynamics of the protein backbone is unimportant for the dynamics inside the pore. In the current study, we are interested in the dynamics ofthe ligand molecule inside the pore. The β-barrel forms a well-defined barrier to separate the system into two compartments: inside the pore where we attempted to simulate the all-atom dynamics of all species involved in full detail and behind the barrel wall, where simplified constrained dynamics of the model lipid bilayer, protein backbone was employed because the influence of this region onto the dynamics inside the pore is expected to be small.